SMEs in Health Research - Synopses of projects funded ... - Europa

project synopsesSMEs in Health ResearchSynopses of projects funded through the SME call for“Life sciences, genomics and biotechnology for health”

Interested in European research?Research*eu is our monthly magazine keeping you in touch with main developments(results, programmes, events, etc.). It is available in English, French, German and Spanish.A free sample copy or free subscription can be obtained from:European CommissionDirectorate-General for ResearchCommunication UnitB-1049 BrusselsFax (32-2) 29-58220E-mail: research-eu@ec.europa.euInternet: http://ec.europa.eu/research/research-euEuropean CommisssionDirectorate-General for ResearchDirectorate F — HealthUnit F1 — Horizontal Aspects and CoordinationContact: Ludovica SerafiniEuropean CommissionOffice CDMA 2/179B-1049 BrusselsTel. (32-2) 29-56759Fax (32-2) 29-95888E-mail: ludovica.serafini@ec.europa.eu

EUROPEAN COMMISSIONSMEs in Health ResearchSynopses of projects funded throughthe SME call for “Life sciences,genomics and biotechnology for health”(FP6-2005-LIFESCIHEALTH-7)2008 Directorate-General for Research EUR 23457 ENHealth

AcknowledgementsThis catalogue has been produced thanks to the essential input from all project coordinators. Special thanks goto Séverine Romain for her highly professional and dynamic assistance, pivotal for the catalogue completion.I am very grateful to Rachida Ghalouchi, Christel Jaubert, Charles Kelly, Kristina Kyriakopoulou, and to all the officersin Health Directorate responsible for the projects included in this synopses, for their efficient co-operation.Finally, my warmest thanks to Stéphane Hogan, Head of Unit F1, Horizontal aspects and coordination inthe Health Directorate, for the commitment and lead provided.Ludovica SerafiniEditorContact details for FP7 activitiesInformation on FP7 Health Theme(including calls, available supports and information on SMEs and innovation):http://cordis.europa.eu/fp7/cooperation/health_en.htmlThe SME Contact Officer in the Health Directorate is Ludovica Serafini, e-mail: ludovica.serafini@ec.europa.euEurope Direct is a service to help you find answersto your questions about the European UnionFreephone number (*):00 800 6 7 8 9 10 11(*) Certain mobile telephone operators do not allow access to00 800 numbers or these calls may be billedLEGAL NOTICENeither the European Commission nor any person acting on behalf of the Commissionis responsible for the use which might be made of the following information.The views expressed in this publication are the sole responsibility of the author and donot necessarily reflect the views of the European Commission.A great deal of additional information on the European Union is available on the Internet.It can be accessed through the Europa server (http://europa.eu) and CORDIS(http://cordis.europa.eu/en/home.html)Cataloguing data can be found at the end of this publication.Luxembourg: Office for Official Publications of the European Communities, 2008ISBN 978-92-79-08803-2DOI 10.2777/13756© European Communities, 2008Reproduction is authorised provided the source is acknowledged.Printed in LuxembourgPrinted on white chlorine-free paper

SME CALLTable ofcontent• Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7• Introduction . . . . . . . . . . . . . . . . . . . . . . . . . 9• AGLAEA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10Development of novel animal modelsof glutamatergic central nervoussystem disorders using in vivosiRNA and transgenic approaches• ANGIOSTOP . . . . . . . . . . . . . . . . . . . . . . . . 12Novel Anti-angiogenic treatmentfor Cancer, Arthritis and OcularNeovascularization based onInhibition of Placental GrowthFactor (PlGF)• ARTEMIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14In Vitro neural tissue systemfor replacement of transgenicanimals with memory/learningdeficiencies• AUTOSCREEN . . . . . . . . . . . . . . . . . . . . . . 16AUTOSCREEN for Cell BasedHigh-throughput and High-contentGene Function Analysis andDrug Discovery Screens• BacAbs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Assessment of StructuralRequirements in Complement-Mediated Bactericidal Events:Towards a Global Approachto the Selection of New VaccineCandidates• BioBridge. . . . . . . . . . . . . . . . . . . . . . . . . . . 20Integrative Genomics and ChronicDisease Phenotypes: modellingand simulation tools for clinicians• CancerGrid . . . . . . . . . . . . . . . . . . . . . . . . . 22Grid-aided computer systemfor rapid anti-cancer drug design• CAPPELLA . . . . . . . . . . . . . . . . . . . . . . . . . . 26Combating cancer through novelapproaches to protein: proteininteraction inhibitor libraries• ChILL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28Chromatin Immuno-linkedligation: A novel generation ofbiotechnological tools for researchand diagnosis• CILMALVAC . . . . . . . . . . . . . . . . . . . . . . . . . 30The Tetrahymena system as aninnovative approach to malariaantigene expression• cNEUPRO . . . . . . . . . . . . . . . . . . . . . . . . . . . 32Clinical Neuroproteomicsof Neurodegenerative Diseases• COBRED . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Colon and breast cancer diagnostics• COMICS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Comet assay and cell array for fastand efficient genotoxicity testing• CVDIMMUNE. . . . . . . . . . . . . . . . . . . . . . . 38Immunomodulation andautoimmunity in cardiovasculardisease and atherosclerosis• DEPPICT . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40Designing Therapeutic Protein:ProteinInhibitors for Brain Cancer Treatments• DeZnIT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Design of zinc metalloenzymetargeted drugs using an IntegratedTechnology approach• Diagnosis . . . . . . . . . . . . . . . . . . . . . . . . . . 44Development of new and costeffective methods for non-invasivediagnosis of human pathogens• DIALOK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Development of Innovative Assaysand Locally acting therapies aimingat critical Kinases in hepatic andrenal fibrosis• DiaNa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Predictive diagnostics for diabeticnephropathy – Novel nanotechnologybased test platforms• Drop-Top. . . . . . . . . . . . . . . . . . . . . . . . . . . . 50Integration of DNA, RNA and proteinmarkers in a tool for the prognosisand diagnosis of human disease• EACCAD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54European approach to combatoutbreaks of clostridium difficileassociated diarrhoea by developmentof new diagnostic tests3

• ENLIGHT . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56New molecular methods and imageanalysis tools for analysis of cancerbiomarkers in situ• EPIVAC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58Development of a multi-stepImproved Epidermis Specific VaccineCandidate against HIV/AIDS• EURO-PHARMACO-GENE . . . . . . . . . 60Design of targeted GenePharmaceutics using self-assemblingfunctional entities• EXERA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62Development of 3D in vitro modelsof estrogen-reporter mouse tissuesfor the pharmaco-toxicologicalanalysis of Estrogen Receptors-Interacting Compounds (ER-ICs)• FASTEST-TB . . . . . . . . . . . . . . . . . . . . . . . . 66Development and Clinical Evaluationof Fast Tests for Tuberculosis Diagnosis• FGENTCARD. . . . . . . . . . . . . . . . . . . . . . . . 68Functional GENomic diagnosticTools for Coronary Artery Disease• GLYFDIS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70Glycans in Body Fluids- Potentialfor Disease Diagnostics• HI-CAM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72Development of a high-resolutionAnger camera for diagnosis andstaging of cancer diseases based onstate of the art detector technology• HighReX . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74High Resolution X-Ray Imaging forImproved Detection and Diagnosisof Breast Cancer• HIVResInh . . . . . . . . . . . . . . . . . . . . . . . . . . 76Preparation and Identification ofNew HIV Reverse TranscriptaseInhibitors Targeted Against HIV StrainsResistant to anti-HIV/AIDS drugs• HIVSTOP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78Development of an Effective RNAInterference-Based Anti-HIV-1 TherapyUsing an SV40-Derived Vector• IBDchip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80Usefulness of a new DNA array(IBDchip) to predict clinical course,development of complications andresponse to therapy in patients withinflammatory bowel disease (IBD)• IMMUNATH . . . . . . . . . . . . . . . . . . . . . . . . 82Translating innate immunereceptor function into diagnosticand therapeutic applications foratherosclerosis• Immuno-PDT . . . . . . . . . . . . . . . . . . . . . . . 84Immunophotodynamic therapyof cancer: concepts and applications• INDABIP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86Innovative diagnostic approachesfor biomarkers in Parkinson disease• INNOVAC . . . . . . . . . . . . . . . . . . . . . . . . . . . 88Highly innovative strategies forvaccination to poverty relateddiseases• INTELLIMAZE . . . . . . . . . . . . . . . . . . . . . . 90High-throughput, fully automatedand cost-effective behaviouralphenotyping of normal, clinicaland genetic mouse models• InVitroHeart. . . . . . . . . . . . . . . . . . . . . . . . 92Reducing Animal Experimentation inDrug Testing by Human CardiomyocyteIn Vitro Models Derived fromEmbryonic Stem Cells• LIGHTS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94Small ligands to interfere withThymidylate synthase dimer formationas new tools for development ofanticancer agents againstovarian carcinoma• liintop. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96Optimisation of liver and intestinein vitro models for pharmacokineticsand pharmacodynamics studies• MagRSA . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98Fully automated and integratedMicrofluidic Platform for Real-timeMolecular Diagnosis of MethicillinresistantStaphylococcus Aureus• MAMMI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100Mammography with molecularimaging• MANASP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102Development of novel managementstrategies for invasive aspergillosis• MEGATOOLS . . . . . . . . . . . . . . . . . . . . . . . . 104New tools for Functional Genomicsbased on homologous recombinationinduced by double-strand break andspecific meganucleases• MEMORIES. . . . . . . . . . . . . . . . . . . . . . . . . . 106Development, characterisation andvalidation of new and original modelsfor Alzheimer’s Disease• Mimovax . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108Alzheimer’s disease-treatment targetingtruncated Aβ 40/42 by activeimmunisation• MODEST . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110Modular Devices for Ultrahighthroughputand Small-volumeTransfection• MUNANOVAC . . . . . . . . . . . . . . . . . . . . . . . . 112Mucosal Nano Vaccine Candidatefor HIV• MYASTAID . . . . . . . . . . . . . . . . . . . . . . . . . . . 114Development of models to improvemanagement of Myasthenia Gravis: Frombasic knowledge to clinical application• MYOAMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116Amplification of human myogenicstem cells in clinical conditions• NanoSense . . . . . . . . . . . . . . . . . . . . . . . . . . 118Moving sensitive immunoassaysfrom slow and expensive to fast andaffordable nanoparticle-based methods• NEOBRAIN. . . . . . . . . . . . . . . . . . . . . . . . . . . 120Neonatal estimation of braindamage risk and identificationof neuroprotectants• Net2Drug . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122From gene regulatory networksto drug prediction4

• NPARI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124Tailoring of Novel Peptide coatingsand therapeutics derived froma newly identified component ofthe human innate immunity AgainstResistant Infections• OMVac . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126Novel prevention and treatmentpossibilities for Otitis Media throughthe comprehensive identification ofantigenic proteins• OptiCryst . . . . . . . . . . . . . . . . . . . . . . . . . . 128Optimisation of protein crystallisationfor european structural genomics• PHECOMP . . . . . . . . . . . . . . . . . . . . . . . . . 130Phenotypical characterisation ofanimal models for neuropsychiatricdisorders related to compulsivebehaviour• PHOTOLYSIS . . . . . . . . . . . . . . . . . . . . . . 132Development of flash photolysisfor deep uncaging in vivo andhigh-throughput characterisationof neurotransmitter gatedion channels in drug discovery• PlasmodiumdUTPase . . . . . . . . . . . . 134Deoxyuridine triphosphatenucleotidohydrolaseas a drug target against Malaria• POC4life . . . . . . . . . . . . . . . . . . . . . . . . . . . 136Multiparametric quantum dotbioassay for point of care diagnosis• PRIBOMAL . . . . . . . . . . . . . . . . . . . . . . . . 138Preclinical studies towards anaffordable, safe and efficacious twocomponentpaediatric Malaria vaccine• PRISM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140Phospholipid and glycolipidrecognition, interactions andstructures by magnetic resonance• PROLIGEN . . . . . . . . . . . . . . . . . . . . . . . . . 142Hypoxic renal proliferation• QuAGSIC . . . . . . . . . . . . . . . . . . . . . . . . . . 144Quantitative analysis of genes insingle cells• RATstream . . . . . . . . . . . . . . . . . . . . . 146European project on thecharacterisation of transgenic ratmodels for neurodegenerative andpsychiatric diseases: Automatedhome cage analyses, live imagingand treatment• RespViruses . . . . . . . . . . . . . . . . . . . . . . 148Immune response to viral respiratoryinfections and vaccination in theelderly• SAGE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150SME-led Antibody Glyco-Engineering• SERO-TB. . . . . . . . . . . . . . . . . . . . . . . . . . . 152Development of a SpecificSerological Kit for the Diagnosisof TB• SMARTER. . . . . . . . . . . . . . . . . . . . . . . . . . 154Development of small modulatorsof gene activation and repressionby targeting epigenetic regulators• STEMDIAGNOSTICS. . . . . . . . . . . . . . 156The development of new diagnostictests, new tools and non-invasivemethods for the prevention,early diagnosis and monitoringfor haematopoietic stem celltransplantation (HSCT)• STREPTOMICS. . . . . . . . . . . . . . . . . . . . 158Systems biology strategies andmetabolome engineering for theenhanced production of recombinantproteins in Streptomyces• SYSCO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160Systematic Functional analysis ofIntracellular Parasitism as a modelof genomes conflict• SysProt . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162System-wide analysis andmodelling of protein modification• TAMAHUD . . . . . . . . . . . . . . . . . . . . . . . . . 164Identification of early diseasemarkers, novel pharmacologicallytractable targets and small moleculephenotypic modulators inHuntington’s Disease• TargetHerpes . . . . . . . . . . . . . . . . . . . . . . . 166Molecular intervention strategies targetinglatent and lytic herpesvirus infections• TargetScreen2 . . . . . . . . . . . . . . . . . . . . . . 168Novel post-genomic cell-based screensfor drug targeting in membrane proteindisorders• TB-DRUG. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170A SME-STREP for Tuberculosis DrugDevelopment• TB-trDNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172Evaluation of transrenal-DNAdetection to diagnose tuberculosis• TEMPO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174Temporal Genomics for TailoredChronotherapeutics• USDEP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176Capture and enrichment of emergingpathogens for multiple and ultrasensitivediagnostic• VALAPODYN . . . . . . . . . . . . . . . . . . . . . . . . . 178Validated Predictive Dynamic Modelof Complex Intracellular PaCell Deathand Survival• VASOPLUS . . . . . . . . . . . . . . . . . . . . . . . . . . 180Placental Growth Factor (PlGF): newdiagnostic and therapeutic applicationsin cardiovascular disease• VITAL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182Development of optimized recombinantidiotypic vaccines for subset-specificimmunotherapy of B cell lymphomas• ZF-TOOLS . . . . . . . . . . . . . . . . . . . . . . . . . . . 184High-throughput Tools for BiomedicalScreens in ZebrafishLate submission:• PREGENESYS . . . . . . . . . . . . . . . . . . . . . . . 186Development of Early Non-InvasiveBiomarkers and Means for the Diagnosisand Progression Monitoring ofPreeclampsia and TailoringPutative Therapies• Index by project number . . . . . . . . . . 188• Index by coordinator. . . . . . . . . . . . . . . 1905

SME CALLForewordThe aim of health research under Framework Programmes is to help Europeexploit the unprecedented opportunities for generating new knowledgeand translating it into applications that enhance human health and boost thecompetitiveness of health-related industries and businesses in support of theLisbon Growth and Jobs strategy.Research intensive SMEs play a key role in the European Union’s economy, interms of competitiveness, innovation, growth and employment. Many of Europe’stop pharmaceutical companies had modest beginnings. Indeed, yesterday’s successfulSMEs are often today’s global giants, employing large workforces andgenerating enormous value.Hundreds of SMEs are active in health-related R&D and, in recognition of theirinnovative potential, scientific strength and strategic importance, a specialeffort to mobilise research-intensive health and biotech SMEs was made duringthe Sixth Framework Programme (FP6).In particular, at the end of the Framework Programme, the Thematic Priority entitled“Life sciences, genomics and biotechnology for health” published a verysuccessful “SME call” with a budget of € 200 million. This call for proposals wasparticularly aimed at funding projects with high numbers of research intensiveSMEs. The call succeeded in mobilising high-tech companies to participate inFramework Programmes: the 86 projects funded involved 270 SMEs, which wereallocated more than 40 % of the budget.Through this call, research-intensive SMEs in the health and biotech sectoracceded to a leading role as key players and driving forces in the researchactivities of EU-funded projects.The momentum achieved through this special call for proposals is expected togenerate an even bigger impact in the Seventh Framework Programme (FP7)projects, with increased participation of SMEs with a key role in research.This publication presents those 86 projects and aims to illustrate the EU’s commitmentto health research, bringing together transnational and multidisciplinaryexpertise from both industry and academia.Manuel HallenActing DirectorHealth Research7

SME CALLIntroductionThrough its Framework Programmes, theEuropean Union has provided support to medicalresearch for more than a quarter of a century,striving to prevent and cure diseases, and helpingto improve patients’ chances of survival and theirquality of life. At the same time, the EU has aidedthe efforts of the European healthcare industryin maintaining a leading role in the world.Between 2002 and 2006, the Sixth FrameworkProgramme (FP6) dedicated € 2.4 billion to theThematic Priority “Life sciences, genomics andbiotechnology for health” to support EuropeanResearch efforts, developing frontier technologies,encouraging excellence in fundamental and clinicalresearch, bringing academics, clinicians andindustry together at every stage of the process– from the laboratory bench to the hospital andto the market.The “Life sciences, genomics and biotechnologyfor health” Thematic Priority emphasised theimportance of innovation and the integration ofindustry, small and medium sized enterprises ( 1 ),by ensuring that new knowledge is disseminatedand translated into new therapies, diagnosticsand clinical practice. Overall, of the € 2.4 billion ofthe budget available for ‘health’, some € 335 millionwas awarded to SMEs participating in EU-fundedprojects, in particular through a special “Call forproposals for STREPs dedicated to SMEs”, in thelast year of FP6. These “SME-STREPs” have beenspecifically designed to support SME effortstowards research and innovation. Such projectswere centred on the reinforcement of SME’sscientific and technological knowledge and onthe validation of innovative solutions. ResearchintensiveSMEs played leading roles – althoughnot necessarily coordinating the projects – andparticipated alongside universities, research centres,other industries and industrial associations.The expected project results had to be of clearinterest and potential benefit to one or moreSMEs. The share of the EU contribution going tothe participating SMEs was expected to bebetween 30 and 50 %.Through this Call, 86 projects, which are the thefocus of this publicationhave been funded fora total contribution of € 200 million, from whicharound 40 % goes to around 270 SMEs. The scientificinvolvement included a wide range ofactivities, such as identification of biomarkers,elucidation of candidate genes and their role,providing microRNA discovery and validationplatforms or bioinformatics and transcriptomicanalysis, developing photonic and electro-optics,designing microchip or magnetic phase platforms,etc. Specialised SMEs with expertise in intellectualproperty management, technology transfer, projectmanagement or training activities also participatedactively in some of these projects.SMEs are the main economic drivers of healthcare,biotechnology and medical technologies.Through EU-funded collaborative research, SMEscan maximise the value of their expertise, networkinternationally, learn from other key players andreduce risk by collaborating with other SMEs andlarger industrial partners and academics from allover Europe and beyond.At the same time, the often pivotal technologicalinput from SMEs, as well as their business orientationand dynamism, will benefit other project participants. In this way, the output and the exploitationof the results can be optimised, and the spirit ofentrepreneurship in research supported.The momentum achieved by this Call to mobiliseresearch intensive SMEs is expected to generatean even bigger impact in the Seventh FrameworkProgramme (FP7) projects on the participation ofSMEs with a key role in research activity.(1) The official EU definition of an SME is anautonomous company with less than 250 employees,an annual turnover of not more than € 50 millionand/or an annual balance sheet total of not morethan € 43 million. For more details see:http://ec.europa.eu/enterprise/enterprise_policy/sme_definition/index_en.htm9

ACRONYMAGLAEAContract number: LSHM-CT-2006-037554 | EC contribution: € 1 198 900 |Starting date: 1 January 2007Duration: 36 monthsSUMMARYGlutamate is the most abundant excitatorytransmitter in the brain. However,very few models exist to explore thepotential of drugs that modulate glutamatetransmission. Because alteredglutamate transmission is involved innumerous psychiatric diseases, there isa strong need for such models to characterisethe effects of hypo- and hyper-glutamatergicstates on the onset anddevelopment of such diseases. AGLAEAwill develop and characterise models ofselective, partial knockdown of specificcomponents of the brain glutamatergicsystem in mice. This will provide a betterunderstanding of the implication of glutamatesignalling in diseases such asschizophrenia, anxiety and cognitive disorders.AGLAEA will lead to breakthroughresearch on the neurobiological and neurochemicalbases of psychiatric disordersand will enable the further testing of newdrugs for treatment. In order to selectivelyturn off specific components of the glutamatergicpathways, an siRNA approachwill be used. The effect of modulation ofglutamate signalling will be characterisedusing functional MRI (fMRI) and microdialysis/microsensoranalysis. Specificbehavioural tests will be carried outon live animals for the assessment ofglutamate-related psychiatric disorders.Furthermore, the data collected fromsiRNA experiments will be applied to thegeneration of transgenic mice, in whichmodulation of glutamate signalling will beinduced at different stages of development.Therefore, AGLAEA will provideboth the pharmaceutical and the academicworld with potent models. Thesemodels will be used to test novel compoundsand assess their therapeuticvalue and will benefit researchers investigatingthe neurobiological and neurochemicalbases of those diseases.The consortium set up to reach the objectivesof AGLAEA gathers 3 high tech SMEs,2 academic groups and one large group forthe management of the project (ALMA),altogether representing 4 Europeancountries (FR, HU, UK, NL).Development of novel animal models ofglutamatergic central nervous system disordersusing in vivo siRNA and transgenic approachesBackgroundModulation of glutamate signalling levels isassociated with many psychiatric disorders.Creation of reliable and practical models ofaltered brain glutamate function has been difficult.Glutamate is the most abundant excitatorytransmitter in the brain and interacts with numerousreceptors and transporters responsible forboth fast synaptic transmission and modulatoryfunctions. However, development of knockout(KO) rodents is expensive and time consuming,and gene KO is often associated with developmentalalterations. Inducible and conditionalknockout technologies have helped to alleviatethis problem. However, the gene is nearly completelysuppressed when the induction occurs.Because glutamate is a ubiquitous excitatorytransmitter, full knockout of a specific glutamatereceptor or transporter often yields a phenotypeincompatible with behavioural testing.AimAGLAEA is aimed at developing models of selective,partial knockdown of specific componentsof the brain glutamatergic system that will resultin hypo- and hyper-glutamatergic states yieldinganimals amenable to behavioural investigation.The results will then drive the creation ofspecific transgenic lines with targeted knockdownof components of the brain glutamate systemyielding mice that can be studied over longperiods of time.Expected resultsAccess to improved animal models of specific psychiatricdisorders will enhance the development ofimproved treatments, in particular for disorderssuch as schizophrenia where existing modelsare often based on limited pharmacological andneurobiological information about the disorder.Targeting the glutamatergic system should lead tomodels that more closely resemble the human situationwith regard to the symptoms that are atpresent not treated by existing drugs (e.g. cognitionin schizophrenia) or when existing drugs haveside effect and/or dependence issues anxiety). Thecreation of these models will also increase fundamentalresearch into the basic mechanisms ofglutamate function. In addition, the techniquesused will expand the use of siRNA in vivo for thecreation of new models in CNS disease, providingnew solutions for the exploration of suchpathologies.Potential applicationsA certain number of CNS disorders, includingschizophrenia, anxiety and cognitive disorderscan be linked to glutamatergic dysfunction. Theexisting treatments for patients suffering fromthese diseases have serious side effects and arenot always efficient. For example, existing drugsare unable to treat the social, emotional andcognitive symptoms of schizophrenia and thereare few marketed treatments for the cognitivedeficits of Alzheimer’s disease. By developingand characterising animal models with hypoandhyper-glutamatergic states, AGLAEA willprovide valuable data on the impact of glutamatergicsignalling on such disorders, thereforeopening the way for better treatment and care ofpatients.10

Key words: animal models, glutamate, siRNA, transgenic miceROLE OF SMEsThree SMEs, representing 60 % of the budget, are key contributors to the project. AddexPharmaceuticals, France, will coordinate the project and will study the effects of interferenceRNA and genetic manipulation of brain glutamate systems on behaviour in mice. Addexhas extensive expertise in the discovery and development of novel medications for centralnervous system diseases and will also examine the effects of experimental and referencedrugs to further validate the mouse models produced in the project. BioTalentum Ltd., basedin Hungary, has in-depth expertise in animal embryology, micromanipulation, embryonicstem cell transgenesis and cryopreservation, which will be applied to the production oftransgenic mice for the project. BioTalentum will use innovative techniques developed inhouseto generate knockdown mice in mouse strains most useful for neurobiological andbehavioural analyses. BioTalentum will also employ the latest techniques in rapid derivationof transgenic mouse lines to provide stable animal models as quickly as possible.Brains On-Line, based in The Netherlands, has broad expertise in the application of microdialysisto in vivo neuropharmacology and pharmacokinetic analysis of drugs in the brain.Brains On-Line will study the neuropharmacological consequences of interference RNA andgenetic knockdown of glutamate system genes in brain regions associated with diseases ofinterest, including schizophrenia, anxiety and cognitive disorders. Brains On-Line will alsoperform detailed immunohistochemical analyses of brain tissue to determine the anatomicaldistribution and extent of genetic knockdown resulting from the interference RNA andtransgenic manipulations. The three SMEs, along with their academic and corporate partners,each bring unique expertise critical to the success of this project.Scientific coordinatorBernard LudwigADDEX Pharmaceuticals France SASBehaviour DepartmentImmeuble Alliance – bat. A&CFR-74160 ArchampsBernard.Ludwig@addexpharma.comwww.addexpharma.comPartnersAndras DinnyesBioTalentum Ltd.Gödöllo, Hungarywww.biotalentum.huCharles MarsdenInstitute of NeuroscienceUniversity of NottinghamNottingham, United KingdomBen WesterinkDepartment of Biomonitoring & SensoringUniversity of Groningen,Brains-On-Line, The NetherlandsBenjamin QuestierALMA Consulting GroupLyon, France| A 2.3 Tesla magnetic resonance imaging (MRI) machineused to investigate the effects of drugs on neuronalactivity in regions of the mouse brain. The method willbe used in the present project to identify the effects ofaltering glutamate activity on brain region function.11

ACRONYMContract number: LSHB-CT-2006-037386 |EC contribution: € 1 993 208 | Duration: 24 monthsStarting date: 1 June 2006ANGIOSTOPSUMMARYANGIOSTOP proposes an approach todevelop a new, safer and more effectiveanti-angiogenic medicine that reducesthe pathological blood vessel formationassociated with solid tumor growth, ocularneovascularization (diabetic retinopathyand macular degeneration) and rheumatoidarthritis. The proposed drug target isPlacental Growth Factor (PlGF) and thecandidate drug is a humanised neutralisingmonoclonal antibody. This drug targetselection is based on recent basicresearch on the role of PlGF in pathologicalangiogenesis and ‘translationalresearch’ that established proof of conceptin experimental animal models.Using a lead candidate anti-PlGF antibody,it has been demonstrated that inhibitionof PlGF reduces solid tumourgrowth, inhibits ocular neovascularisationand alleviates arthritis symptoms.ANGIOSTOP will assure the developmentof an anti-PlGF antibody that may constitutea new, safer and efficacious medicinefor the treatment of diseases that dependon PlGF driven angiogenesis such as cancer,ocular disease and arthritis.Novel Anti-angiogenic treatment for Cancer,Arthritis and Ocular Neovascularization basedon Inhibition of Placental Growth Factor (PlGF)BackgroundMost anti-angiogenic strategies are focused onblocking the interaction between VEGF and itsreceptor VEGFR-2. Despite the success of Avastin,it is unlikely that VEGF-inhibitors alone will be sufficientto halt tumour angiogenesis. First, anincreasing number of studies document that blockingthe VEGF pathway leads to the induction ofalternative angiogenic signals. Secondly, it hasbeen reported that treatment of cancer patientswith Avastin significantly upregulates the levels ofPlGF. Finally, the currently available angiogenesisinhibitors have serious side effects, thus mandatingthe development of additional angiogenesisinhibitors. Due to the potential application ofangiogenesis inhibitors in disorders other thancancer, where the treatment is expected to start atearlier times after the disease onset and continuefor longer periods, safer anti-angiogenic drugswithout the risk of serious side effects are needed.Through gene targeting studies in mice, it has beenshown that loss of PlGF does not cause any vasculardefect during development, reproduction ornormal adult life, while it severely impairs angiogenesisand arteriogenesis during pathologicalconditions including ischemia, inflammation andcancer therefore indicating that the ANGIOSTOPanti-angiogenic strategy targeting PlGF couldrepresent a safer and more effective approach.AimANGIOSTOP aims to elaborate a comprehensiveapproach to the accelerated development of newefficacious and safer anti-angiogenic medicinesthat reduce the pathological blood vessel growthand can be used for the treatment of major progressivedisorders such as cancer, ocular neovascularisation(as observed in diabetic retinopathy andage-related macular degeneration) and arthritis.The overall objective of ANGIOSTOP is to developan anti-PlGF monoclonal antibody. The roadmapcomprises ‘translational research’ to validate previousproof of concept studies in new therapeuticallyrelevant small animal models, both in terms ofsafety and efficacy, to evaluate PlGF expression andits possible upregulation in cancer patients, and todevelop an industrial production process at theGMP level for critical path development.The project aims to perform extensive validationstudies of its drug candidate to reduce the risk offailure as the drug advances into clinical trials andto manufacture this product for clinical trials. Theultimate goal of ANGIOSTOP is to develop an anti-PlGF monoclonal antibody for the safe and effectivetreatment of cancer, ocular disease andarthritis. The research will focus on a selected drugcandidate but the new models and strategies willbe of more general utility for the development ofnew medicines aimed at increasing or reducingblood vessel formation, as well as for the advancementof the project’s understanding of pathologicangiogenesis.12

Key words: angiogenesis, cancer, ocular disease, arthritis, PlGFROLE OF SMEsBioInvent is the project coordinator.The purpose of the present consortium is to align a partnership strictly confined to participantswith unique essential assets (uniquely qualified academic research groups, SMEsowning intellectual property as well as essential know-how, and experienced clinical trialexperts) to allow a rapid focused development of new safe and efficacious medicines formajor diseases (i.e. solid tumours, AMD and diabetic retinopathy, and arthritis). The complementaritiesand synergy between the academic groups and SMEs will allow a focusedstreamlined development strategy, avoiding levels of bureaucratic decision making that isan unavoidable handicap of large networks and Big Pharma.Expected results• A lead humanised anti-PlGF antibody will be validatedin appropriate animal models.• Toxicology studies will identify a safe clinicaldose and document the cross-reactivity profileand any toxic effects of the lead candidate antibody.• Process development and industrial GMP manufacturingof the lead candidate antibody for criticalpath development will be carried out.• The protein expression of PlGF will be examinedin patient tumour samples. If PlGF levels correlatewith certain tumour types and associatewith grade and prognosis, such information maybe beneficial for identification of appropriatepatients groups.• Development of a fully human back-up antibodywith a similar or better pharmacological profileas compared to the lead candidate antibody willbe performed for contingency purposes.Scientific coordinatorTitti Martinsson-NiskanenBioInvent International ABLund, Swedentitti.martinsson.niskanen@bioinvent.comwww.bioinvent.comPartnersJean Marie StassenThromboGenicsLeuven, BelgiumPeter CarmelietFlanders Interuniversity Institutefor Biotechnology VZWLeuven, BelgiumChristian FischerCharité Universitaetsmedizin BerlinBerlin, GermanyEric Van CutsemKatholieke Universiteit LeuvenLeuven, BelgiumWen JiangCardiff UniversityCardiff, United KingdomPotential applicationsANGIOSTOP has both strategic and specific deliverablesand milestones. The new animal models andacquired knowledge on pathologic and therapeuticangiogenesis will transcend the specific aims of thedrug development programs and be of strategicsignificance for angiogenesis research in general.The translational and critical path research programhas a clearly defined ultimate deliverable:a new medicine based on PlGF-neutralizing antibodyfor anti-angiogenic treatment of certain solidtumours, ocular diseases and arthritis.| ANGIOSTOP is exploring the therapeutic potential andpleiotropic mechanism of anti-PlGF, antibodies againstplacental growth factor (PlGF), a VEGF homologue, whichregulates the angiogenic switch in disease but not in health.Anti-PlGF antibodies inhibit tumour growth by blockingangiogenesis. Distinct from VEGF inhibitors, however, targetingPlGF has been found to prevent infiltration of angiogenicmacrophages, and thus do not switch on the angiogenicrescue program responsible for resistance to VEGF inhibitors.This mechanism is illustrated with anti-PlGF (depicted in blue)preventing PlGF (green) binding to its receptor VEGFR-1 + (red)expressed on macrophages (orange).13

ACRONYMContract number: LSHM-CT-2007-037862 | EC contribution: € 1 984 900 | Duration: 36 monthsStarting date: 1 March 2007ARTEMISSUMMARYThe ARTEMIS project aims to design,develop and optimise an in vitro system toreplace the use of animals in transgenicsand toxicology experiments, and in studiesrelated to the effects of genes, chemicals,and neural tissue structure and function,such as memory and learning. From a scientificperspective, the ARTEMIS partnerstarget the development of a three-dimensionalneural tissue-like construct, which isformed by the synaptic connections developedamong neurons produced frommouse embryonic stem cells.For its operational goal, the consortiumseeks to replace transgenic animals withmemory and learning deficiencies withthe in vitro developed neural tissues.ARTEMIS will develop the tissue in vitrofrom embryonic cell lines with the genesinvolved in memory and learning ‘switchedoff’. The consortium will assess and comparethe ability of transgenic tissue tomemorise electrical stimuli with that ofnormal tissue.Assessing the role of genes in memory andlearning in vitro provides preliminary informationat tissue level, so as to determinethe design of the transgenic animalstowards the optimal ones with a higherprobability of having altered phenotypes.This would effectively reduce the numberof transgenic animals that are currentlyproduced by trial-and-error methods.The proposed in vitro system can effectivelyintegrate biochemical damage withbehavioural damage.In vitro neural tissue system for replacementof transgenic animals with memory/learningdeficienciesBackgroundIn vitro systems composed of synaptically interconnectedneurons have already been developedand used for pharmacological and toxicologicalstudies, based on the extracellular recording ofcell electrical activity. The neurons used in thesesystems are usually taken from animal tissues,because a readily renewable cell source such asthe tumour-derived neuronal cells, is of limitedapplicability due to their altered physiology.Consequently such approaches do not replacethe use of animals, since the cells they use mustbe taken from animals each time a test or a numberof tests is performed. In addition to this limitation,the existing in vitro neuronal systemscannot currently be considered as alternatives,but rather as complementary to in vivo procedures.This is because they provide only partialanswers to more complex problems, where intercellularsynaptic network level processes are critical– rather than intracellular ones – in assessinghuman hazards, for example the chemical effecton sensory or cognitive functions.AimThe development of an in vitro system of bioartificialneural tissue made from mouse embryonicstem cells with memory/learning capabilities.The in vitro system consists of a three-dimensionalneural tissue-like construct. It is formed by thesynaptic connections developed among neuronsgenerated from mouse embryonic stem cells. Theneurons are inside a porous biomaterial which containsmolecules that guide the development of thesynaptic network. The tissue is interfaced on twoopposite sides, with multi-electrode arrays forelectrical stimulation and response recording.During the development of the synaptic connections,an electrical stimulation is applied so that thefinal synaptic connectivity pattern will be stimulusspecificand will generate a stimulus-specific electricalresponse. Based on the signal features of theresponse, it can be evaluated when the tissue has‘memorised’ the electrical signal.The objective is to use in vitro developed neuraltissues instead of transgenic animals havingmemory and learning deficiencies. For this reason,the tissue will be developed in vitro fromembryonic cell lines that have the genes involvedin memory/learning ‘switched-off’, (transgenictissue). The ability of the transgenic tissue tomemorise electrical stimuli will be checked andcompared with this of normal tissue. In this way,the role of genes in memory/learning can bechecked in vitro, providing preliminary informationat the tissue level to orient the design oftransgenic animals towards optimal ones thathave a high probability of having an altered phenotype,therefore decreasing the number oftransgenic animals currently generated by trialand-errormethods.Due to the controlled complexity and the ease ofbiochemical analyses in the in vitro system comparedto in vivo experiments, the system will beused in tests aimed at providing information onthe biochemical mechanisms of memory defectsin neural tissue generated from trangsenic celllines, for which such defects in vivo experimentsfailed to clarify the mechanisms. If this task issuccessfully undertaken, the in vitro systemcould replace the use of transgenic animals insome cases of memory/learning deficiencies.In addition, the system will be used in neurotoxicitytests because it has the advantage of measuringtoxicity end-points at various levels of theorganisation of neural tissue such as sub-cellular,cellular and synaptic network levels, as wellas behavioural-like in memory/learning, whichare currently measured in separate in vitro systems(batteries), with the behavioural onesmeasured only in animal experiments. Specifictests with neurotoxic compounds will be performedin the system, to find what set of endpointbiochemical measurements are necessaryand sufficient for the prediction of memory damage,checking in this way the completeness ofthe complementarity of in vitro system-batteriescurrently in use. The developed in vitro systemis proposed as a system which can integrate14

Key words: bioartificial neural tissue, embryonic stem cells, multielectrode arrays, in vitro neuronal development,memory acquisition-learning, neurotoxicity, developmental toxicityROLE OF SMEs• Electronic Technology Team, (eTT)eTT is responsible for the signal analysis of the response of the synaptic network, so thatcriteria to detect the memory/learning ability will be formulated.• Bio Talentum Ltd., (BIO)BIO develops transgenic cell lines that have deficiencies in neural development andmemory, so that an assessment of the in vitro system will be made as a pre-screeningsystem to switch-off genes before the generation of transgenic animals.• Histopathology Ltd., (HISTO)HISTO performs all the histochemical analyses of the project for the detection of cellsinside the hydrogels and their state of differentiation.• BSL Bioservice Scientific Laboratories GmbH, (BSL)BSL participates in the design of the tests and performs the tests and various biochemicalmeasurements and off-line analyses needed for the correlation of the end points.• Quattromed, (QM)QM develops transgenic cell lines and memory function tests in the in vitro system, in orderto test the ability of the system to be used as transgenic tissue instead of transgenic animals.Scientific coordinatorPetros LenasComplutense University of MadridDepartment of Biochemistry and MolecularBiology IV, Veterinary FacultyParque Científico de MadridSantiago Grisolía, 228760 Tres Cantos, Madrid, Spainpetros.lenas@opt.ucm.eswww.ucm.esPartnersJanusz Marian RosiakInstitute of Applied Radiation ChemistryDivision of Applied Radiation ChemistryPolitechnika LodzkaLodz, Polandwww.p.lodz.plDaniel HorakDepartment of Bioanalogous and SpecialPolymers Group of Polymer Particles,Institute of Macromolecular Chemistry,Academy of Sciences of the Czech RepublicPrague, Czech Republicimc.cas.czAntonio NovellinoElectronic Technology TeamRome, Italywww.ettsolutions.combiochemical damages with behavioural ones.Based on the results of this project, a proposalfor formal pre-validation studies will be prepared,so that in the near future the system will be validatedand used instead of animals, in order topredict behavioural damages.Expected resultsAn in vitro neural tissue consisting of a threedimensionalnetwork of synaptically interconnectedneurons that exhibit higher-level, braintissue-like functionalities in memory acquisitionand learning. This tissue could replace the use ofmemory/learning deficient transgenic animals(in vitro transgenics), and the use of animals inneurotoxicity test related to behavioural-like(memory/learning) end points.Potential applications• Assessment of toxic or pharmacological effectson the neuronal functions in direct relation withthe in vivo situation, i.e. the impairment ofmemory or learning instead of end-point biochemicalmarkers when it is not known to whatextent they influence higher-level functions.15• Development of in vitro transgenic neural tissueas memory/learning disease model systems,using genetically modified instead ofnormal embryonic stem cells.• Neurotoxicity studies related to the developmentwith application of neurotoxic substancesat different developmental stages.• Drug tests directed at deciphering the effect atthe network level; for example, the anticonvulsantdrugs for epilepsy, which is caused by amalfunction of a network of neurons instead ofdefects in particular neurons, or the effects ofagents used in anaesthesia due to the inhibitionof the oscillations of the synaptic networkinstead of electrical activities of single neurons.• Development of intelligent biosensors for thedetection of biohazards training the network toneurotoxic compounds as stimuli, instead ofelectrical signals.• Development of neuroprostheses of the centralnervous system, intended to replace brain functionsthat have been lost due to disease ortrauma.Andras Janos DinnyesBio Talentum Ltd.Gödöllo, Hungarywww.biotalentum.huGeorge SzekeresLaboratory of HistopathologyHistopathology Ltd.Pecs, Hungarywww.histopat.huThomas HartungEuropean Centre for the Validationof Alternative Methods (ECVAM)Institute for Health and Consumer ProtectionIspra, Italywww.jrc.cec.eu.intThomas BeckerBSL Bioservice Scientific Laboratories GmbHPlanegg, Germanywww.bioservice.comErnest ArenasDepartment of Medical Biochemistry andBiophysics Division of Molecular NeurobiologyKarolinska InstituteStockholm, Swedenki.seEero VasarTiit TalpsepQuattromed A. S.Tartu, Estoniawww.quattromed.comJosé MendesDepartment of Physics, University of AveiroCampus Universitario de SantiagoAveiro, Portugalwww.ua.pt

ACRONYMContract number: LSHG-CT-2006-037897 | EC contribution: € 3 217 280 | Duration: 60 monthsStarting date: 1 January 2007AUTOSCREENSUMMARYThe overall objective of the AUTOSCREENproject is the establishment of an innovativeand automated screening instrumentfor high-throughput and high-contentscreens. This instrument will allow standardised,robust, automated and ultrasensitivehigh-resolution analysis of RNAsand proteins at cellular and subcellularresolution. The AUTOSCREEN consortiumis composed of six academic partners(Research Institutes and Universities) andfour SMEs.AUTOSCREEN for Cell Based High-throughputand High-content Gene Function Analysis andDrug Discovery ScreensBackgroundAs more and more genomes are being sequenced,efficient methods to elucidate the functions of themany unknown genes need to be developed. Suchmethods will be crucial in future attempts to aligngenes of unknown functions in biochemical pathwaysand networks that carry out the essentialprocesses in all living organisms. These methodswill also be an essential prerequisite for turningbiology from a qualitative, mostly descriptive science,into a quantitative, ultimately predictive,science.Although quantitative tools such as DNA microarraysfor transcriptome analysis of biological systemshave been available for some years, they havenot yet been used to their full potential due to theoverwhelming complexity and indeterminate compositionof biological systems. Such intricacy hasoften prevented the integration of this informationinto comprehensive and cohesive models.Cells are built from thousands of different proteinsthat are expressed, both temporally andspatially, over an extremely wide dynamic range.Proteins and other cellular components are regulatedthrough variations of their location, theiractivity and their state of modification. AlthoughDNA microarrays have proved to be importanttools for gene discovery on the tissue level, and,moreover, hold great promise for diagnosticapplications, they have major shortcomings intheir lack of cellular resolution. In order to obtainqualitative and quantitative data on cellular pathways,equipment that allows recording of transcriptsand proteins at the high precision and athigh-throughput needs to be developed.AimThe main goal of the project is to develop an innovativescreening platform suitable for highthroughputand high-content cell-based assaysand to demonstrate its suitability for high-resolutionin situ techniques. This instrument, calledAUTOSCREEN, will not only provide the basis forintelligent and efficient high-content screens, butwill also be designed for low cost genetic, medical,chemical and pharmaceutical screens. The integrationof novel technologies into a common platformconcept, the development of efficient cell-basedscreens, and the demonstration of the feasibility ofthis approach will constitute a significant competitiveadvantage for the European pharmaceuticaland agrobiotechnological industry.Expected resultsThe main expected result of the project is the generationof an innovative screening instrument,called AUTOSCREEN. This instrument, which willconsist of the modular iMIC imaging microscopyplatform as a future microscopy standard, will integrateultra-sensitive CCD-technology and novelsoftware concepts that allow an adaptive, i.e.results-based, shaping of the ongoing experiment.This will facilitate the reduction of an otherwiseuninterpretable datastream. An ultra-sensitive fluorescence-basedscanning device for single-moleculemeasurements and a fully automated platefeeder station for automated sample handling andtracking will increase the flexibility and wide utilityof AUTOSCREEN. This system will be tested ina large number of applications for performance andexcellence.The project is expected to permit the qualitativeand quantitative monitoring of cellular constituents(RNA, proteins, and metabolites) in livingcells at the highest possible cellular andsubcellular resolution and with maximal sensitivityand specificity. This will allow quantifyingprotein expression and monitoring its subcellularlocalisation, its state of modification and itsassociation with other proteins and ligands.Furthermore, it will allow measuring of the changeof these processes over time. Characterisationof the toponome will overcome major limitationsof contempory functional genomic and proteometechnologies, which do not provide cellular orsubcellular resolution, and will permit highcontentscreens for pharmacological substanceswith fewer side reactions.16

Key words: high throughput analysis, imaging, screening, genomics, proteomics, drug screeningROLE OF SMEsWithin the AUTOSCREEN project, the partner SME companies will establish a widelyapplicable robot-automated screening tool by conceptualising and assembling a firstAUTOSCREEN prototype. The SMEs will develop a full automation of the prototype,improve the innovative iMIC microscope platform in iterative improvement steps, anddevelop a variety of optimisations, assays and applications. The following partners areinvolved in AUTOSCREEN as SMEs: TILL, MANZ, ANDOR and ARO.The contribution of TILL will be the development of novel concepts for overcoming the currentlimitations of high throughput imaging, and to contribute to the development of new adaptivesoft- and firm-ware concepts for automated imaging. Later, TILL will integrate new developmentsboth from within and outside the consortium, evaluating the overall performance ofall evolutionary stages of the process and specifying future activities. TILL is also involved inthe exploitation and dissemination of results and in the management of the project.MANZ will concentrate on defining substrates, handling objects and system specificationsand on automated handling of substrates.ANDOR will be responsible for further enhancing the new price/performance, single photonsensitive Luca EMCCD camera and will cooperate with TILL in developing novel readout patterns.ARO will be involved in several WPs to assess the quality of AUTOSCREEN under a broad varietyof experimental conditions, specifically with respect to proteome visualisation capabilities.Scientific coordinatorKlaus PalmeUniversity of FreiburgCenter for Applied BiosciencesInstitute for Biology IIFaculty of BiologySchanzlestr. 179104 Freiburg, Germanyklaus.palme@biologie.uni-freiburg.dewww.uni-freiburg.dePartnersStefanie KlemmTILL ID GmbHMunich, Germanywww.till-photonics.comAndras FilepManz KftDebrecen, Hungarymanzautomation-c.cegbongeszo.hu/nyito-en.htmJan HesseUpper Austrian Research GmbHLinz, Austriawww.uar.atColin CoatesAndor Technology PlcBelfast, United Kingdomwww.andor.comPotential applicationsAUTOSCREEN will have a strategic impact on functionalgenomic, biotechnological and biomedicalresearch by permitting qualitative and quantitativemonitoring of cellular constituents in cells atthe highest possible cellular and subcellular resolutionand with maximal sensitivity and specificity.This will allow, for example, quantifyingprotein expression, monitoring of its subcellularlocalisation and state of modification, and characterisationof the toponome.The demonstration of the wide applicability ofAUTOSCREEN to the quantitative monitoring ofbiological processes, within living cells, at highestcurrently possible resolution and with sensitivityto the limit set by the laws of physics, will havea significant impact on biomedical research ingeneral. By combining interdisciplinary activitiesfrom academic and industrial sources and byinterfacing biological research with nanotechnology,computing and engineering, the team expectto create an important tool for biomedicalresearch. Moreover, AUTOSCREEN-based assayswill allow the monitoring of cellular networks andincorporate in vivo protein interaction assays andfeatures like protein concentration and kineticparameters. Thus, available information on geneexpression networks will not only be useful foridentifying points of the network affected by thedrugs and for simulations of cellular processes,but will also allow the assessment of drug sidereactions at an early stage and facilitate thedesign of novel, less toxic compounds.The project will reveal new, faster and better waysto determine gene functions and regulatory networksin a much shorter period of time. The implementationof these technologies will lead to ahigher competitiveness of European biomedicalSMEs, in the sense that the instrumentation to bedeveloped and assembled in this project willenable many European SMEs to efficiently performtheir screens. The estimated low cost of thisinstrument is expected to be of great benefit forSMEs as it will promote their market success. Theproject will also provide the opportunity for establishinga new industry standard for automatedmicroscopy and thus provide opportunities notonly on an individual basis, but also for largermanufacturers who will benefit from the innovativeapproach for which currently there is no equalon the world market.Carmen PlasenciaAromics S.L.Barcelona, Spainwww.aromics.es/eng/index.htmMartin OheimInstitut National de la Santé etde la Recherche Médicale (INSERM)Neurophysiology andNew Microscopy LaboratoryParis, Francewww.biomedicale.univ-paris5.fr/neurophysiologie/labo/oheim.phpHartmann HarzLudwig-Maximilians-UniversitätBioImaging ZentrumMunich, Germanywww.biz.uni-muenchen.deBenedetto RupertiUniversity of PadovaPadova, Italywww.unipd.itLadislav NedbalInstitute for Systems BiologyNove Hrady, Czech Republicwww.greentech.cz17

ACRONYMBacAbswww.bacabs.orgContract number: LSHB-CT-2006-037325 | EC contribution: € 2 269 999 |Starting date: 1 January 2007Duration: 36 monthsSUMMARYHigh throughput cloning and expressionof large sets of genomic ORFs hasbecome a preferred industrial strategyfor genome-wide searches of new vaccinecandidates. For invasive infectionsin particular, the aim is to find proteinseliciting antibodies capable of binding tothe bacterial cell surface and, throughinteraction with the complement system,effectively kill the bacteria. However,current data accumulating from reversevaccinology studies (targeting of possiblevaccine candidates starting fromgenomic information) show that onlya small fraction of surface-exposed proteinsappears to elicit antibodies withbactericidal activity. By using informationgenerated by reverse vaccinologyprojects within the Consortium, theBacAbs project will apply a novel multi -disciplinary approach to single out thestructural requirements for viable bactericidalvaccine candidates and willdevelop bioinformatics tools to predictcompliance with such structural requirements.To this end, a systematic analysisof sequence, structure, dynamics andinteractions of selected protein targetswill be undertaken using model systemsof medical interest such as serogroup-BNeisseria meningitidis, a pathogencausing septicemia and meningitis forwhich no effective vaccine exists. TheConsortium comprises an industrialpartner with extensive experience onvaccine development, three SMEs withstrong expertises on several of the keytechnological aspects of the project, andfive academic partners with internationallyrecognised tracks on experimentaland theoretical studies of protein structureand interactions.Assessment of Structural Requirements inComplement-Mediated Bactericidal Events:Towards a Global Approach to the Selectionof New Vaccine CandidatesBackgroundThe development of antibiotic resistance in pathogenicbacteria is potentially one of the most seriousthreats in modern medicine( 1 ). One approach tominimize the use of antibiotics is to vaccinateagainst pathogenic strains of bacteria. A clear candidateto this approach is Neisseria meningitidis,a major cause of bacterial septicemia and meningitis.N. meningitidis is a Gram-negative bacterium,capsulated in its invasive form, classified into fivemajor pathogenic serogroups on the basis of chemicalcomposition of distinctive capsular polysaccharides( 2,3 ). Although a promising candidate ison clinical trials ( 4 ), there is not yet an effective vaccineagainst serogroup-B N. meningitidis (MenB),responsible for over 50% of all meningococcal diseasein Europe( 5 ). The capsular polysaccharide ofMenB is identical to a widely distributed human carbohydrate,making its use as the basis of a vaccinefor prevention of MenB diseases problematic( 6 ). Asa consequence, most efforts have turned to developmentof vaccines based on surface-exposed orexported proteins( 7 ).A bactericidal response, i.e. one which leads to bacterial-celldeath, can be triggered through a varietyof mechanisms. For meningococcal infections, invitro bactericidity assays with immune sera correlatewith protection in humans( 8 ). Although in vivoprotection against MenB may not be solely achievedby complement-dependent bacteriolysis( 10,11 ), anantigen that elicits (murine) antibodies capable oftriggering bacterial-cell death in vitro in a complement-dependentmanner is normally considered acandidate for human vaccine development( 11,12 ).In this context, one major obstacle to vaccine development,besides sequence and antigenic variability(13 ), is the difficulty to identify antigens that willgenerate a bactericidal response. Typically, onlya very small fraction of the antibodies raised inlarge-scale antigen-screening studies are bactericidal(14 ). Thus, while potential antigens can be readilyidentified this information is of little use unless weare also able to predict which antigens can lead tothe production of bactericidal antibodies.In principle, the capacity of a protein antigento raise bactericidal antibodies may depend on(a combination of):• size, shape, structural complexity, abundance,solubility, and propensity to oligomerization; and• sequence, structure, dynamics and location ofspecific protein regions (epitopes).These factors may in turn modulate the propertiesof the Ag-Ab complex and its susceptibility to berecognised by the C1q component. The BacAbsproject aims at deciphering possible correlationsbetween these factors and bactericidity.AimFollowing the framework outlined above, theBacAbs project is concerned with the identificationof (surface-exposed or exported) proteinantigens that may elicit complement-mediatedbactericidity in vitro. This includes early discriminationof antigens that may induce production ofnon-bactericidal antibodies. To achieve this goal,the Consortium will investigate the requirementsfor productive Ag-Ab-C1q complex formation andproposes to find relevant answers by studyingwith a multidisciplinary and comparative approachthe structure of a number of these complexes,taking the MenB vaccine-development project ofNovartis Vaccines & Diagnostics as a model andsource of useful data and reagent molecules. Tosingle out possible structural determinants,focus will be put on groups of antigens with similarsize, abundance, solubility, etc. (eliciting andnot eliciting bactericidal antibodies).Although initially centred around group-BN. meningitidis, the specific target of the projectis the development of tools that can be effectivelyapplied to genome-wide identification of vaccinecandidates against any bacterial pathogensusceptible of complement-mediated lysis.18

Key words: vaccines, structural biology, computational biology, antigen, monoclonal antibody, complement system, bactericidity, proteincrystallogenesis, X-ray crystallography, NMR, mass spectrometry, molecular modelling, molecular-dynamics simulation, molecular dockingROLE OF SMEsThe three SMEs involved in the BacAbs project have a principal technological role. The ITcompany INFOCIENCIA S.L. will be implementing the management and dissemination webservers of the Consortium, performing bioinformatics analysis of antigen and epitopesequences, implementing algorithms, protocols and data emerging from the Consortium’swork into computational tools and databases within a web-based technological platform,and evaluating the commercial interest of this platform via demonstration. Two biotechs willbe working on sample preparation and protein-structure determination. ASLA Biotech Ltd.will be performing protein expression and labelling, screening and optimisation of sampleconditions for NMR analysis, monoclonal antibody generation, and sequential backboneassignment and structure determination via NMR. Bio-Xtal S.A. will be performing proteinexpression and purification, especially in connection to derivatives (seleno-methioninelabelled) for X-ray analysis, expression and solubilization screens on highly hydrophobic orpoorly soluble targets, exploration of protein crystallogenesis using nanodrop scale roboticstechniques based on commercially available and proprietary screening approaches, developmentand optimization of robotic processes for crystallization plate storage and drop visualization,refinement of crystal growth conditions for selected hits to yield diffraction qualitycrystals, and X-ray data collection and structure solution.Scientific coordinatorXavier DauraUniversitat Autònoma de BarcelonaCampus UAB s/n08193 Bellaterra (Cerdanyola del Vallès)SpainXavier.Daura@uab.eswww.uab.esPartnersGuido GrandiNovartis Vaccines and DiagnosticsSiena, Italywww.novartisvaccines.comAnatoly SharipoASLA BIOTECH, Ltd.Riga, Latviawww.asla-biotech.comEtienne L’hermiteBio-Xtal S.A.Mundolsheim, Francewww.bioxtal.comExpected resultsThe BacAbs project shall provide:• Structural information on a set of proteins thatare components of the cell surface (the bacterialorgan for interaction with eukaryotic host cells)of a major human pathogen.• Improved experimental protocols and techniques,bioinformatics tools and databases toassist the development of vaccines againsthuman bacterial pathogens in general, andgroup-B Neisseria meningitidis in particular.• A framework in which experimental and in silicomethods for determining protein structure andstudying macromolecular recognition, immunologicalresponse mechanisms, and sequencestructure-functionrelationships can be furtherdeveloped.• A web-based technological platform integratingthis knowledge, with a potential to improving theeffectiveness and reducing the costs of vaccinecandidatesearches.Potential applicationsThe results of the BacAbs project have potentialapplication in the selection of new vaccine candidatesagainst group-B Neisseria meningitidis andother bacterial pathogens.References(1) Borchardt, Drug. News Perspect. 2004, 17, 219; (2) Gotschlichet al., J. Exp. Med. 1969, 129, 1349; (3) Gotschlich et al., J. Exp. Med.1969, 129, 1367; (4) Giuliani et al., Proc. Natl. Acad. Sci. USA 2006,103, 10834; (5) Cartwright et al., Vaccine 2001, 19, 4347;(6) Hayrinen et al., J. Infect. Dis. 1995, 171, 1481; (7) Jodar et al.,Lancet 2002, 359, 1499; (8) Goldschneider et al., J. Exp. Med.1969, 129, 1307; (9) Welsch et al., J. Infect. Dis. 2003, 188, 1730;(10) Vermont & Dobbelsteen, FEMS Immunol. Med. Microbiol.2002, 34, 89; (11) Pizza et al., Science 2000, 287, 1816; (12) Welschet al., J. Immunol. 2004, 172, 5606; (13) Poolman, Infect. AgentsDis. 1995, 4, 13; (14) Rappuoli, Science 2003, 302, 602.Giorgio ColomboConsiglio Nazionale delle RicercheIstituto di Chimicadel Riconoscimento MolecolareMilano, Italywww.icrm.cnr.itMartin ZachariasJacobs University Bremen GmbHSchool of Engineering and ScienceBremen, Germanywww.jacobs-university.deMartino BolognesiUniversità degli Studi di MilanoDipartimento di Scienze Biomolecolarie BiotecnologieMilano, Italywww.unimi.itAlexandre BonvinUniversiteit UtrechtDepartment of ChemistryUtrecht, The Netherlandswww.uu.nlJose Manuel MasINFOCIENCIA S.L.Barcelona, Spainwww.infociencia.com| Solution structure of the antigenic domain of GNA1870,a 28-kDa surface-exposed lipoprotein of Neisseriameningitidis. This is one of the most potent antigensof Meningococcus discovered by reverse vaccinology(Protein-Data-Bank entry 1YS5).19

ACRONYMContract number: LSHG-CT-2006-037939 | EC contribution: € 1 800 000 | Duration: 30 monthsStarting date: 1 December 2006BioBridgeSUMMARYBioBridge will focus on the application ofsimulation techniques on top of multileveldata, in order to create models forunderstanding how molecular mechanismsare dynamically related to complexdiseases at the systemic level. The projectwill explore and identify gaps in information,and develop and apply standardsfor the transfer and filtering of data fromexisting molecular biology databasesand new high-throughput experiments(microarray, in vivo metabolic profilingand proteomics data) into metabolicmodels of complex diseases. SMEs areinvolved in BioBridge from its inception,so that newly developed protocols will becommercially exploitable. The project willtherefore drive the standardisation ofanalysis of relevant aspects of disease.Integrative Genomics and Chronic DiseasePhenotypes: modelling and simulation toolsfor cliniciansBackgroundChronic diseases are usually the result of interactionsbetween individual susceptibility and differentenvironmental and/or lifestyle factors, and areoften modulated by multiple genes. The interplaybetween these factors determines disease phenotypeand hence, the prognostic and therapeuticimplications of the disease. This interplay betweengenetically predetermined susceptibility and diseasephenotype can, in turn, be revealed by computeranalysis integrating clinical and biomedicaldata. Computer analysis related to clinical problemsis currently in a phase of accelerated growth.Some examples of the application of computeranalysis to clinical practice are the classificationand prognosis of ovarian cancer( 1 ), the analysis ofmyocardial perfusion images and cardiograms ( 2 )and the development of a screening device for thediagnosis of heart murmurs( 3 ). In addition, severalprojects in the European Union are implementinginformation technology-based services for diabetesmanagement ( 4 ).However, all the approaches currently implementedin clinical practice use very limited datasets, despitethe availability of vast amounts of data from variouslife science disciplines since the ‘-omics’ revolution.Only by integrating genomic, proteomic andmetabolomic data, can knowledge that is useful forthe understanding and treatment of complexhuman pathologies begin to be obtained. This is thegoal of the BioBridge project.AimThe BioBridge objectives are twofold. First, a bioinformaticaspect will involve the development ofsoftware for integrated genomic, proteomic,metabolomic and kinetic data analysis, in order tobuild a bridge between basic science and clinicalpractice. Secondly, a biomedical aspect will focuson understanding the distortion of cellular metabolismthat is associated with certain target diseases.The diseases in question are congestiveheart failure (CHF), chronic obstructive pulmonarydisease (COPD) and type II diabetes. The availablefacts strongly indicate that these diseases comprisea cluster of chronic conditions, all of whichare associated with nitroso-redox imbalance. Theintegration of data into a dynamic framework willenable the development of the first kinetic modelof the metabolism shared by COPD, CHF and typeII diabetes, thereby revealing the common andindividual traits of these three complex diseases.Expected resultsAfter 30 months, BioBridge will have achievedthe following goals:• creation of a structured database for the collectionof clinical information relating to COPD, CHFand type II diabetes;• identification of the metabolic pathways implicatedin the target diseases;• recording of genomic, proteomic, metabolomicand kinetic information onto the relevant structureddatabases;• development of a software product designed forspecific disease-related data searching;• development of standards for the different levelsof data, which will be useful for their integrationfrom genomic and metabolomic databases, andfrom specific proteomics and metabolomics profilingexperiments, including microarray analysisand stable isotope tracer data. These will bemainly Bayesian networks and multivariateanalysis tools;• development of protocols for transferring datafrom the structured databases into dynamicmodels;• using a differential equation approach, thedesign and development of an innovative simulationenvironment that will accommodate thedynamic behaviour of complex networks, and inparticular the metabolic pathways that arealtered by the target diseases;• development of generic tools that will be clini callyuseful beyond the target diseases addressedduring the lifetime of the project. BioBridge willalso focus on interfacing with end-users, in particularclinical researchers and clinicians.20

Key words: diabetes, chronic obstructive pulmonary diseases, chronic heart failure, systemic effects, genomics,proteomics, metabolomics, modelling, bioinformaticROLE OF SMEsThe Biobridge consortium brings together 3 selected SMEs with complementary skills inthe domains of semantic interoperability, heterogeneous data integration and simulationtechnologies.MathCore Engineering AB develops integrated tools in modelling, simulation, control, andvisualization of complex systems. This expertise is fundamental in the project tasks relatedto the creation of Mathmodelica Metabolic Pathway simulator. This tool will positionMathCore very solidly in the biological simulations field.Biomax Informatics AG provides state-of-the-art software for the biopharmaceutical industrywith a focus on data integration, data retrieval, knowledge aggregation and generation.The Biobridge project uses its BioXMTM Knowledge Management Environment to integrateand organize heterogeneous data types. Additionally, its software BioRSTM allows ubiquitousretrieval of data for project participants.Genfit is a leading European drug discovery company in the field of cardiovascular, metabolic,inflammatory and CNS disorders. Genfit brings its LSGraph® technology to the projectthat facilitates the handling of information individual graph nodes and integration ofinformation from NCBI Gene, PubChem, Uniprot, GO, KEGG etc. This technology also features:data mining capabilities, tracking of relations and evidence and an associated searchengine to elucidate the regulatory mechanism(s) behind the observed effects.Scientific coordinatorJosep RocaDepartment of PneumologyInstitut d’InvestigacionsBiomèdiques August Pi i SunyerBarcelona, Spainjroca@clinic.ub.esPartnersPeter AronssonMathCore Engineering ABLinköping, Swedenwww.mathcore.comJohn BrozekGenfit LaboratoriesGenfit S.A.Loos, Francewww.genfit.comAndrea RamgeDieter MaierBiomax Informatics AGMartinsried, Germanywww.biomax.com/company/company.phpJordi Villà i FreixaComputational Biochemistryand Biophysics Laboratory,Universitat Pompeu FabraBarcelona, SpainPotential applicationsThe main outcome of the project will be a protocolfor organising multilevel data related to the targetdiseases into a convenient form for use in the constructionand refinement of kinetic models ofintracellular metabolic pathways. The softwaredeveloped will be applicable to more generalcases of multilevel data integration.In helping to provide insights into the key molecularmechanisms that determine poor prognosisin the CHF/COPD/type II diabetes disease cluster,BioBridge will generate novel strategies for personalisedprevention and enhanced delivery ofpatient care.Existing computational models have alreadyproved powerful in this context. For example, oneof the BioBridge partners has recently developeda statistical framework for analysis of multivariatemodels from large-scale datasets. This softwareenvironment (GALGO) uses a genetic algorithmsearch procedure, coupled with statistical modellingmethods, for supervised classification andregression. GALGO is relatively easy to use, canmanage parallel searches and has a toolset forthe analysis of models. Another partner hasdeveloped methodologies for biologically-drivenvariable selection, also using a genetic algorithmsearch strategy. BioBridge will build on andimprove these and other computational models.References(1) Wu et al, 2003; (2) Fletcher et al, 1978); (3) (Bhatikar et al,2005); (4) (Bellazzi et al, 2004).Pranav SinhaInstitut für Medizinische undChemische Labordiagnostik,Landeskrankenhaus KlagenfurtKlagenfurt, AustriaFrancesco FalcianiSchool of BiosciencesUniversity of BirminghamBirmingham, United Kingdom| The increasing size and complexity ofbiological database and the capacity ofnew experimental designs to determinehigh throughput data for specificemphasises the significance of the threelevels in the figure: a) the need forstructured databases related with theproblem, b) the need for formats, likeSBML, able to translate the structureddata into dynamical models, and c) thedevelopment of powerful modelingtechniques ultimately able to make use ofand to interpret clinical data. Note thatthe connecting SBML spans both thestructure of the database and themodeling environment, gluing togetherall the pieces of the puzzle.21

ACRONYMContract number: LSHC-CT-2006-037559 | EC contribution: € 2 804 075 |Starting date: 1 January 2007Duration: 36 monthsCancerGridwww.cancergrid.euSUMMARYIn the three years of this multidisciplinaryresearch project, the 10-member Consor -tium plans to develop and refine methodsfor the enrichment of molecular librariesto facilitate discovery of poten tial anticanceragents. Using grid-aided computertechnology, the likelihood of findinganti-cancer novel leads will sub stantiallyincrease the translation of basic knowledgeto application stage.In particular, through the interaction withnovel technologies and biology, the R&Dconsortium aims at:• developing focused libraries with a highcontent of anti-cancer leads;• building models for prediction of diseaserelatedcytotoxicity and of kinase/HDAC/MMP and other enzyme (i.e. HSP90)inhibition or receptor antagonism usingHTS results;• developing a computer system based ongrid technology, which helps to accelerateand automate the in silico design oflibraries for drug discovery processes,and which is also suitable for futuredesign of libraries for drug discoveryprocesses that have different biologicaltargets (the result is a new marketabletechnology).Grid-aided computer systemfor rapid anti-cancer drug designBackgroundAfter the completion of the sequencing stage ofthe human genome project, the major focus ofdiscovery efforts turned to the identification ofthe ‘druggable’ portion of the genome that islinked to pathological states and is able to interactwith the drug-like chemical space, restoringnormal functions.Apparently, the druggable genome is a subset ofthe 30 000 genes in the human genome thatexpress proteins and represent, in many ways, anunprecedented gift and exceptional opportunity fordrug discovery scientists and for patients who arehoping for therapies of diseases currently uncured.That subset (estimated as ca. 3 000 proteins) isable to bind drug-like molecules as characterisedby the Lipinski’s rule-of-5 criteria.In order to find more rapidly small molecule modulatorsto the newly emerging validated targets,the high-throughput screening provides a reasonablesolution to screen large compound libraries.However, it seems most of the targets can be classifiedinto large target families such as kinasesand GPCRs: thus, development of target focusedlibraries could dramatically increase the hit rateas well as open the way to identify selectiveinhibitors/antagonists within the target families.The idea of ‘focused libraries’ or ‘targetedlibraries’ of molecules emerged in recent yearsas a ‘compromise’, or as an attempt to bridgebetween two seemingly conflicting approachesto drug discovery:• High Throughput Screening (HTS), by whichhundreds of thousands of compounds, mainlyin big pharma, were tested against a (hopefullyvalidated) biological target such as a protein ora cellular system. The basic assumption of HTSis that large numbers and diversity shouldcover chemical space well enough to find, atleast, ‘hits’ (that are active in micromolar concentrations)which may subsequently be transformedto ‘leads’ (with affinities in thenanomolar range and with reasonable drug-likeproperties) and finally to drug candidates.Combinatorial chemistry has also been on theside of HTS, presenting the ability to synthesisehuge amounts of derivatives based on specific‘scaffolds’.• Rational drug design approaches such as structure-baseddesign and ligand-based design.The first takes into consideration the detailedatomic structure of the target and the possibilitiesfor forming physical interactions (i.e.,hydrogen bonds, Van der Waals interactions,electrostatic complementarity, hydrophobicity,etc.) between small molecules and specificsites on the targets, while the second dependsmore on properties of known active moleculesand uses similarity ideas (including ‘pharmacophore’searches) to discover new active molecules.The substantial reduction in discoveringnew chemical entities by big pharma in recentyears has been in part attributed to the failuresdue to very low hit rate in both the HTS andCombichem, on the one hand, and on theinability to properly taking into account thepharmacokinetic (ADME/Tox) effects as well asfor entropy, solvation and target flexibility instructure- and ligand-based designs.A landmark in introducing pharmacokinetic considerationsto drug design and developmenthas been the ‘Rule of 5’ of Lipinski. This idea,which is now less than a decade old, also providedan immediate tool to reduce the size ofcombinatorial libraries and of HTS candidates by‘filtering’, i.e., requiring that all molecules mustpass the Lipinski rule (three out of four conditionsfor the limiting of molecular weight, calculatedlipophilicity, and the numbers of H-bond donorsand acceptors) in order to be in the properbioavailability range.22

Key words: ?? bioinformatics, pharmacology, grid technology, library design, in-silico prediction of drug-like properties,prediction of ADME parameters, predictive toxicology, creation of virtual librariesROLE OF SMEs|AInte:Ligand (Austria) will provide in silico screening of compound databases of commerciallyavailable small drug-like molecules, consulting in compound profiling, and decisionsupport tools for medicinal chemistry. The company will generate virtual libraries for theconsortium partners and will distribute its library generation software tools to the membersof the consortium. Inte:Ligand will also market the enhanced versions of its software andexploit its enlarged competences in ligand target interaction modelling.GKI Economic Research Co. (Hungary) gained experience in leading international consortiaby acknowledging the importance of interactivity and proactive communication in facilitatingprojects with a variety of key actors. In CancerGrid, a similar approach will be taken.From the social science standpoint, it is also important to raise awareness towards theobjectives and anticipated results of CancerGrid. With this in mind, GKI will prepare andpublish a case study of the project, targeting a wide audience beyond the direct stakeholders.GKI will also be responsible for organising the involvement of direct or indirect stakeholdersin the area of CancerGrid (such as healthcare providers and physicians, industry,regulatory authorities, experts in ethics, law and social sciences, health economics, publichealth, patient organisations, policy-makers etc.) as appropriate.|BDAC (Italy) is a biopharmaceutical company, founded in 2004, specialized in the identificationof new anti-tumour drugs. In particular, DAC is developing new proprietary smallmoleculecompounds with inhibitory activity against chromatin remodeling enzymes(histone deacetylases) and against HSP90, key players in cancer and non-cancer diseases.As a partner of the CancerGrid consortium, DAC will initially develop target-based assaysin order to perform screenings of compounds previously identified as hits in the cellbasedscreening. Moreover, DAC Srl will design, synthesize and weigh-out a focusedlibrary (1500 compounds) for which the target based screening will be repeated.The molecules that passed the Lipinski filter werethus targeted on oral bioavailability, and theirnumbers were much smaller than those for the initiallyplanned experiments. The idea of ‘filters’thus gained momentum, and additional filterssuch as those of Veber (limiting the number ofrotatable bonds and the size of polar surfacearea), also for bioavilability, were suggested.Both Lipinski and Veber rules did not considerdirectly any conformational aspects (3-dimensionaldescriptors of the molecules to be tested,but pharmacophore searches (ligand-baseddesign) and virtual docking and scoring (structurebased design) serve as subsequent filteringprocesses in 3D that cover the ‘affinity’ part ofdrug action, while the other filters mostly dealwith ‘drug transport’ issues.These two properties are, to a large extend, orthogonal.Thus, one may regard the filtering process asbeginning with huge numbers of molecules, whichare reduced to a smaller set by chemical descriptors.This smaller set may then be studied withmore detailed conformations at the pharmacophorelevel, reducing it further to a group ofmolecules which may be docked virtually to theassumed target, finally leaving a small set of substantially‘focused’ or ‘targeted’ lead candidates.The main ‘focusing’ activity has been howeverconcentrating on molecular scaffolds that are usefulfor probing families of targets such as GPCRs,tyrosine kinases, MMPs etc.But, even that approach suffers from many drawbacks.Lipinski and Veber rules can not distinguishwell between drugs and non-drugs, and areclearly not appropriate indicators of ‘drug-likeness’.Neural networks have been applied specificallyto this problem and managed to distinguishproperly between drugs and non-drugs, but havethe disadvantage of ‘hidden layers’ which do notenable to plan and design novel molecules.| A Typical fold of matrix metalloproteinasesstructured in 3 α-helices (red) and 4 parallel and1 antiparallel β-sheets (yellow). The binding siteis represented by a white surface while the zincion is shown as a light-gray sphere and the threecatalytic histidines are rendered as ball-and-stick.| B Coordination between zinc and the threecatalytic histidines and the phosphonate group ofthe ligand extracted from the 1ZS0 is highlighted.23

ACRONYMCancerGridA drug-like index has been suggested but is basedon fragment identification and therefore limited inits ability to discover novel structures. Structurebasedapproaches can consider small moleculeflexibility, but are still inappropriate for dealing withthe flexibility of the protein targets, especially withthe flexibility of backbone and of larger loops. Thescorings in docking methods have recently beenexposed to much criticism. Using single conformationsin pharmacophore searches is clearly inappropriate,because it has been shown that smallmolecules bind to proteins in conformations thatare higher in energy than their global minima.Toxicity predictions have not yet reached enoughreliability to prevent major toxicity threats by drugs.The need for selectivity has not yet been properlyaddressed in the preparation of focused libraries.Therefore, although many companies nowadaysare offering focused libraries for kinases, GPCRsand other families of molecules, there is a greatneed to improve the production of such librariesin order to shorten the time for discovery and tosave enormous expense. A main stumbling blockon the way to solving such issues is the complexcombinatorial nature of the problem of libraryconstruction and drug design.In this proposal, we include methods that dealdirectly with the combinatorial nature of the problems,that have been shown to solve combinatorialproblems in a highly satisfactory manner, that discoverthe global minimum in most cases andretain a large set of best results, many of themexcellent alternatives to the global minimum.Expected resultsNovelties and added values of the IT part of theproject:• virtual focused libraries of anti-cancer agents;• potential anti-cancer agents;• HTS technology;• data for model building purposes;• models able to predict anti-cancer properties;• CancerGrid System: a grid-based computer aidedtool that able to provide anti-cancer candidatesfaster and in a more efficient way, also suitable todevelop candidates for other targets.Potential applicationsThe models developed within the frame of thisproject can be used for filtering large discoverylibraries to find anti-cancer drug candidates,and to design anti-cancer focused libraries. TheCancerGrid computer system will be able to supportthe design of lead compounds in general, notonly in the anti-cancer field, but in any otheractivity area. Thanks to its grid-based architecture,the system will be able to predict moleculardescriptors for compound libraries, containinga large number of molecular structures, in a shorttime. When calculating 3D molecular descriptors,the system will take all major conformers intoaccount. This enables the calculation of information-richmolecular descriptors, and the developmentof reliable linear and non-linear models.The system will also be able to apply these modelsto predict the biological activity or chemical/physical property of the compounds.24

Scientific coordinatorGyörgy DormánAssistant Director of Science and TechnoloyAMRY HungaryZahony u. 7 Budapest HU 1031, Hungarygyorgy.dorman@amriglobal.comwww.amriglobal.comProject managerIstván BágyiManager, Grants & IPAMRY Hungaryistvan.bagyi@albmolecular.huPartnersThierry LangerInte:Ligand Software-Entwicklungsund Consulting GmbHMaria Enzersdorf, Austriawww.inteligand.comMati KarelsonTallinn University of TechnologyTallin, Estonia| Workflow Scheme of Computer Aided Drug Discovery in CancerGrid.Mart SaarmaUniversity of HelsinkiHelsinki, FinlandBalazs BorsiGKI Economic Research Co.Budapest, Hungarywww.gki.hu/en/index.htmlPeter KacsukComputer and Automation Research InstituteHungarian Academy of SciencesBudapest, HungaryAmiram GoldblumUniversity of JerusalemJerusalem, Israel| Grid Based IT Support for Drug Discovery.Saverio MinucciDAC S.R.L.Milano, Italywww.genextra.it/dac.htmlwww.dacresearch.itAngelo CarottiUniversity of BariBari, ItalyFerran SanzUniversity Pompeu FabraBarcelona, Spain25

ACRONYMContract number: LSHC-CT-2006-037251 | EC contribution: € 3 361 300 | Duration: 36 monthsStarting date: 1 January 2007CAPPELLAwww.cappellabio.euSUMMARYThe inhibition of protein:protein interactions(PPI) is one of the most promisingapproaches to the developmentof novel cancer therapies. This projectbrings together some of Europe’s leadingbiotech SMEs and several highly recognisedacademic institutes. By combiningfive distinct chemical approaches andtesting them on three different targets(all from different partners) a series ofinnovative small-ligand tools and librariesthat allow new approaches to the inhibitionof PPI in cancer will be developed.The project is a unique opportunityto integrate novel in silico, chemical,genetic and ADME-based approaches tothe design, synthesis and optimisationof libraries and compounds.Combating cancer through novel approachesto protein: protein interaction inhibitor librariesBackgroundMost protein:protein interactions occur withinthe cell and thus can only be targeted by smallmolecules. Furthermore, PPI differ structurallyfrom more classic drug targets such as enzymesand receptors, and consequently existing compoundshave generally delivered disappointingresults. Therefore, new approaches are neededto develop novel small molecules which inhibitPPI in cancer.Expected resultsInnovative tools for designing PPI inhibitors• Five different PPI-inhibitor library creation tools,based on five complementary approaches:– in silico;– genetic chemistry;– advanced natural product technologies;– retro-synthesis of natural scaffolds and;– ADME improvement.AimThe objective of this project is to develop a seriesof innovative small-ligand tools and libraries thatallow new approaches to the inhibition of proteinproteininteractions in cancer. A key theme is theutilisation of structural motifs found in naturalPPI-inhibitor compounds. This is coupled withhigh content testing of the resultant structures onthree distinct PPI targets relevant to differenttypes of cancer, to allow compound rule-sets tobe developed and improved. We want to developsmall-ligand libraries focused on PPI inhibitorsof relevance to cancer. Furthermore, we willdevelop innovative tools that allow improvedlibrary design in this area by integrating in silicoapproaches, bio-informatics, new approaches tocompound synthesis and pharmacology. The projectwill also cover the scientific areas such as insilico prediction of drug-like properties, predictionof ADME parameters, predictive toxicologyand creation of virtual libraries.• Cross-fertilisation of approaches so that each ofthe five approaches learns lessons from the othersand incorporates relevant leanings into itsapproach.• Three high-content assay systems for threeimportant PPI cancer targets (p53-Mdm2, Betacatenin-TCF4, BRCA2-RAD51).• Design rules for PPI inhibitor compound libraries(mass, diversity composition, lipophilicity, compoundclass etc.) generated from 15 complementarydata sets.Novel small-ligand libraries andpre-clinical candidates• Several ‘PPI inhibitor’ compound libraries.• Different candidate compound families fromwithin these libraries that can subsequently betaken forward into pre-clinical testing by theSME partners.26

Key words: identification of novel compounds, natural products, inhibition of protein:protein interactions, high throughput screeningROLE OF SMEsThere are five SMEs within the CAPPELLA project consortium. Generally speaking, the SMEsprovide very specific scientific know-how and technological platforms to the project, withoutwhich the project would be rendered incoherent. SMEs bring to the project the results oftheir in-house developments. By combining the know-how of these different companies, theproject has made a pharmaceutical development which would not have been possible byone of the companies acting alone.With regard to the SMEs involved in the CAPPELLA project:PharmaMar is a pharmaceutical company specializing in the detection and development ofpharmaceutical products from extracts obtained from marine organisms. The company possessesa huge collection of marine specimens from which previously unknown natural compoundsare extracted and characterized. Structural data on such new natural compounds actas a very important database for the CAPPELLA project.Analyticon is a provider of methods for the fractionation and analysis of highly complexextracts from biological samples and concomitantly a provider of computer-based methodsfor the processing of data obtained.Inte:Ligand contributes to the project with a computer-based in-silico analysis of potentialpharmaceutically relevant drugs. The analysis will permit the prediction of drug behaviourin toxicological or pharmacokinetic studies and will allow the computer-based evaluation ofpotential drug analogues.BioLigands is the provider of a highly efficient in vitro assay for the interaction betweena tumor suppressor protein and its antagonist. The screening assay provides compounddata which will be incorporated into a computer-based drug evaluation.Evolva contributes its chemical evolution platform, which permits chemically evolved metabolicpathways to be expressed in yeast. It is expected that chemically evolved expressionlibraries will give access to new pharmaceutically active small molecular weight compounds.The elucidated chemical structure obtained from such compounds will be passedthrough the in-silico development procedure developed by Inte:Ligant.Scientific coordinatorSanne JensenEvolva S.A.Hagmattstrasse 64123 Basel, SwitzerlandProject managerTanja Thyboinfo@cappellabio.euwww.evolva.comPartnersJens Peter MullerAnalytiCon Discovery GmbHPosdam, Germanywww.ac-discovery.de/english/go.htmlKarsten KristiansenBioLigands ApSOdense, DenmarkThierry LangerInte:Ligand Software-Entwicklungsund Consulting GmbHVienna, Austriawww.inteligand.comBirger Lindberg MollerRoyal Veterinary & Agricultural UniversityUniversity of CopenhagenCopenhagen, DenmarkSimon MuntPharmaMar S.A.Madrid, Spainwww.pharmamar.com/language.cfmAshok VenkitaramanUniversity of CambridgeCambridge, United KingdomAriel Ruiz i AltabaUniversity of GenevaGeneva, SwitzerlandJuhan SedmanUniversity of TartuTarku, Estonia27

ACRONYMChILLContract number: LSHG-CT-2006-037462 | EC contribution: € 1 800 480 | Duration: 36 monthsStarting date: 1 October 2006SUMMARYThe objective of this project is to developand validate a new technology based onthe Chromatin Immuno-Linked Ligation(ChILL) method that will transform theway the molecular analysis of chromatinis performed and will not only facilitateanalysis of very small sample sizes, suchas early embryos or diagnostic samplesfrom patients suffering from a range ofdiseases, but also radically improve theresolution of the epigenetic marks.Chromatin Immuno-linked ligation:A novel generation of biotechnologicaltools for research and diagnosisBackgroundThe sequence of an organism’s genome does notdirectly determine how the genome is used tobuild the organism. A second, more complex regulatorycode – the epigenetic code – is encryptedin the chromatin structure and the 3D nuclearorganisation of chromosomes. Epigenetic informationis encoded in DNA modifications (namelymethylation), chromatin composition and modification,and nuclear topology, or the dynamicorganisation of the genome within the nucleus.Epigenetic information not only provides the firstcue to allow a cell to interpret the genome, it canalso be heritably transmitted through cell divisionto maintain cellular identity. Moreover, whilemany heritable disorders in humans are causedby DNA sequence changes (mutations) that abolishgene expression, a number of diseases arecaused by inappropriate gene silencing, broughtabout by epigenetic modifications. Indeed, mostcancers involve the epigenetic silencing of genesthat normally control cell proliferation. The principalforms of epigenetic modification are DNA andhistone methylation.A challenge that is central to modern biology is theidentification of the spatial and temporal dynamicsof epigenetic factors in a number of physiologicalsituations. The Chromatin Immuno-Precipitation(ChIP) assay has played a pivotal role in decipheringpatterns of epigenetic marks that govern genetranscription. Besides 'classical’ ChIP, several similartechniques have been described in the literature.Recently, new technologies designed toimprove on the existing ChIP and native ChIP(NChIP) technologies, have emerged.In addition, low resolution and reproducibility problemsare often encountered. These severe limitationsof the ChIP method are overcome by theChromatin Immuno-Linked Ligation (ChILL) method,which could provide the foundation for a new generationof biotechnology tools and methods.AimThe objective of this project is to develop andvalidate a new technology which has the potentialto replace the various ChIP technologies, and totransform the way the molecular analysis ofchromatin is performed. The ChILL technique hasbeen patented by one of the partners of this project,leaving the consortium free to operate withregard to intellectual property rights. The ChILLmethod is based on specific ligations which occurbetween DNA stretches under diluted conditions.In this environment, ligation partners can onlyinteract if they are in close proximity.This proximity is created by new oligonucleotideantibodyconjugates (nucleoproteic probes, oroligo-ab), which physically place the target DNAin contact with the oligonucleotide reportersequences. The ligation products are then amplifiedby the polymerase chain reaction and analysedwith real-time instruments and/or classical gelelectrophoresis.Due to the ligation step taking place under dilutedconditions, the ChILL method will generate datacomparable to those obtained with ChIP, but withincreased sensitivity and a simplified protocolthat omits the tedious immuno-precipitation step.As a proof of principle, the ChILL method hasalready been shown to be at least 100 times moresensitive than the regular ChIP assay.ChILL will not only facilitate analysis of very smallsamples, such as early embryos or diagnosticsamples from patients, but will also radicallyimprove the resolution of the epigenetic marks.In addition, strong detergents used in the ChILLassay open up the chromatin structure, renderingit more accessible to antibodies than in conventionalChIP assays.Another major advantage of ChILL will be its abilityto interrogate several parameters in a singlesample. For this purpose, a variant of ChILL called28

Key words: chromatin remodeling, transcription regulation, epigenetic, ChIP assay, histones, DNA methylationROLE OF SMEsFor the ChILL project, Diagenode has three main objectives:• First, as coordinator of the research project, the company aims to create strong scientificsynergies among the participants.• As the SME participant, Diagenode ensures that research is oriented towards possiblefinal commercial applications. In the case of ChILL, the interest is concerned with betterunderstanding of how an innovative technology can be translated into a diagnostic tool.• Last but not least, one of Diagenode’s roles is to create ‘added value’ within the SME,by gaining scientific experience and know-how in a ‘high-tech’ field. The new scientificexpertise created by the EU funded research projects is also recognised and acceptedoutside the company, by the scientific community and, in a broader sense, by thecommercial community.Scientific coordinatorDidier AllaerDiagenode S.A.Avenue de L’Hopital, 1 Tour Giga B344000 (Sart Tilman)Liège, Belgiumdidier.allaer@diagenode.comwww.diagenode.comPartnersRolf I. OhlssonUppsala UniversityDept. of Development & GeneticsEvolution Biology CentreUppsala, SwedenHenk G. StunnenbergRadbout University NijmegenDept. of Molecular BiologyNijmegen, The Netherlandscombinatorial ChILL will be developed. This willrepresent a major breakthrough, because it willmean that several epigenetic marks can be collectedfrom a single tube, making it easier to buildup what might be called an ‘epigenetic profile’ ofthe biological material in question.Expected resultsThe Chromatin Immuno-Precipitation (ChIP) assayplays an absolutely pivotal role in decipheringpatterns of epigenetic marks that govern genetranscription. While the ChIP assay is a versatiletool, it suffers from low resolution and low sensitivity.These strong limitations of the ChIP methodare overcome by the Chromatin Immuno-LinkedLigation (ChILL) method. ChILL will not onlyfacilitate analysis of very small sample sizes, suchas early embryos or diagnostic samples frompatients suffering from a range of diseases, butalso radically improve the resolution of the epigeneticmarks. The ChILL approach also offersopportunities to examine simultaneous co-localisationof two or more factors on the same chromatintemplate, and the epigenetic marks will beresolved in unprecedented detail.The expected results of the programme wouldbe to make ChILL technology accessible to allEuropean research laboratories via validated procedures,reagents or kits. The project also expectsto launch diagnostic kits using ChILL technologyfor the diagnosis of diseases linked to epigeneticdisorders.Potential applicationsThe immediate impact of ChILL will be a betterunderstanding of the epigenetic code. The longerterm commercial impact of the ChILL methodmight also be very important for Diagenode withpossible development of tools for the research ordiagnostic market.F. FuksUniversité Libre de BruxellesFaculty of Medicine Laboratoryof Molecular VirologyBrussels, BelgiumD. ClarkGeneSys Ltd.Camberley, United Kingdom29

ACRONYMContract number: LSHP-CT-2007-037304 | EC contribution: € 1 271 664 |Duration: 36 monthsStarting date: 1 January 2007CILMALVACSUMMARYThis STREP, co-ordinated and led by anSME, will focus on the development of newmalaria vaccine candidates with the aim oftaking at least one product to the stage ofpilot scale. Products showing most promise,once expressed in the Tetrahymena system(or Ciliate system), will proceed to antigentesting in vitro and in vivo, to assess theirstructure and antigenic integrity. At leastone product is expected to reach lead optimisation,safety and toxicology testing.Combining the expertise of the two academicmalaria research laboratories withthe novel Ciliate-based expression systemunder development by the SME willgenerate recombinant Tetrahymena thermophilastrains expressing malaria antigensbased primarily upon MSP-1 and thevar2CSA genes of Plasmodium falciparum.To utilise the capabilities of the participantsto greatest efficiency, this STREPwill comprise, besides the ProjectManagement, work packages dealingwith the generation of antigen expressingCiliate strains, pilot scale production andpurification of the antigens and the testingand validation of candidate vaccines.This STREP application, co-ordinated byCilian AG, will provide an expression platformthat can easily combine antigens todevelop new combination vaccines thatmay be more promising than vaccines currentlyunder development. Ciliate-basedexpression of Plasmodium falciparumproteins in secreted, membrane bound orcytosolic forms will complement the workdone under the larger European malariavaccine development project.The Tetrahymena system as an innovativeapproach to malaria antigene expressionBackgroundMalaria kills over one million children in Africaalone each year, with an addition of up to 500 millionepisodes of clinically significant illness due tomalaria annually. Worldwide deaths are estimatedat between 2 and 3 million per annum. Fewother infectious diseases place such a burden onthe social, economic and healthcare systems ofdeveloping countries. Therefore there is a pressingneed for the development of a vaccine againstmalaria, to ease at least part of this overwhelmingburden on the continent of Africa, which suffersthe majority of the deaths and illness caused bythe malaria parasite.AimThe aim of this project is to use an innovative newexpression platform based on the CiliateTetrahymena thermophila in conjunction with twonovel malaria vaccine candidates, as a method ofadvancing these antigens to pre-clinical testing,prior to testing in humans. It will produce novelTetrahymena organisms expressing Plasmodiumfalciparum antigens at pilot-scale production levels.The two antigens selected are novel yet promisingcandidates based on the N-terminal regionof MSP-1 and the Var2 CSA variant of the PfEMP-1antigen family.Expected resultsThe main objective of this STREP is to producewithin three years at least two candidate vaccineantigens against the blood stage of the malaria parasitePlasmodium falciparum, ready to use for preclinicalevaluation. The candidate antigens (MSP-1and VAR2CSA) will be expressed by the novelexpression platform Tetrahymena thermophila,a free-living Ciliate, which expresses Plasmodiumfalciparum antigens efficiently. Partial results willbe: vector constructs that are suitable for expression;appropriate reproducible lab scale purificationprotocols; optimised host strains; a firstup- and downstream process up to pilot scale; andimplementation of the first steps of a quality managementfor potential later GMP production.Potential applicationsThere are no effective vaccines for malaria currentlyavailable. Vaccination trials conducted inhumans with existing candidates have been metwith limited success. This stresses the need forcontinuing efforts towards testing novel candidates.This project offers a novel biotechnologicalapproach to vaccine development and respondsto the demands of developing countries, nonprofitorganisations and charity foundations, totechnologically contribute to actions targeted atthe major poverty-related diseases, includingmalaria. One goal of the approach is to apply theunderlying technological concept of this project tothe later industrial development and productionof new and highly effective vaccine candidatesagainst malaria.30

Key words: Malaria, Plasmodium, vaccines, Ciliates, Tetrahymena, MSP-1, VAR2CSA, biotechnology, bioproductionROLE OF SMEsThis project is driven by the coordinating German SME Cilian AG which has developeda novel protein expression platform based on recombinant eukaryotic ciliate cells whichexcrete the desired product either membrane-bound or in cytosolic form. Under this projectthe quality and immunogenicity of the secreted proteins will be tested for two currentmalaria vaccine antigens. The project will thus allow the SME to validate the utility of theirnovel expression system and, at the same time, deliver GLP scaled-up processes for twopromising malaria vaccine candidates, provided by the European partners of the project.Scientific coordinatorMarcus HartmannRemco BrandtCilian AGJohann-Krane Weg 42D-48149 Muenster, Germanycilmalvac@cilian.dewww.cilian.dePartnersDavid CavanaghInstitute of Cell, Animaland Population BiologyUniversity of EdinburghEdinburgh, United Kingdomhomepages.ed.ac.uk/eang15Thor TheanderCentre for Medical ParasitoolgyUniversity of CopenhagenCopehagen, Denmarkwww.euromalvac.org/profiles/theander.htm© Shutterstock31

ACRONYMContract number: LSHM-CT-2006-037950 | EC contribution: € 3 000 000 | Duration: 36 monthsStarting date: 1 Janvier 2007cNEUPROSUMMARYAlzheimer’s Dementia (AD) is one of themost common brain diseases in the elderly.Dementias pose a major health problem inEuropean countries, with currently 5.7 millionaffected dementia patients in the EU25.No curative therapies are currently availablefor these dementias; however, firstdis ease-modifying treatment strategiessuch as Aβ-immunisation have enteredclinical trials. These novel treatments willbe most effective if they are offered ata very early dementia stage. Currently,however, the reliable clinical differentialdiagnosis of very early dementia stages isnot satisfactory. Here, recent research hasclearly demonstrated that multiparametricneurochemical dementia diagnostics(NDD) in cerebrospinal fluid (CSF)clearly improves the early and differentialdiagnosis of dementias.cNEUPRO will apply advanced proteomictools to discover novel neurochemicaldementia markers (BIOMARKERS) in bloodand CSF for the improved early, as well aspredictive, diagnosis of AD. A predictivedementia diagnosis is essential in orderto optimise the effectivity of forthcomingpreventive therapeutic strategies. Ourinitiative will establish European standardoperating procedures (SOPs) for currentneurochemical dementia diagnostics(NDD) and we will establish the first NDDreference centres in Portugal and Hungary.A strong methodological impact is placedon the quality of pre-analytical sample handlingand clinical phenotyping, which hasbeen neglected in industry-driven discoverystudies. cNEUPRO integrates innovativebiotech and bioinformatic companies withleading clinical and proteomic dementiaresearch centres. cNEUPRO will also supportthe discovery of new diagnostic targetsand, furthermore, will provide a promisingapproach to identify novel scaffolds foradvanced molecular neuroimaging.Accordingly, cNEUPRO will contributeconsiderably to the welfare, health andquality of life in Europe, and concomitantlyit will reinforce the competitiveness of theEuropean biotech industry.Clinical Neuroproteomicsof Neurodegenerative DiseasesBackgroundEurope has to face a threatening increase in theprevalence of the most common dementia, i.e.Alzheimer’s Dementia (AD). There is an urgentneed for novel disease- modifying treatments,which will be most effective if offered at a veryearly dementia stage, preferentially as preventivetherapy during the prodromal stage of mild cognitiveimpairment (MCI). However, the reliable clinicaldifferential diagnosis of very early AD is notsatisfactory and conventional diagnostic tools donot offer predictive diagnostics for AD. Here,recent research has clearly demonstrated thatmultiparametric neurochemical dementia diagnostics(NDD) in cerebrospinal fluid (CSF) clearlyimproves the early and differential diagnosis ofAD. Moreover, recent studies have also indicatedthat incipient AD can be predicted several yearsprior to dementia onset. However, these promisingresults of CSF-based NDD need to be validatedby additional studies. Furthermore, additionalneurochemical biomarkers have to be identifiedfor the improved early differential diagnosis ofdementias and, most importantly, first assaysfor blood-based NDD need to be developed.Moreover, only blood-based NDD will allowa widely applicable monitoring of therapy efficacy.Meanwhile, CSF-based NDD has entered neurochemicalroutine diagnostics of dementias inEuropean expert centres. However, there isa strong need to develop first standard operationprocedures (SOPs) for CSF-based NDD, which significantlydepends on the quality of preanalyticalsample handling, storage conditions and samplestorage. It is noteworthy that the success of thisnovel approach for the improved diagnosis ofvery early dementias has also stimulated strongresearch activities in the US.AimcNEUPRO is designed to discover innovative proteinbiomarkers and to develop novel CSF andblood multiplex assays for the accurate early, differentialand possibly predictive diagnosis of AD.Moreover, cNEURPO will develop first EuropeanSOPs for CSF-based NDD.Expected resultscNEUPRO consists of two R&D modules:Module I is dedicated to the discovery of novelprotein biomarkers, the generation of high-affinityligands and the implementation of biomarkersinto novel ELISA or Multiplex Assays. The discoveryof biomarkers is differentiated into the developmentactivities: definition of high-qualitysamples, identification of candidate biomarkersin blood and CSF by multi-dimensional state-ofthe-artproteomics, and validation of the candidatebiomarkers (→ biomarker). The validation ofa biomarker comprises its protein chemical (structural)validation by advanced mass spectrometryand its clinical validation within a re-test study.For validated biomarkers we will devise novelpoly- and monoclonal antibodies as well as highaffinitymolecules. The latter highly stable smallbinding proteins are designed using a proprietarytechnology and may possibly also be used astherapeutic tools or scaffolds for molecular neuroimaging.Finally, the biomarkers will be integratedinto novel ELISA and, most importantly,Multiplex-Assays. Applying advanced bioinformaticstools (proprietary technology), cNEUPRO willdesign a prototype predictor system for AD.32

Key words: Alzheimer’s Dementia, biomarker, neurochemical dementia diagnostics, cerebrospinal fluid, medical proteomics,blood-based bioassays, multiplex assays, predictive diagnostics for preventive therapy, quality controlROLE OF SMEsThe SME Protagen (Germany), Farallone Therapeutics B.V. (The Netherlands), MicroDiscovery(Germany) and Matrix Advanced Solutions (Germany) are partners in cNEUPRO. They contributecommercially tuned management skills, as well as specialist scientific experience toassist in mass spectrometry-driven candidate biomarker identification (Protagen), developmentof high-avidity and highly stable small binding proteins (Farrallone Therapeutics B.V.)and sophisticated multidimensional bioinformatic data analysis (Microdiscovery, MatrixAdvanced Solutions). In several areas of the project’s research SME involvement is crucialsince it provides unique proprietary technology, which is essential to the success of theresearch initiative. The cNEUPRO project has realised a close and synergistic networkbetween the SME and academic partners of the research initiative. Moreover, the SME partnersare centrally involved in the scientific management of the consortium.| Core facility mass spectrometry unit of one of thelaboratories of cNEUPRO partners for identification ofbiomarkers.© 2007 Dr. Oliver Ratajczak – strukturwelt.deModule II is dedicated to improving the performanceof current CSF-based NDD, by definingEuropean SOPs for pre-analytical sample handling,sample storage and assay conditions. Aspart of module II, CSF quality surveys will be conducted,‘gold standard’ CSF samples devised, andwe will establish two new NDD reference centresin Hungary and Portugal.Potential applications• Improved early and predictive diagnosis ofAlzheimer’s Dementia.• Development of first blood-based NDD fordementia diagnostics and therapy monitoring.• Identification of potential therapy respondersby indicative biomarker phenotypes.• Discovery of novel scaffolds, which may possiblyalso be used as therapeutic tools or scaffoldsfor molecular neuroimaging.• Elucidation of the molecular mechanisms involvedin AD.• Implementation of first European SOPs for CSFbasedNDD.Scientific coordinatorJens WiltfangUniversity of Erlangen-NurembergSchwabachanlage 6D-91054 Erlangen, Germanyjens.wiltfang@psych.imed.uni-erlangen.dewww.uni-erlangen.orgPartnersSylvain LehmannCentre Hospitalier Universitaire de MontpellierMontpellier, FranceKaj BlennowSahlgrenska Academy at Göteborg UniversityMölndahl, SwedenCharlotte TeunissenVU University medical centreAmsterdam, The NetherlandsConnie JimenezVrije Universiteit AmsterdamAmsterdam, The NetherlandsMarkus OttoUniversitätsklinik UlmUlm, GermanyDavid Burn (clinics),Chris Morris (proteomics)University of Newcastle upon TyneNewcastle, United KingdomMartin WiesenfeldtMatrix Advanced Solutions Germany GmbHLondon, United Kingdomwww.matrix-as.comEdgar F. da Cruz e Silva (Proteomics),Odete A.B. da Cruz e Silva (NDD referencecenter Portugal)University of AveiroAveiro, PortugalLaszlo VesceiUniversity of SzegedSzeged, HungaryJohannes SchuchhardtMicroDiscovery GmbHBerlin, Germanywww.microdiscovery.deLucilla ParnettiUniversity of PerugiaPerugia, ItalyHelmut E. Meyer, Katrin MarcusRuhr-Universitaet BochumBochum, GermanyMichel BerghFarallone Therapeutics B.V.Amsterdam, The Netherlandswww.farallone.comCarsten KorthHeinrich Heine University of DuesseldorfDüsseldorf, GermanyTuula PirttilaUniversity of KuopioKuopio, FinlandLuc BueeInstitut de la Santéet de la Recherche MédicaleLille, FranceStefan MüllnerProtagen A.G.Dortmund, Germanywww.protagen.de33

ACRONYMContract number: LSHB-CT-2007-037730 | EC contribution: € 2 985 102 | Duration: 36 monthsStarting date: 1 March 2007COBREDwww.cobred.euSUMMARYCOBRED aims at discovering colon cancer(CRC) and breast cancer (BC) biomarkersfor patient follow-up (monitoring markers),by exploiting the capacity of three stateof-the-arthigh-throughput technologies inan integrated systems biology approach.The specific RTD objectives are to:• design a clinical protocol for prospectiveclinical CRC and BC collections that fitthe needs of the three high-throughput‘omics’ technologies used, namely trans -criptomics, proteomics and metabolomics;• identify biomarker candidates (metabolites,proteins, PBL derived mRNAs)capable of detecting and assessing thestatus of minimal residual disease,metastases and recurrence after surgeryand chemotherapy;• develop a centralised database to integratethe data generated by the threetechnology platforms, to include the clinicaland pathological information on thecollections;• discover biomarkers with better speci -ficity and sensitivity, using cross-platformadvanced data-mining techniques on thecombined data from the consolidateddatabase; and• validate the biological relevance and diagnosticpotential of the identified biomarkersby testing their specificity on tissuearrays and in relevant preclinical models.COBRED gathers the expertise and RTDresources of three biotech SMEs, leadingacademic partners and two leading cancertreatment centres renowned for theirexpertise in BC and CRC treatment. After3 years, COBRED will deliver a set of biomarkercandidates verified in preclinicalstudies and ready for large scale clinicalvalidation and further development forcommer ciali sation by the respective SMEpartners. Furthermore, COBRED will havedemonstrated the potential to exploreconsolidated data resulting from differenthigh-throughput technologies and clinicalprofiles with advanced data mining technologiesfor enhanced biomarker discovery.Although within the project scope,COBRED focuses on biomarkers for follow-updiagnostics, which have the potentialto evolve into early cancer detection &screening tools.Colon and breast cancer diagnosticsBackgroundAn apparent paradox of current cancer epidemiologyis that while new therapies and diagnosticsimprove survival rates in common cancers, e.g.colon and breast cancer, the incidence rates arealso increasing and thus the net effect is negative.Colorectal cancer (CRC) is the third most commoncancer type worldwide; in the year 2000 theglobal incidence was around 1 million, close to10 % of all cancers, resulting in about 0.5 milliondeaths, totalling almost 8 % of all cancer mortality( 1 ). Lifetime risk of developing colorectal adenocarcinomais one of the highest of all cancers,approximately 6%, and of colorectal adenoma,the benign but precancerous lesion, is approximately50%. The risk of CRC rises with age, particularlyafter the age of 60.Breast cancer (BC) is the most common canceramong Western women. In these patients, it is notthe primary tumour, but rather its distant metastasesthat are the main cause of mortality. Theyearly incidence rate is over 0.5 million (630 000new breast cancer cases) which result in around0.2 million deaths. Recently, the rates of metastasisand mortality in BC patients have decreased asa result of early diagnosis by mammographicscreening and the implementation of systemicadjuvant therapy similarly to CRC. However, asthe population ages, the incidence of breast cancerincreases ( 2 ).Continuous improvements in the treatment ofanother major life threatening illness, namelycardiovascular disease, leads to an increase inthe overall life expectancy. This contributes tothe increase of the incidence rate, in CRC and BCamong others, due to population ageing. Thespeed of population ageing is higher than thedecreased mortality due to the accumulatedtreatment benefits from new cancer diagnostics( 3 ) and therapies ( 4 ) thus leading to a paradoxicallynegative net effect.There is ample, but only circumstantial, evidencederiving from survival data of patients with earlystages of cancer, suggesting that earlier diagnosiswould allow a 10-20 % survival rate increase. Infact, the potential benefits of early CRC and BCdiagnosis are so high that a wide range of communityand governmental efforts have beenimplemented for population wide screening.Biomarkers are substances found in the blood,other bodily fluids (e.g. urine) or tissues that eitheralone or in combination may signal the presence ofcancer or the risk of cancer. Diagnostics based onbiomarkers have the potential to significantlyimprove current cancer diagnostic means, providinga higher sensitivity (i.e. much smaller tumourscan be detected), more easily, faster and at a muchlower cost ( 5 ).Biomarker discovery and validation, in the sameway as drug discovery and validation, is a longprocess with a high rate (60-80%) of attrition ofcandidate biomarkers along the major steps ofqualification that ultimately ends in the approvalby the Food and Drug Administration (FDA) in theUS and the European Agency for the Evaluation ofMedicinal Products (EMEA) in the EU. Often,seemingly good candidates that have been identifiedand found valuable in one study do not showthe expected predictive values in the secondstudy. In fact, the number of new diagnosticsapproved per year is decreasing, in sharp contrastto the intensifying efforts to discover biomarkers.Therefore, despite having the highest potentialvalue, COBRED chose not to pursue the discoveryof screening markers because of economic andlogistic impracticalities of a large scale screeningmarkervalidation in BC and CRC. Instead, the projectfocuses on the second largest clinical need,namely the improvement of patient follow-up,through the discovery of monitoring markers,which are expected to report relapse, metastasisand minimal residual disease at earlier stages,which are more amenable to surgical andchemotherapy treatment, and which are morelikely to improve cancer patient survival.34

Key words: cancer, biomarker, monitoring markers, breast, colon, transcriptomics, proteomics,genomics, metabolomics, dataminingROLE OF SMEsAimBioSystems International, a French SME, is the coordinator of COBRED.The three SMEs involved (BioSystems International, Biocrates Life Sciences and Ipsogen)are research-intensive SMEs who play leading roles given their expertise in ‘omics’(genomics, proteomics and metabolomics) technologies, an issue which is at the heart ofthe COBRED project and the technological basis for the achievement of the project’s objectives.The targeted project results are clearly of interest and potential benefit to SMEs, sincebusiness opportunities will be created for them in the field of diagnostic tools and methods(and related IPR).A fourth SME (ARTTIC) is responsible for the project management.COBRED aims at discovering colon cancer andbreast cancer biomarkers for patient follow-up(monitoring markers) by exploiting the capacity ofthree state-of-the-art high-throughput technologiesin an integrated system biology approach.The goal is to identify biomarker candidates(metabolites, proteins, PBL derived mRNAs) capableof detecting and assessing the status of minimalresidual disease, metastases and recurrenceafter surgery and chemotherapy.Expected resultsCOBRED will deliver candidate protein, metaboliteand mRNA biomarkers tested in preclinicalstudies, ready for large-scale clinical validationand further development for commercialisationby the respective SME partners: Ipsogen formRNA derived markers, BioSystems Internationalfor protein markers and Biocrates Life Sciencesfor metabolomics markers.Specific project results will include:• sets of biomarkers (gene signatures, proteins,metabolites, or a combination of these) that willbe considered clinically relevant for early diagnosisof primary BC and CRC and relapses;• central repository system hosting the resultsfrom the technological platforms and the relevantclinical data;• prospective clinical collection of BC and CRC;• clinical validation for the diagnostic potential ofsubsets of the identified biomarkers in comparisonto existing biomarkers and to currentlyavailable imaging techniques;• preclinical models for the biomarker evaluationand biological studies.Potential applicationsDiagnostic kits for BC and CRC patient follow-up.References(1) Midgley R. et. al. Nat Clin Pract Oncol. Jul; 2(7):364-9 (2005);(2) Parkin D.M, et. al. Int J Cancer 1999; 80: 827-841. (1999),Elmore J.G. et. al. JAMA. 293:1245-1256 (2005); (3) Shen Y, J et. al.Natl Cancer Inst. 17;97(16):1195-203 (2005); (4) Nygren P et. al.Acta Oncol. 44(3):203-17. (2005); (5) Baker M. Nat Biotechnol.23(3):297-304. (2005).Scientific coordinatorLaszlo TakacsBioSystems International S.A.S.4 rue Pierre Fontaine,91058 Evry cedex, Francelaszlo.takacs@biosys-intl.comwww.biosys-intl.comPartnersKlaus WeinbergerBiocrates Life Sciences A.G.Innsbruck, Austriawww.biocrates.comFabienne HermitteIpsogenLuminy Biotech EntreprisesMarseille, Francewww.ipsogen.comXavier Sastre-GarauInstitut CurieParis, Francewww.curie.frDavid MalkaInstitut Gustave RoussyVillejuif, Francewww.igr.frLászló FésüsUniversity of DebrecenDebrecen, Hungarywww.unideb.huAndras GuttmanUniversität InnsbruckInnsbruck, Austriawww.hlbs.orgJaak ViloUniversity of TartuTartu, Estoniabiit.cs.ut.eeBruno CucinelliARTTIC S.A.S.Paris, Francewww.arttic.com35

ACRONYMContract number: LSHB-CT-2006-037575 | EC contribution: € 3 189 385 | Duration: 36 monthsStarting date: 1 January 2007COMICScomics.vitamib.comSUMMARYA battery of reliable and validated in vitroassays is needed to test for genotoxic andcytotoxic effects of chemicals, withoutresorting to animal experiments. Thecomet assay, a sensitive indicator of DNAdamage, will be combined in this projectwith the Cell Array system, to establishand validate high capacity assays suitablefor chemical testing. Up to 800 cell sampleswill be processed for comets on a singlemicroscope slide. Arrays will use cellswith different metabolic capabilities, withdata on cytotoxicity obtained in parallelwith DNA damage. A medium-throughputassay will also be developed. Cometanalysis by differential staining of damaged/undamagedDNA using establishedand novel dyes combined with automatedimage analysis will be faster and morereliable than at present. A crucial aspectof the cellular response to DNA damage isDNA repair; variations between peoplecan affect cancer risk, while genotoxicchemicals can act by interfering withrepair. Two methods for measuring repair,one based on the comet assay, the otherusing a ‘Repair Chip’ approach, will becompared. In addition, fluorescent probeswhich lock onto the DNA after hybridisation(‘padlock probes’) will be appliedto study gene-specific DNA repair. Themodified comet assay methods will beassessed for reproducibility and sensitivityin an inter-laboratory prevalidationtrial, using a coded set of standard chemicals,to satisfy regulatory bodies, as wellas industrial users of the technology. Theresult will be robust, validated, highthroughputin vitro genotoxicity tests.This proposal brings together academicpartners and SMEs, together with a largeindustrial concern, and the EuropeanCentre for the Validation of AlternativeMethods (ECVAM). Dissemination throughprofessional and trade publications, regulatorychannels, and scientific conferenceswill lead to widespread adoption of thenew methods.Comet assay and cell array for fastand efficient genotoxicity testingBackgroundThe comet assay for DNA damage is widely used,but has a major drawback as it is labour-intensive,and therefore can be used only in studies in whichthe numbers of samples are relatively small. Thedevelopment of high-throughput variants willincrease its applicability in both genotoxicity testingand population biomonitoring. DNA damage isa good marker of exposure to genotoxic chemicals;measuring cellular repair of this damagegives additional information on the mode ofaction of genotoxic agents and on individual susceptibilityto carcinogens.AimThe overall objective is to develop reliable andtested genotoxicity and cytotoxicity assays that,combined, will reduce the need for animal experimentsin assessing the safety of chemicals.Specific aims include:• to increase the throughput of the comet assayup to 20-fold;• to develop further the cell array system as a parallelassay for cytotoxicity;• to seek optimal cell types for use in genotoxicityand cytotoxicity testing;• to increase the speed of scoring of comets;• to use lesion-specific enzymes and inhibitors tomeasure different kinds of DNA damage;• to develop and compare methods for measuringDNA repair activity;• to develop an approach to measure gene-specificDNA damage and repair;• to validate the comet assay in its various forms;• to develop reference and internal standards foruse in the comet assay;• to make the various innovative products availablefor use by companies and researchersinvestigating DNA damage and repair.Expected resultsValidated assays for DNA damage and repair thatwill be accepted by regulatory authorities for usein genotoxicity testing and will thereby reducereliance on experimental animals.Potential applicationsCommercial genotoxicity testing, biomonitoring inhuman population studies, basic research in DNAdamage and repair.36

Key words: DNA damage, DNA repair, genotoxicity, comet assay, biomonitoringROLE OF SMEsOut of the seven industrial participants to this project, five are SMEs and they contribute tothe key activities in the project, devising new software for image analysis as required by thenovel methods of scoring of comets (IMSTAR); providing suitable cell lines (Biopredic); providingcustom-made DNA-damaging chemicals for calibration purposes (Severn Biotech);providing dyes for differential staining of intact and damaged DNA plus running trainingworkshops (TATAA Biocenter); pre-market product development and testing (Thistle).Scientific coordinatorAndrew CollinsDepartment of NutritionUniversity of OsloPB 1046 Blindern0316 Oslo, Norwaya.r.collins@medisin.uio.noPartnersBrigitte FouqueCommissariat à l’Énergie AtomiqueGrenoble, FranceFrançoise SoussalineIMSTAR S.A.Paris, Francewww.imstarsa.comThomas HartungJoint Research CentreIspra, ItalyGunnar BrunborgNorwegian Institute of Public HealthOslo, NorwayChristiane GuillouzoInstitut National de la Santéet de la Recherche MédicaleRennes, FranceKatarina VolkovovaSlovak Medical UniversityBratislava, SlovakiaJon Eigill JohansenChiron ASTrondheim, Norway| The principle of the ‘padlock probe’. The probe(left panel) has at its ends sequences complementaryto adjacent parts of the target DNA. After hybridisation,these ends are ligated and the probe thus locked ontothe target. These probes can be designed to lock ontodefined gene sequences, and so permit an examinationof damage and repair in those specific genes.[Figure provided by Prof. Mats Nilsson.]Neven ZoricTATAA Biocenter ABGöteborg, Swedenwww.tataa.comElizabeth MartinAstraZenecaMacclesfield, United KingdomGalen MilneThistle Scientific LimitedGlasgow, United Kingdomwww.thistlescientific.co.ukAndrew SmartSevern Biotech Ltd.Kidderminster, United Kingdomwww.severnbiotech.comChristophe ChesneBiopredic InternationalRennes, Francewww.biopredic.comMats NilssonUppsala UniversityUppsala, SwedenKarel AngelisInstitute of Experimental BotanyPrague, Czech Rep.37

ACRONYMContract number: LSHM-CT-2006-037227 | EC contribution: € 2 700 000 | Duration: 36 monthsStarting date: 1 August 2006CVDIMMUNEwww.cvdimmune.comSUMMARYThe CVDIMMUNE project aims at: Investi -gating novel risk markers for CVD inEuropean patient cohorts of in about15 000 patients including unique cohorts asthe Swedish Twin registry, the MORGAMstudyand SLE. Investigating immunomodulationas a therapeutic strategy for ofCVD. Developing documentation for registrationof diagnostic ELISA kits in EU andthe US. Developing proof of concept for atleast one pharmaceutical product candidate.Providing a strong research foundationand knowledge on mechanisms.Immunomodulation and autoimmunityin cardiovascular disease and atherosclerosisBackgroundCardiovascular disease, mainly caused by atherosclerosis,is the main cause of death in theWestern world and also increasingly in developingcountries. Even though progress has beenmade in prevention of the disease, the inflammatoryand immunological nature of atherosclerosisis not reflected by available diagnostic measures.Furthermore, treatment has been improved bylipid lowering drugs, e.g. statins, but novel treatmentmodalities aiming at the pathologicalinflammatory and immune reactions characterisingatherosclerosis are yet to be developed.Likewise, the understanding of the mechanismsleading to atherosclerosis and causing the immunereactions are poorly characterised. This applies tothe general population but also to SLE, an autoimmunedisease where the risk of CVD is very high.AimAtherosclerosis, the major cause of cardiovasculardisease (CVD) is an inflammatory disease,where the immune system plays an importantrole. Autoantibodies as protection or risk markers,and therapy through immunomodulationcould be a major advance in the prevention andtreatment of CVD and is a focus of this project.One type of antibodies are natural antibodiesagainst phosphorylcholine (aPC), an antigenexposed in some bacteria and in phospholipidswith platelet activating factor (PAF)-activity, e.g.in oxidised LDL. The project’s clinical and experimentalstudies indicate that aPC, mainly of IgMtype, are protection factors against human atherosclerosisand CVD. The project’s plan is thereforeto develop aPC as a diagnostic tool, which will betested in several unique cohorts, includinghealthy individuals and high risk individuals. Theproject also thinks aPC could represent a noveltherapeutic modality, where both polyclonal andmonoclonal aPC are possibilities. Both kinds ofaPC antibodies will be developed and tested inmouse animal models for atherosclerosis.In contrast to natural antibodies (which are germline encoded), antiphospholipid antibodies (aPL)are risk markers for both arterial and venousthrombosis, and the main focus is novel types ofaPL against platelet activating factor (PAF) or PAFlikelipids (aPAF). These novel risk markers (aPAF)will be tested in the same cohorts as aPC and, inboth cases, robust kits will be developed. Thegenetic background of aPC and aPAF will be studied,e.g. in the Swedish Twin Registry. In a prototypicautoimmune disease, namely SLE, where therisk of CVD is very high, such aPL are raised.Annexin A5 is a plasma protein, interfering withphospholipid surfaces and acting as an anticoagulant.The project has demonstrated that aPLinhibit Annexin A5 binding to endothelium, aneffect neutralised by intravenous immunoglobulins(IVIG) and that Annexin A5 is present in atheroscleroticlesions, especially at sites prone torupture. Based on these findings, the project hashypothesised that raising Annexin A5 binding,either by administration of neutralising antibodiesfrom IVIG in individuals with high aPL levels, orby administration of Annexin A5 per se, couldprevent plaque rupture and atherothrombosis.Taken together, the project combines diagnosticand therapeutic projects and is focused on therole of the immune system, especially autoantibodies,in atherosclerosis and atherothrombosis.This project combines academic and industrialexpertise and objectives, aiming at developing:• a novel protection marker for atherosclerosis,natural IgM antibodies against phosphorylcholine(PC) and novel risk markers, IgG autoantibodiesagainst phospholipids (aPL): plateletactivating factor (PAF) and PAF-like lipids (aPAF);• these markers will be investigated in uniquepatient cohorts. Documentation for registrationof diagnostic ELISA kits in EU and the U.S. will bedeveloped;• novel immunomodulation therapy against atherosclerosisand CVD in direct association withthese factors will be developed, along with the38

Key words: atherosclerosis, atherothrombosis, natural antibodies, antiphospholipid antibodies, SLE, immunomodulationROLE OF SMEsSMEs play a pivotal role in CVDIMMUNE. Athera Biotechnologies AB is in collaboration withKarolinska Institutet, the originator of the majority of the project ideas and product candidatesexplored in the project. Athera develops the two diagnostic risk markers and therapeutic candidatesto be investigated. Furthermore, Athera is the main party responsible for the commercialisationof the results of these efforts. The second SME in the project, IsoSep AB, plays an integralrole by developing the chemistry solutions vital to several of the programmes in the project.administration of atheroprotective aPC and theincrease of Annexin A5 binding to endotheliumthrough the neutralisation of aPAF and other aPLor administration of Annexin A5 per se, a plasmaprotein that may prevent rupture of atheroscleroticplaques and CVD;• proof of concept for at least one of these pharmaceuticalproduct candidates.Expected results• Development of robust and quantitative test kitsin ELISA format for analysis of IgM antibodies toPC and IgG antibodies to PAF or PAF-like lipids inserum.• Epidemiological data on aPC and aPAF from severalwell characterised and, in several cases,unique cohorts of healthy and high-risk individuals.• Assessment of genetic variability of aPC andaPAF and identification of candidate genes.• Establishment of in vitro and in vivo models forstudies of aPC and Annexin A5 relating to atherosclerosisand atherothrombosis.• In vivo data for drug candidates for atherosclerosisand atherothrombosis and data compiledto submit an IND application from one of thedrug candidates investigated in the project.Potential applicationsThe project expects its novel protection and riskmarkers to reflect inflammatory and immunologicalfactors in plaques and to be useful as tools forrisk assessment for CVD, as a complement to classicalrisk factors as dyslipidemia, hypertension,diabetes, and smoking. The project also proposesthat treatment relating to these factors could bea major step forward, in addition to establishedones such as lipid lowering drugs.| Resting levels of EC intracellular calcium before leukocytes were allowed to interactwith ECs is shown in individual cells through continuous registration of fluorescenceintensity with a widefield microscope. Endothelial cell borders are shown by labellingECs with Alexa 488-conjugated anti VE Cadherins antibodies. ECs (GREEN) wereloaded with Calcium sensitive probe.| Leukocytes, freshly isolated from venous blood of healthy donors on Ficoll/Hypaquegradients were allowed to settle on the monolayers at 37 °C were allowed to transmigratethrough IL-1 β treated EC at 37 °C. Leukocytes,labeled (Red) and are at differentstages of diapedesis process.Scientific coordinatorJohan FrostegårdDepartment of Medicine,Karolinska University Hospital, HuddingeCenter for Infectious Medicineand Rheumatology Unit,141 86 Stockholm, Sweden.johan.frostegard@medhs.ki.seProject managerNarinder Gautamnarinder.gautam@medhs.ki.sePartnersHans GrönlundAthera Biotechnologies ABStockholm, Swedenwww.athera.sePeter SeverImperial College LondonLondon, United KingdomStefan BlankenbergJohannes Gutenberg-University MainzMainz, GermanyEwa NinioInstitut National de la Sante etde la Recherche Medicale, U525Paris, FrancePaul QuaxTNO Netherlands Organization forApplied Scientific ResearchLeiden, The NetherlandsMarta E. Alarcón-RiquelmeUppsala UniversitetUppsala, SwedenThomas NorbergIsoSep ABTullinge, Swedenwww.isosep.com/home.shtmlWouter JukemaLeiden University Medical CenterLeiden, The NetherlandsJörg BlaeserPhadia GmbHFrieburgh, Germanywww.phadia.com| Changes in EC intracellular calcium were measured during leukocytes extravasationon individual cells through continuous registration of fluorescence intensity witha widefield microscope. Leukocytes were allowed to transmigrate through IL-1 βtreated EC monolayers at 37 °C. A transient increase in Enthothelial cells- [Ca2+]i isshown. ECs (GREEN) were loaded with Calcium sensitive probe. Localized increase inEC Calcium in individual cells is shown (GLOWING GREEN).39

ACRONYMDEPPICTwww.deppict.euContract number: LSHC-CT-2007-037834 | EC contribution: € 3 640 293 | Duration: 36 monthsStarting date: 1 March 2007SUMMARYProtein:protein interactions (PPI) are centralelements in cellular processes andimportant targets for selective therapeuticagents. They constitute a rich area fordiscovery of novel small ligand-basedtherapies. This proposal seeks to utilisesuch interactions, in particular those featuringa α-helix binding groove such asp53-MDM2, or more novel targets, e.g.nm23-prune, to develop targeted smallmoleculelibraries with physico-chemicalproperties appropriate for therapeuticeffect against various tumour types suchas the brain cancers of glioblastoma andmedulloblastoma.Combination of the concepts below shouldprovide an opportunity to unlock the potentialof protein interactions as key componentsin signalling pathways via designof selective small-molecule modulatorstargeting the kinase-effector interactioninstead of the ATP active site.• Develop an understanding of the elementscontrolling selectivity in protein:protein signalling networks by developingapproaches for design of small moleculesthat target α-helix binding grooveinteractions through use of structurebasedand fragment-based approaches.• Data-mining of ADME and drug-druginteractions to build a predictive databasefor library design.• Develop quantitative structure/propertyrelationships, with an emphasis on CYPmediatedmetabolism, ABC transportersat the blood/brain and brain/tumourinterfaces, mutagenicity, solubility, pKa,and passive permeability, and predictivetools for mutagenicity and other genetictoxicology end-points.• Develop predictive PK and PBPK modelsto improve understanding of BBB andtumour penetration.• In vitro and in vivo PK/PD and TK/TD characterisationof compounds, to increaseunderstanding of their mechanism ofaction and reduce the use of laboratoryanimals.Such knowledge-based approaches willalso be applicable to design of small moleculesfor other protein:protein interactionsutilising a α-helix binding grooveboth for peripheral tumours and othertherapeutic areas.Designing Therapeutic Protein:Protein Inhibitorsfor Brain Cancer TreatmentsBackgroundAmongst the range of cancer types, brain andperhaps pancreatic cancers are especially lackingin effective treatments. In particular braintumours are:• the leading cause of death from childhood cancersamong persons under 19;• the second leading cause of cancer-relateddeaths in males aged 20-39;• the fifth leading cause of cancer-related deathsin women aged 20-39.Although onset of disease varies with tumourtype, it can occur at a relatively young age causingadditional and significant social and economicproblems for both patients and their families.Current standard treatments include surgery,radiation therapy and chemotherapy. These maybe used either individually or typically in combination.Brain cancers however present uniqueproblems due to the location of the tumours: surgeryand radiotherapy carry considerable risk tothe patient and resection is not always possible.Chemotherapy is faced with the problem of penetrationof drugs across the blood-brain barrier(BBB) and of lack of specificity. The focus forthese patients is therefore on more effective therapiesto prevent relapse, and on more efficientscreening and diagnosis to halt the disease at anearly stage.AimThe main objective of the proposed project is toprovide more effective anti-tumour therapies bydeveloping targeted small ligand libraries withappropriate physico-chemical properties for therapeuticeffect targeted against protein:proteininteractions implicated in various tumour types.The research activities will concentrate on knowledge-basedapproaches supporting translationalresearch aimed at bringing basic knowledgethrough to applications in clinical practice andpublic health. The project will thus focus on providingsmall molecule ligands with minimal sideeffects as treatments for the brain tumoursglioblastoma (GBM) and medulloblastoma.Expected resultsThe successful integration of the various aspectsof this proposal will provide a robust knowledgebasedstrategy for exploiting protein:proteininteractions as drug targets in the treatment ofbrain tumours. The strategy should however besufficiently generic to be transferable to other diseaseareas, especially within the CNS, where protein:proteininteractions provide an entry pointinto disease-modifying therapies.Potential applicationsThe design of selective small molecule modulatorsof protein:protein interactions should providethe basis for developing new therapeuticstrategies against brain cancers. They will allowfor improving current libraries and for buildingpredictive databases for library design of newspecific drugs and therapeutic agents with highcentral nervous system penetration, necessary toreach a higher efficacy, selectivity, responsivenessand lower toxicity. In addition these approacheswill represent a powerful system for preclinicaldata collection, leading to an optimisation ofclinical trials setting and development.40

Key words: protein:protein interactions, small molecule inhibitors, knowledge driven drug design, blood/brain, tumour penetrantROLE OF SMEsThe project is specifically designed to increase SME efforts towards research and innovation,to encourage collaborations between SMEs and to expand their scientific and technologicalknowledge base. The four SMEs involved in the project, Sienabiotech S.p.A. (SIBI),Molecular Discovery (MD), Crystax (Crystax), and Aureus Pharma (AUR) take leading rolesin driving and managing the planned library design and drug discovery programme. Theactive and serious involvement of a SME working in drug discovery such as SIBI guaranteesthe rapid application of the research results. Specifically, SIBI researchers will be involvedin library design, construction of in silico paradigms, setting up of experimental metabolismmodels and screening of libraries for ADME attributes. Molecular Discovery will providehigh quality software tools and chemoinformatics procedures aimed at the prediction of thephysicochemical profiling of the investigated compounds with potential anti-tumour activity.Crystax will perform all the necessary processes (cloning, expression, purification and crystallisation)to obtain the 3D structure of the pharmacological targets proposed in this project.This will allow the correct characterisation of the active sites, where small moleculescan bind and have a pharmacological effect. The Aureus Pharma team will set up a databasefrom scientific literature in order to perform data-mining of ADME and drug-drug interactionsto build predictive tool sets; design and implement predictive models based ondatasets from the knowledgebase developed; and collect pertinent data from literature tobuild predictive toxicology models and filters. In combination, the four SMEs carry out crucialroles in the DEPPICT project.Scientific coordinatorGraeme RobertsonSiena Biotech S.p.A.Fiorentina, 153100 Siena, Italygrobertson@sienabiotech.comwww.sienabiotech.it/index/index.jspPartnersGabriele CrucianiMolecular Discovery Ltd.Pinner,Middlesex, United Kingdomwww.moldiscovery.com/index.phpMassimo ValotiUniversity of SienaSiena, ItalyJuan AymamiCrystax Pharmaceuticals S.L.Barcelona, Spainwww.crystax.comRoberto PellicciariUniversity of PerugiaPerugia, ItalySophie OllivierAureus PharmaParis, Francewww.aureus-pharma.comProf. Herbie NewellUniversity of NewcastleNewcastle, United Kingdom| Iterative Research Cycles where data will be used to construct robusttestable hypotheses in the context of the pathophysiology of braintumours. To achieve this it is necessary to look for trends – StructureActivity Relationships. The discovery and exploitation of site/mechanismof action and developing knowledge at multiple levels – Target, Cell,and Pathway will be key to achieving this.41

ACRONYMContract number: LSHB-CT-2007-037303 |EC contribution: € 3 189 400 | Duration: 36 monthsDeZnITStarting date: 1 January 2007SUMMARYThe objective of DeZnIT is to develop andapply new methodology for the rationaland accelerated design of novel drugs targetedagainst zinc-containing enzymes.These enzymes are key modulators ofmany serious human diseases includingcancer, glaucoma, obesity, and rheumatoidarthritis. Despite some successes,many major technological challengesremain in the development of effectivedrug therapies against this enzyme family.DeZnIT will address these challenges bydeveloping and integrating key technologiesfrom pharmacogenomics, computermodelling, structural and molecular biologyand chemistry, combined with drugdiscovery infrastructure and expertise. Inparticular, highly novel computationalapproaches taken from the field of computerscience will be applied to drugdesign for the first time.The consortium members combine all thenecessary competencies to achieve thegoals and objectives of DeZnIT.Design of zinc metalloenzyme targeted drugsusing an Integrated Technology approachBackgroundZinc-containing metalloenzymes have a widerange of specific biological activities. They areimplicated in several types of diseases such ascancer, atherosclerosis, neuronal degenerativediseases, glaucoma and inflammation. In this proposal,the project concentrates on the therapeuticallyimportant zinc-containing enzyme families ofcarbonic anhydrases, histone deacetylases and theADAM (A Disintegrin And Metalloprotease domain)family of proteinases, in particular ADAM17, alsoknown as TACE (TNF-α Converting Enzyme).Whilst many computer-assisted drug designmethods have been developed over the past severaldecades, their application to the medicinallyimportant class of zinc-containing enzymes hasbeen challenging. The nature of the interactionbetween the potential drug molecule and a metalsuch as zinc requires a very time consuming calculationand obtaining accurate results is difficultto achieve in a real-world setting.Expected resultsDeZnIT is highly focused on the identification ofnovel and more effective drug candidates, whichwill be further developed for serious human diseases.The other outcomes of DeZnIT are improvedmethods for computational drug design and otherplatform technologies such as crystallography,molecular biology (including development of biomarkers)and chemical synthesis. The success ofDeZnIT would lead to significantly reduced costsand timelines for drug discovery processes, withconsequent health and economic impacts.Potential applicationsIn addition to the specific applications outlinedabove in the area of zinc metalloenzymes, anymethods developed during the course of DeZnITmay be applicable to other classes of metal containingenzymes of therapeutic importance.Aim• To develop modern, sophisticated computerisedmethodology for high-throughput drugscreening in silico, focussing on Zn-containingenzymes.• To isolate and characterise target proteins withinthe Zn-containing enzyme families (includingnewly identified members) for the screening ofmore efficient drugs.• To design and create new classes of enzymeinhibitors.42

Key words: zinc metalloenzymes, drug design, computer-assisted drug design, cancer, inflammationROLE OF SMEsThere are three SME participants in DeZnIT, each playing a key role. One of the SMEs,InhibOx, is the project co-ordinator and, in addition, will focus on the delivery of novel computationalmethodology. KeyDP will provide molecular and structural biology expertise,whilst TopoTarget will provide drug screening technology. Together, the SMEs provide significantexpertise in the commercial development of small molecule therapeutics in a highlysynergistic manner with the academic partners.Scientific coordinatorPaul FinnInhibOx Ltd.Pembroke house36-37 Pembroke streetOxford OX1 1BP, United Kingdompaul.finn@inhibox.comwww.inhibox.comPartnersSteven ButcherTopoTarget A/SCopenhagen, Denmarkwww.topotarget.comFlip HoedemaekerKey Drug Prototyping B.V.Amsterdam, The Netherlandswww.keydp.comPeteris TapencierisLatvian Institute of Organic SynthesisRiga, LatviaSeppo ParkkilaUniversity of TampereTampere, FinlandAndrea ScozzafavaUniversity of FlorenceFlorence, ItalyWilliam Graham RichardsUniversity of OxfordOxford, United Kingdom| A detail from the crystal structure of carbonic anhydrase II, a key enzyme of interest to the projectand the first crystal structure produced by the consortium.43

ACRONYMContract number: LSHB-CT-2006-037212 |EC contribution: € 2 499 999 | Duration: 36 monthsStarting date: 1 January 2007DiagnosisSUMMARYInfectious diseases continue to be a seriousburden around the world, in bothdeveloping and industrialised countries.Development of new and cost effective methodsfor non-invasive diagnosis of human pathogensThe main objective of DIAGNOSIS is to contributeto the above need by developinga novel easy to use, low cost, mostly noninvasive biotechnological platform for thedetection of infectious diseases. The challengingaim is to reach a short and efficientsample treatment implemented into existingand newly developed portable PCR laboratoryfor multiplex fluorescent pathogendetection. The concept will be proven onhuman critical pathogens but will beapplicable also for animals, and plantspathogens. The concept will be applicablefor samples taken from affectedorganisms as well as from food/feed andenvironments (water, air, soil etc.).The scientific and technological objectiveswill include the development of:• new principles of nucleic acids sorption/desorption;• innovative concentrating methods andmaterials for the enrichment of viruses,micro-organisms and nucleic acids;• the adaptation of the phosphoramiditechemistry to alternative fluorescencedyes in order to broaden the labellingassortment for multiplex PCR analyses,a portable non-dependent on externalpower supply PCR laboratory;• exemplary demonstration of the wholetechnological chain on several groupsof human pathogens, including theMycobacterium complex, the periodontalpathogens, the causal agents of populationshifts within the intestinal microfloraassociated with inflammatory boweldiseases and Fungal skin infections,completed by the diagnosis of mainrepresentatives of food-born pathogens.BackgroundInfectious diseases are a global concern. Of theannual 12 million deaths attributable to infectiousdiseases on the planet, 95% occur in the developingworld, particularly in the most impoverished areaswhere individual and general hygiene standardsremain very low and prevention policies are nonexistent,poorly adapted or insufficiently funded. Onthe other hand, economic and industrial developmentalso accounts for the emergence of infections,such as food-borne pathogens that take advantageof the increasing industrialisation of the food chain,nosocomial infections in the increasingly complexhospital environment and travel-related infections.In addition, the demographic trend towards anageing population in Europe enhances the risk ofincreasing infection as elderly people are prone toinvasive medical procedures and are, in general,more susceptible to infectious diseases.European science must play a major role in this fightto curb infectious diseases, particularly throughthe establishment of a stronger and more coherentsurveillance and control system and througha substantially increased investment in researchto underpin this endeavour.Only with this investment will Europe be able tomanage infectious diseases within its own boundaries.In addition, Europe will also be able to helpprevent the emergence and spread of infectionsprevailing elsewhere on the globe and to pursueits historical tradition of giving assistance to thepoorest countries.AimThe main strategic objective of DIAGNOSIS is to contributeto the above need by developing a novel,easy to use, low cost and non invasive biotechnologyfor infectious diseases diagnosis, i.e. pathogensdetection.The challenging aim is to reach a short and efficientsample preparation followed by highly sensitive,accurate, cost efficient multiplex diagnosis implementedi.a. into a portable PCR fluorescent laboratory.The concept will be proven on human criticalpathogens but will be applicable also for animals,plants and environmental, and food samples.Expected resultsNovel technologies• New principles for NA separation andpurification• New sorbent methods and materials• Protocols for sample preparation• Protocols for samples target concentration• Chemistry for oligonucleotides synthesis• Multiplex PCR• Protocols for diagnostic assays• Protocols for POC (point of care) samplepreparationNew products• Kits for ultra-rapid separation and purificationof DNA and RNA• Kits for separation and purification of NA fromdifficult (inhibitor rich) samples• Kits for separation of different classes of NA• Kits for non-cultural enrichment ofmicro-organisms• Kits for diagnostic assays of critical pathogens• Prototype instrument for fluorescent detection• Portable PCR laboratory• Kits for sample preparation outside thelaboratoryPotential applicationsThe application workpackage will concentrate butnot limit its activities to the following groups ofpathogens and critical sample sources for multiplexPCR systems with fluorescence detection,thus approving and demonstrating the broadand beneficial universal applicability of the technologicaldevelopment in the work packagestechnological work packages:• mycobacterium complex:in sputum;• difficult culturable fastidious periodontalpathogens in gingival crevicular fluid;• predominant food-borne human pathogens;• gut flora pathogens in stool samples for analysesof intestinal microbiota associated with inflammatorybowel disease;• fungal pathogens in hair, skin and nail samples.44

Key words: infectious diseases; diagnosis; nucleic acids, sample preparation, monolithic sorbent; DNA, RNA, PCR,real-time; fluorescence detection; multiplex PCR; phosphoramidite chemistry; portable instrument; Mycobacterium;gingival crevicular fluid, food-born pathogens; gut flora Pathogens; Fungal pathogensROLE OF SMEsDIAGNOSIS is enhancing the competitiveness of Europe’s biotechnology industry by thedevelopment of fast and reliable nucleic acids separation and purification, new methods forseparation from inhibitor enriched samples and new instruments and kits for fast and costeffective detection of critical human pathogens.Most of the partners are industrial partners, thus taking the outcome of the project directlyto the European biotechnology industry.• The consortium consists of 73 % SMEs, all of which are based on innovative technologiesand research, with 67 % of the budget allocated to SMEs. The main idea is to promote theirtechnologies and develop new products by enhancing their business plans.• The project management is undertaken by two SMEs: one an expert with the technologicalwork, and the other an expert in administrative management and coordination of EUfounded projects. This company is led by a woman.• DIAGNOSIS is allocating one WP to exploitation and dissemination by its SMEs partners,including internal workshops and staff exchange between the relevant entities. A detailedplan of staff exchange will be implemented during the project.• International Cooperation is assured through the participation of 3 partners from INCOcountries (Russia and Armenia); one of which is a Russian SME (DNAT), while the othertwo are research institutes which will provide essential know-how for the project.Scientific coordinatorRobert-Matthias LeiserAgrobiogen GmbHThalmannsdorf 25,Larezhausen86567 Hilgertshausen, Germanymatthias.leiser@agrobiogen.dewww.agrobiogen.dePartnersDenis RebrikovDNA-Technology jscMoscow, Russiawww.DNA-Technology.comClaus-Detlev BauermeisterLabor Dr. Bauermeister & CoMoers, GermanyRadovan HaluzaGeneri Biotech s.r.o.Hradec Kralove, Czech Republicwww.generi-biotech.comCamilla GiammariniDIATHEVA SrlFano, Italywww.diatheva.comMartin GehriPreentTec AGFribourg, Switzerlandwww.preentec.chRonald Arthur BoschHilbrands Laboratorum B.V.Wijster, The Netherlandswww.hlbbv.nlSergey ZavrievM.M. Shemyakin-Yu.A.Ovchinnikov Institute of Bioorganicchemistry of RASMoscow, Russiawww.ibch.comHamlet BalayanInstitute of Fine Organic Chemistry of NASYerevan, Republic of Armeniawww.sci.am/resorgs.php?oid=14&langid=1Ulf GoebelCharité – Universitätsmedizin BerlinInstitut für Mikrobiologie und HygieneBerlin, Germanywww.charite.de/imhPnina DanOSM-DAN Ltd.Rehovot, Israelwww.osmdan.com45

ACRONYMDIALOKContract number: LSHB-CT-2007-036644 | EC contribution: € 1 978 070 | Duration: 36 monthsStarting date: 1 October 2006SUMMARYThe DIALOK consortium consists of twoSMEs (based in The Netherlands andHungary) and five academic participants(based in The Netherlands, Germany andSpain) and is dedicated to the developmentof innovative drugs that displaya restricted action within specific targetcells or organs. Such locally acting drugswill have an improved safety and efficacy,as side-effects in other tissues willbe prevented.Development of Innovative Assays and Locallyacting therapies aiming at critical Kinases inhepatic and renal fibrosisBackgroundKinases are a class of enzymes that play a key rolein intracellular responses to stress and growthfactors. Kinases catalyse the transfer of phosphatefrom ATP to proteins, which may either beother kinases, transcription factors or other regulatoryproteins. As such, the activation of kinasesleads to a cascade of activating signals that regulatemany physiological processes, e.g. cell divisionand differentiation. Aberrant kinase activityis associated with many diseases such as cancer,diabetes, and chronic inflammatory disorders.Kinases have been identified by the pharmaceuticalindustry as important targets for drug development,with major investment having been madein basic research and drug design in this area,estimated at 20 % of the total R&D budget in thepharmaceutical industry. Over 500 kinases havebeen identified in the human genome and manynew kinase inhibiting drugs will be developed inthe coming decades. Indeed, some of the mostsuccessful drugs introduced in the past years arekinase inhibitors, such as Gleevec and Irresa.Within the development of this class of highlypotent drugs, some critical problems have arisen.For example, even kinase inhibitors with highspecificity for a specific kinase sometimes haveadverse effects that prevent the further developmentof safe drugs. This problem is inherent to theclass of compounds, since kinases often play animportant role in both pathophysiological andnormal physiological processes.AimThe DIALOK consortium is dedicated to thedevelopment of innovative drugs that displaya restricted action within specific target cells ororgans. Such locally acting drugs will constituteimproved safety and efficacy, since side-effects inother tissues will be prevented. The project willinvestigate this therapeutic strategy for kinaseinhibitors, a class of drugs that has tremendoustherapeutic potential but that is also associatedwith unacceptable side effects. Kinase inhibitorswill be conjugated in two classes of carrier systems,directed towards either the liver or kidney.In this way, the project will develop locally actingdrugs for the treatment of either hepatic or renalfibrosis, aiming to prove this concept in experimentalanimal models.An important novel aspect of the project is thelinker used for coupling the drug to the carrier.DIALOK will employ Kreatech’s Universal LinkerSystem (ULS), a novel patented drug-linker whichenables straightforward coupling with mostkinase inhibitors (broadly applicable) withoutchanging the original drug structure. Anotherunique property of ULS is that it provides controlledrelease of the conjugated drug overa period of days, which is of great importancefor effectiveness of the delivered drug.In parallel to development of locally acting kinaseinhibitors, DIALOK will develop novel assays fordetecting activation of kinases. Such assays willbe of great value to the project, accelerating andstrengthening the validation of kinase inhibitorbasedtherapeutics. Kreatech’s ULS-based (fluorescent)reporter molecules are particularlysuitable for the detection of phosphorylatedkinase substrates, and therefore enable broadlyapplicable, non-radioactive detection of activatedkinases, as compared with traditional kinaseactivity assays, which use radiolabeled ATP orphosphoaminoacid-specific antibodies.46

Key words: drug delivery, kinase inhibitors, kinases, liver disease, renal disease, drug safety, inflammation, fibrosisROLE OF SMEsThere are two SMEs in this project, namely Kreatech and Vichem Chemie. They are experts,respectively, in linking bio-organic molecules based on coordinative chemistry, and in thedesign and synthesis of kinase inhibitors. Taken together, new cell specific therapeutic compoundsare developed to be tested for specificity and effectiveness by the RTD partnersof the consortium. Kreatech also plays a key role in managing the project as a whole andsafeguarding intellectual property rights.Expected resultsThe DIALOK consortium proposes the improvedsafety and efficacy of kinase inhibitors by meansof local drug delivery. By restricting the activity ofthe inhibitor to the diseased tissue only, the balancebetween therapeutic effects and sideeffectscan be altered dramatically (Fig. 1). Sincethe locally delivered drug will provide adequatedrug levels within the targeted organ, in combinationwith much lower levels in the other partsof the body, the safety and efficacy of the drugswill be improved.Local diseases require local drug treatment.This can be effectuated by drug delivery.Potential applicationsIn this project, participants will explore the deliveryof kinase inhibitors for the treatment of bothliver and renal fibrosis, since no adequate pharmacotherapyyet exists for these types of diseases.The technology will be also applicable tothe treatment of other diseases in which kinasesplay an important role, e.g. cancer, or inflammatorydiseases such rheumatoid arthritis.Scientific coordinatorJack VeuskensKREATECH Biotechnology B.V.Vlierweg 201032 LG Amsterdam, The Netherlandsj.veuskens@kreatech.comwww.kreatech.comPartnersK. PoelstraGroningen University Institutefor Drug ExplorationDept. of Pharmacokineticsand Drug DeliveryGroningen, The NetherlandsG. KériVichem Chemie Ltd.Budapest, Hungarywww.vichem.huM. TemplinNatural and Medical Sciences Instituteat the University of TuebingenReutlingen, GermanyR. BatallerIDIBAPS (Institut d’InvestigacionsBiomèdiques August Pi i Sunyer)Laboratory of Liver FibrosisBarcelona, SpainM. RuizUniversity Autonoma MadridVascular and Renal Research LaboratoryMadrid, SpainRJ KokUtrecht UniversityDept. of PharmaceuticsUtrecht, The Netherlands| Fig. 1 Schematic depiction of how wewant to improve the safety and therapeuticefficacy of kinase inhibitors.47

ACRONYMContract number: LSHB-CT-2006-037681 |EC contribution: € 2 977 400 | Duration: 36 monthsDiaNawww.diana-eu.fiStarting date: 1 December 2006SUMMARYDiaNa combines the accumulated expertisefrom the previous FP5 EU project,Mechanisms of Proteinuria (QLG1-2000-00691) and the FP6 project, ADDNET(LSHB-CT-2003-503364). The latest know -ledge on the pathophysiology of diabeticnephropathy and newly identified urinarymarkers are utilised to developpredictive diagnostic tests to follow diseaseprogression. By using metabolomicapproaches, the project aims to findadditional markers from diabetic urine.In parallel, two separate approaches willbe used to develop diagnostic tests, onebased on nanobead technology, and theother on a multiplexing platform allowingthe combination of several parametersin a single test. This will translateinto early identification of patients athigh risk of rapid loss of kidney function.After validation with clinical material,subsequent steps will include transfer ofthe test into patient use by an SME. Thisapproach, which directly aims at developinga clinical urinary test, will be supportedby extensive basic research onthe mechanisms/biomarkers of diabeticnephropathy.Predictive diagnostics for diabeticnephropathy – Novel nanotechnologybased test platformsBackgroundDiabetic nephropathy is the main cause of endstagerenal failure in the Western world. TheWorld Health Organization (WHO) estimates thatcurrently there are over 200 million people withdiabetes worldwide. The prevalence is constantlyrising and estimated to reach over 300 million bythe year 2025. Overall, up to 40 % of diabeticpatients will develop debilitating kidney complications.Diabetic nephropathy is becoming notonly a severe health problem for individualpatients, but also a major economic burden of allsocieties. The project aims to achieve a betterunderstanding of the pathophysiologic mechanismsunderpinning the development of diabeticnephropathy, a major complication shared byboth type I and type II diabetes.AimThe ultimate goal of the project is to developnovel diagnostic tests, based on the best molecularunderstanding reflections in urine to revealthe early diabetic damage during the premicroalbuminuricstage of the disease.Expected resultsThe ultimate goal of the project is to developnovel diagnostic tests based on the best molecularunderstanding reflections in the urine toreveal the early diabetic damage during the premicroalbuminuricstage of the disease.Potential applicationsThe applications will include novel magnetosensorsfor the detection of diabetes-diabetic kidneydamage.48

Key words: kidney, cardiovascular disease, diabetes, urinary markers, rapid diagnostics, magnetosensors, disease managementROLE OF SMEsThree SMEs are involved, plus a subsidiary of a large company:• Philogen SpA utilising their expertise to extract antibodies specific for the moleculesinvolved in the pathogenetic sequelae of diabetic nephropathy and used for diagnostics;• Future Diagnostics B.V. combining the antibodies produced to novel test platforms, includingthe appropriate packaging into existing and to-be-developed concepts;• United Laboratories Ltd. developing and screening for appropriateness of the platformsdeveloped for daily routines with incoming patient samples; and• Philips Electronics Netherlands B.V developing novel magnetosensors for detecting lowamounts of target molecules in patients’ urine.In addition, market analysis and surveys, IPR strategies, and competitor analysis will beprovided by an additional party as a subcontractor of project partner, University of Helsinki.Scientific coordinatorHarry HolthoferHaartman InstituteHaartmaninkatu 3University of HelsinkiFI-00014 Finlandharry.holthofer@helsinki.fiwww.Helsinki.fiNational Centre for Sensor Research/BioAnalytical SciencesDublin City UniversityDublin 9, Irelandharry.holthofer@dcu.iewww.cbas.iePartnersPer-Henrik GroopSamfundet FolkhälsanHelsinki, Finlandwww.folkhalsan.fiRob van der HeijdenUniversiteit LeidenLeiden, The Netherlandswww.leidenuniv.nlDario NeriSwiss Federal Institute of TechnologyZurich, Switzerlandwww.ethz.chReinerio GonzalesPhilogen SpASiena, Italywww.philogen.itMenno PrinsPhilips Electronics Nederland B.V.Eindhoven, The Netherlandswww.philips.comMike MartensFuture Diagnostics B.V.Wijchen, The Netherlandswww.future-diagnostics.nl© ShutterstockJussi VilpoUnited Laboratories Ltd.Helsinki, Finlandwww.yhtyneetlaboratoriot.fi49

ACRONYMContract number: LSHB-CT-2006-037739 | EC contribution: € 1 834 331 |Duration: 36 monthsStarting date: 1 January 2007Drop-TopSUMMARYThe management of patients with superficialbladder cancer is difficult. No reliablemeans exist to determine whethera tumour will progress towards an infiltrativeform, which requires radical surgery(cystectomy), or whether it willremain superficial, which requires onlyconservative surgery (resection). In addition,no dependable marker exists topredict whether a primary tumour willreappear or not during the years followingsurgical resection, forcing patientsto undergo constant revisions that reducetheir quality of life and overburden healthcare systems.Studies have identified biomarkers withpotential for the prognosis (progressionand recurrence) of superficial tumours.However, the analyses have often beenlimited to a single type of marker (e.g. proteinor genotypic markers) or even toa single marker. To the best of the project’sknowledge, no study has attemptedto integrate different types of markers foran increased predictive power.The main scientific goal of DRoP-ToP is toidentify a set of markers (at protein-, RNA-,and DNA level) with high predictive powerfor tumour progression and recurrence. Inaddition, DRoP-ToP pursues an ambitioustechnological challenge: the developmentof a prognosis microarray, based solely onnucleic acid probes, for the detection ofthe above mentioned predictor set.Integration of DNA, RNA and protein markersin a tool for the prognosis and diagnosisof human diseaseBackgroundWith an ever increasing incidence, cancer is thesecond major cause of death in the Westernworld. Although advances in our understanding ofthe mechanisms of tumour onset and progressionhave been enormous, major impact on survivalhas been mainly restricted to sertain kinds oftumours. Besides advances in different therapies,the improvement in survival can also be attributedto improvements in diagnosis and the identificationof high-risk groups, which allow for earlierand better treatment selection.In contrast to therapies and diagnosis, the overallprognosis of the most common cancers, such aslung, colon, prostate, breast and bladder cancersremains poor, particularly when the tumour cannotbe cured by surgery. The ‘post-genomic era’has brought many promises that this situation willchange, but it has also given the emphasise to theneed to make appropriate and better use of information,technology and clinical resources. Theproject believes that resources are often wastedbecause of inappropriate approaches and inadequatecollaboration between clinical, academicand industrial partners.Transcriptome analysis by DNA microarrays hasbeen successfully used for the identification of biomarkersof tumour progression. However, due tovarious inconsistencies from study to study, theirapplication to common clinical practice has not yettaken place. The DRoP-ToP project intends to overcomethese limitations by a two-fold approach:• prospective validation of the informationacquired through retrospective studies. For this,a collaborative multicentre effort is essential;• integration of biomarkers from genome, transcriptomeand proteome analysis in a single predictorset. Even though each of these threeanalyses by itself will likely contribute, it isexpected that the combination of biomarkertypes will result in an enhanced predictivepower.AimDRoP-ToP has two major objectives, one technologicaland one scientific. Regarding the former,the project proposes to develop a tool for multiparametricanalyses (mRNA levels, large geneticrearrangements, genetic mutations, genetic polymorphisms,protein levels and post-translationalmodifications) of biological samples, to betterpredict tumour progression and recurrence. Theevaluation of such heterogeneous parameterswill be performed on a single microarray: thetriple microarray, an oligonucleotide microarrayfor simultaneous DNA, RNA and protein assessment).The triple microarray constitutes the testsurface of a workstation that integrates technologyfor the hybridization, scanning and detectionof biomarkers. Its simplicity should facilitatea wide implementation of this tool in the clinic.As scientific objective, the project proposes toidentify a set of biomarkers with power for theprediction of clinical behaviour of bladder cancer.Selection of such set of biomarkers will be the endpoint of a five-phase endeavour:• identification of candidate biomarkers for bladdercancer progression and recurrence from thescientific literature and from existing data generatedby two DRoP-ToP partners specialised inbladder cancer;• pre-selection of biomarkers on the basis of thestrength of their association to tumour behaviourand on the scientific and technical quality ofthe study;• measurement and validation of said candidatebiomarkers in a set of samples from patientswith a detailed clinical record and follow-up;• application of bioinformatics and biostatisticstools for the identification of a set of biomarkerswith a strong association to tumour behaviour.The DroP-ToP strategy should be applicable to thestudy of any tumour type, and more generally to anydisease with a genetic or gene-expression component.However, and as a proof of concept, theproject proposes to apply it to bladder carcinomabecause it represents a paradigm of the need foruseful biomarkers in the clinical setting:50

Key words: ?? urology, clinical analysis, anticancer therapy, prognosis, microarrayROLE OF SMEsThe DRoP-ToP consortium is made of 8 multi-disciplinary partners coming from 3 EuropeanMember States (France, Spain, and Germany), 2 Associated States (Israel and Switzerland),and one INCO Country (Former Yugoslav Republic of Macedonia).Among the partners, the participation of 3 European High-Tech SMEs (Progenika Biopharma,Genewave and NuAce Technologies) must be noted. Progenika Biopharma is the coordinatorof the DRoP-ToP consortium.Progenika is a leading company in Functional Genomics and has wide expertise in microarraytechnology, which is critical to the success of the project. The company disposes also ofa relevant know-how in genomics technology and has gained an outstanding level of experiencein sample preparation from almost all human, plants and animal models, in microarrayprocessing and data mining, both in Expression and Genotyping projects. In particular,beside acting as coordinator for the DRoP-ToP project, Progenika is committed to lead thework on the design, validation and optimization of gene specific probes (for mRNA expressionanalysis) as well as allele specific probes (for genotyping). Progenika is also responsiblefor the mRNA expression analysis and protocol optimization for the to-be developed probes.The SMEs Progenika and Genewave are together responsible for the production of the finalchip functionalized with the three different detection probes.Genewave is developing and commercializing new biophotonic instruments and systems forgenomic, proteomic and post-genomic applications. Conscious that the sensitivity of detectionconstitutes one of the major hurdles preventing biochips from reaching mass applications,Genewave has developed an amplifying substrate for biochip (AmpliSlide) basedon an original optical design and its associated high-throughput reader (AmpliReader).Within the scope of this project, Genewave will further develop and optimized these technologieswith a main goal to obtain highly sensitive substrates with a coating chemistryoptimized for the efficient simultaneous binding of RNA, DNA and Aptamers and integratedinstruments dedicated to the use in clinical diagnostics (integrated microarray analysisstation). This will represent a major advance as such a tool will allow much more powerfuldiagnostics than available today aiming at less invasive, screening and diagnostic tests.NuAce has developed a unique technology for synthesizing Dinucleotide-based Aptamers(DBAs), which can be employed as target-specific binders for genomic, proteomics andtherapeutics applications.The DBAs are highly suitable for creating protein recognition agents that can be used in proteinchips. NuAce’s expertise will support the project in building up its basic concept, andprovide technological components including the task to generate DBAs to be immobilizedon the chip that specifically detects protein markers identified within the project.51

ACRONYMDrop-Top• it is one of the best models of tumour progression;• its incidence ranks fifth among all cancer types(the fourth most common in males and the ninthin females);• despite widely variable outcome, the diagnosisand prognosis tools used in the clinic are few andthe same, and they are invasive even for asymptomaticpatients (cystoscopy);• it is the most expensive cancer type, as it can recurmany times after treatment;• its evolution is very difficult to predict, whereasthe therapeutic approach for its two forms is completelydifferent: when invasive at the time ofdiagnosis, it has a poor prognosis and requiresaggressive surgery (cystectomy); when non-invasive,prognosis is favourable and it only requiresconservative surgery (resection);• its recurrence is also difficult to predict, whichleads to unnecessary visits and cystoscopies forabout 50% of patients, whose tumours will neverrecur;• a number of highly promising biomarker candidateshave already been identified and reportedin the literature.Expected resultsCancer is the second leading cause of death worldwide.In the year 2002 there were 10 million newcases of cancer in the world, 6 million deaths andapproximately 22 million people living with cancerworldwide. It is estimated that by year 2020 therewill be 15 million new cases per year, and 10 millionsdeaths. Bladder cancer is a highly common neoplasia,mainly among men, and its incidence is rising inseveral countries in Europe. Approximately 125 000new cases with bladder cancer are diagnosed eachyear in the EU.Despite continued interest in the development ofnovel tests to better predict bladder cancer prognosis,there has been very limited progress. This is inpart due to the fact that all tests developed untilpresent are based on the detection of only one typeof biomolecule (i.e. RNA, DNA or protein). Ourapproach is radically different: from a systematicreview of current knowledge on biomarkers of bladdercancer and existing research results of the participatingacademic partners, we propose todevelop a microarray that can detect the 3 majortypes of molecules in human biological samples.This should provide a much more solid basis toidentify molecular predictors of the disease.The DRoP-ToP proposed technology will bringabout three main improvements:• the number of invasive tests will be stronglyreduced, leading to a reduction in costs bydecreasing hospital admissions and the numberof occupation hours lost;• reduction in the number of invasive tests will alsodiminish morbidity and improve the quality of lifeof patients;• a better prognosis will allow more adequate choiceof treatment i.e. avoiding therapy to patients whodo not need it and applying more aggressive therapyto patients at risk.While most patients develop bladder tumours witha relatively good prognosis in terms of survival,their management is very expensive because of themultiple recurrences that most patients suffer, theneed for invasive follow-up procedures, and the frequenthospitalisations. Overall, bladder cancerpatients generate the highest cost/patient and lifetimeamong patients with cancer. In conclusion,bladder cancer generates very high costs to society.At the present time, there is no test recommendedor approved to help establish the prognosis ofpatients with bladder cancer. Over the past 10 yearsseveral products have been approved by the FDAfor use in the early detection of bladder cancerrecurrence (i.e. nmp22, BTA, Diagnocure Immunocyt,Vysis). However, none of these tests is yet usedroutinely in the clinical setting because they do notprovide a substantial benefit. Therefore, there isa tremendous need for better tests.Patients with bladder cancer develop multiple (upto 30) tumour recurrences, thus requiring continuedfollow-up after the initial diagnosis. For thisreason, most patients undergo at least two medicalvisits over the first few years after diagnosis.Subsequently, the frequency of medical examinationsvaries according to the evolution of the disease.Therefore, a test that would allow the earlydetection of recurrences and an improved establishmentof prognosis would be applied very frequentlyto the patients. The DRoP-ToP proposedtest could even be used more commonly than cystoscopiesare performed today, given that it wouldnot be invasive. Its availability would allow demonstrationof the concept that early detection oftumour recurrence is associated with improvedoverall outcome.Potential applicationsDiagnosis and prognosis for the bladder cancerand other diseases.52

Scientific coordinatorGorka OchoaProgenika Biopharma, S.A.Parque Tecnológico de BizkaiaEdificio 801 BDerio-Vizcaya48160, Spaingochoa@progenika.comwww.progenika.comPartnersFrancois RadvanyiInstitut Curie-CNRSParis, France| Triple microarray and Integrated station for improvedmultiparametric analysis of biological sample.| Comparison between a standard glass slide and anAmpliSlide. In a standard glass slide a large portion ofthe emitted fluorescence by substrate-attached fluorophoresescapes into the glass substrate. Constructive interferenceallows AmpliSlide to amplify and redirect this emittedfluorescence towards the reader’s optics. This amplification,up to a 20-fold increase in signal, results in enhancedsensitivity. (Top and middle: illustration and computerisedsimulation of light emission from fluorophore placed onthe slide. Bottom: side by side comparison of images fromscanned slides hybridised under identical conditions).Nuria MalatsInstitut Municipal d’Investigacio MedicaUniversitat Pompeu-FabraBarcelona, SpainGordana CerovicGenewave S.A.S.Palaiseau Cedex, Francewww.genewave.comMelanie HilanioUniversity of GenevaGeneva, SwitzerlandZivko PopovUniversity Cyril andMethodius-Faculty of MedicineDepartment of UrologySkopje, Former Yugoslav Republicof MacedoniaHader KlessNuAce Tecnologies, Ltd.Rehovot, IsraelJoerg HoheiselDeutsches KrebsforschungszentrumHeidelberg, Germany53

ACRONYMContract number: LSHM-CT-2006-037870 |EC contribution: € 1 771 000 | Duration: 36 monthsEACCADwww.cdiff.nlStarting date: 1 December 2006SUMMARYClostridium difficile-associated disease(CDAD) has become the most frequentnosocomial infection in many Europeanhospitals. In 2004, the situation wasexacerbated by the arrival in Europe ofa new hypervirulent strain (PCR ribotype027) previously confined to N. America,where it has been responsible for a massiveincrease in CDAD incidence andassociated deaths. Central to the controlof epidemics are the deployment ofassays able to rapidly diagnose andmonitor the presence and spread of theorganism. No such tests currently existfor these new hypervirulent C. difficilestrains. It is the overall objective of thisproposal to develop the urgentlyrequired rapid, diagnostic assays inclose collaboration with 3 SME’s.European approach to combat outbreaks ofclostridium difficile associated diarrhoea bydevelopment of new diagnostic testsBackgroundC. difficile is resistant to various antibiotics andcapitalises on the ensuing disruption of the normalintestinal flora to colonisation and cause disease.The spectrum of disease ranges fromasymptomatic carriage to a fulminant, relapsing,and increasingly fatal colitis. The effects of CDADare devastating, both in terms of morbidity/mortalityand the high costs of disease management.Presently, C. difficile may only be treated witheither metronidazole or vancomycin. A number offactors have contributed to the worrying escalationin the incidence of CDAD. The elderly andimmuno-compromised are particularly at risk(80 % of cases occur in the over 65s). The proportionof the population in these high-risks groupsis rapidly rising. Strains exhibiting greater virulenceare also beginning to emerge, which in someinstance has been attributed to the production ofadditional virulence factors, e.g. binary toxin. Thesituation has now been exacerbated by the arrivalin Europe during 2004 of a new hypervirulentstrain and antibiotic resistant strain (ribotype027, toxinotype III) previously confined to Canadaand the USA. The occurrence of this strain is associatedwith an excessive use of cephalosporinesand quinolone antibiotics, and has been responsiblefor a massive increase in CDAD incidence in N.America and associated deaths, e.g. the proportionof patients with CDAD who died within30 days after diagnosis rose from 4.7 % in 1991-92to 13.8 % in 2003. This epidemic strain isolatedin Canada, USA, UK, Belgium, France and TheNetherlands was characterised as toxinotype III,North American PFGE type 1, restriction-endonucleaseanalysis group type BI and PCR-ribotype027. The strain produces toxins A and B and containsa 18 bp deletion in the toxin regulator geneTcdC. It is imperative that an overall strategy tocombat this and similar novel variant(s) isdevised. Central to control of epidemics by suchnew C. difficile strains with increased virulence isa strategy that will include not only a rapid detectionbut also a specific recognition of virulentstrains. Diagnostic assays for CDAD rely either onthe detection of C. difficile products (toxins),C. difficile genes, or the culture and toxin testing ofthe isolates. Toxins can be detected either by theirbiological properties (cell cytotoxicity assay) or byimmunological methods (latex agglutination,immunoassay). The cell cytotoxicity test is the‘gold standard’. However, there are significantdrawbacks. Laboratories must have access to culturedmonolayers, and results vary according tothe cell line, dilution factors, reagents used andstorage conditions. Additionally, the turnaroundtime is very slow. Enzyme immunoassaysconsistof conventional enzyme immunoassays and membraneimmunochromatographic tests. The sensitivitiesand specificities of enzyme immunoassaysare within 85-95 % of the cell cytotoxicity test, andnumerous commercial kits are available. However,their performance relative to each other has notbeen subjected to a rigorous meta-analysis.Immuno-chromatography tests are extremely simple,can be performed at the bedside and givea result within 30 minutes. This may be of crucialimportance in an epidemic situation to recogniseinfected patients. DNA-based tests are focussedon the detection of the C. difficile genes encoding16S RNA, GDH or the toxin genes (tcdA & tcdB).AimThe recognition of suitable targets and developmentof a commercial rapid test that will distinguishvariant hypervirulent and antibioticresistant strains from ordinary C. difficile strains isthe main aim of this project. The objective will beachieved through the complementary skills ofa consortium composed of 3 SMEs and 4 publicsector institutes, each experts in their fields.There will be a close collaboration in the form ofsubcontractors with the European Study Group ofC. difficile (ESGCD). Suitable diagnostic markers(DNA- and antigen-based) will be identified usinga combination of targeted approaches (focusingon toxin and antibiotic resistance determinants),and empirical approaches (DNA arrays and HT-AFLP) to identify unique strain differences. Assaydevelopment will be led by the SMEs, using proprietarytechnologies. Clinical validation will beperformed in a certificated reference laboratory.54

Key words: clostridium difficile, hypervirulent type 027, CDAD, diagnostics, outbreaksROLE OF SMEsThe consortium consists of a balanced mix of public sector scientists that have worked onC. difficile for most of their professional careers (taken from four institutes), together withthree SME’s with highly developed technology on bacterial toxin preparation, moleculardiagnostics and enzyme-immunoassays. Therefore, complementary expertise, and ‘stateof-the-art’technology is supplied by partners specialised in diagnostics, epidemiology,genomics and drug susceptiblity screening.The three SMEs participating in the project, tgcBiomics, PathoFinder and Coris BioConcept,will mainly contribute to the development of molecular tests and rapid membraneimmunoassays for detection of the target in patient material and in bacterial isolates.The programme outputs will allow the formulationof a European strategy to combat the considerablethreat now being posed to European qualityof life by C. difficile.Expected results• Recognition of targets for new diagnostic testsby characterisation of hypervirulent and drugresistant C. difficile strains. The targets are basedon toxins, toxin coding regions, or unique othergenes of C. difficile.• The availability of molecular tests and rapidmembrane immunoassays for detection of thetarget in patient material and in bacterial isolates.• Validation of new developed tests for clinicaldiagnostics and strain characterisation. The newmolecular tests and rapid membrane assays willbe investigated in faeces samples of patientswith various forms of C. difficile associated diarrhoea.The newly developed tests will also beused to recognise hypervirulent isolates andantibiotic resistance of clinical isolates obtainedby prospective surveillance studies in Europe.Potential applicationsand prevent an outbreak. The genomic approaches(DNA Array and HT-AFLP) will provide fundamentalinformation on the genetic make-up of hypervirulentC. difficile strains and will lead to greaterinsight into pathogenesis which will in turn allowthe development of more effective therapeuticcountermeasures and IPR spin-offs. Additionally,European guidelines will be formulated to diagnoseCDAD and to combat outbreaks. The introductionof these tests and European guidelinesincrease the awareness of CDAD as an importantnosocomial infection and will be of help to preventthe development of large outbreaks by newhypervirulent variants, as currently occur in USAand Canada. Application of the new tests andupdated guidelines will contribute to insights inthe epidemiology of CDAD and will be of generalsupport to prevent over-prescription of antibioticsin hospitals. Application of the new developedtests will provide a platform for automation ofdiagnosis. A further stimulant for effective DNAbaseddiagnostic tests is to extend testing onthe same faecal sample for other non-bacterialcauses of infectious diarrhoea, such as viral diarrhoeaand parasitic diarrhoea. It is possible to automatenucleic acid extraction and use a commonextraction for all subsequent analyses.Scientific coordinatorEd J. KuijperDepartment of Medical MicrobiologyLeiden University Medical CenterPO Box 9600, 2300 RCLeiden, The Netherlandsejkuijper@gmail.comPartnersMaja RupnikDept. Med. Microbiol. Immunol.University of MariborMaribor, SloveniaNigel MintonInstitute of InfectionImmunity and InflammationUniversity of NottinghamCentre for Biomolecular ScienceNottingham, United KingdomPaola MastrantonioIstituto Superiore di Sanità, ISSRome, ItalyCristoph von Eichel-StreibertgcBiomics GmbH,Mainz, Germanywww.tgcbiomics.deThierry LeclipteuxCoris BioConceptGembloux, Belgiumwww.corisbio.com/index.aspGuus SimonsPathofinder B.VMaastricht, The Netherlandswww.pathofinder.nl| Toxin A (TcdA) and toxin B (TcdB) areencoded on large chromosomal regionPaLoc, which encompasses two toxingenes (tcdA and tcdB) and threeadditional genes coding for regulatoryand putative transport function(tcdR,E,C). In nontoxigenic strains,PaLoc is replaced by 115 bp sequence.The new diagnostic tests will overcome the lackof sensitivity and specificity of current diagnostictests. The new immunoassay offers an alternativefor those laboratories which lack capabilityin molecular biology. Recognition of variant 027is not possible with the currently available diagnostictests. Rapid recognition of CDAD and itsvariant 027 will result in appropriate patienttreatment and specific measures to prevent nosocomialspread and the development of outbreaks.The rapid molecular test will provide the first indicationof the presence of type 027, allowing adequateinfection control measures to be undertaken55

ACRONYMContract number: LSHB-CT-2006-037545 | EC contribution: € 2 978 810 | Duration: 36 monthsStarting date: 1 August 2006ENLIGHTwww.olink.com/content/Enlight/Enlight.htmlSUMMARYThe ENLIGHT project aims to developanalytical procedures with the sensitivityand specificity required to study individualnucleic acid and protein molecules,and also interacting molecules, in theirnormal context in cells and tissues (insitu) and in tissue lysate microarrays.A spectrum of reagents will be developedfor the analysis of specific markers of particularinterest in oncology. Furthermore,software and algorithms will be establishedfor automatic user-independent insitu image analysis of single moleculeevents.These methods and algorithmswill be applied to evaluate candidate biomarkersof special relevance for tumourbiology and cancer pathology.New molecular methods and image analysis toolsfor analysis of cancer biomarkers in situBackgroundIn situ analysis of cells and tissues has been anessential part of pathological research and diagnosisprimarily within cancer for many years, anda number of specific biomarkers of predictiveand prognostic value for various cancers havebeen identified. In situ analysis of nucleic acidsequences is dominated by in situ hybridisation,while in situ analysis of proteins is dominated byimmunohistochemistry where sections of tissuesare tested for the presence of proteins by specificantibodies. Due to limitations in these technologiesthere is a significant need in the scientificcommunity for new efficient techniques and proceduresfor more advanced analyses. A majorchallenge is to develop improved means formore detailed studies of biomolecules in situ, inorder to determine their abundance, sub-cellularlocalisation, and secondary modifications, aswell as how they interact with other moleculesand participate in signalling and control of cellularfunction.AimThe first aim is to develop new molecular methodsand assays for the analysis of individual DNA andprotein molecules in situ. The project is based ontwo fundamental technological inventions, padlockprobing and proximity ligation. These are thefirst technologies to offer the sensitivity and specificityrequired for studies of single bio-moleculesin situ. The padlock probe technology is used tointerrogate nucleic acids and to distinguish closelysimilar sequence variants, while the proximity ligationassay (PLA) is applied to analyse individualproteins, interactions between proteins, and posttranslationalprotein modifications.Finally, the new methods and image analysisprocedures will be used to clarify the role ofmolecular biomarkers in tumourigenesis, primarilyconcerning the AP-1 and HER protein familiesand for mitochondrial DNA. The methods will alsobe tested in a high-throughput microarray analysissystem. The cancer biomarker will primarily beinvestigated in a research setting, but the utility ofthe markers for diagnostic analyses will also beexplored.Expected resultsThis project is expected to provide new means tostudy biomarkers for oncogenesis, and to generatenovel insights in cancer biology. It is expectedthat the in situ techniques developed in this project,and the scientific knowledge created, in thelonger run will lead to improved disease prevention,more rapid and accurate cancer diagnosis,and better treatment opportunities.New analytical means will be developed to analysecancer biomarkers in situ. Relative to state-of-theartprocedures, these methods are expected toprovide significantly improved in situ analyses interms of specificity, sensitivity (single moleculedetection), possibility to study biomarker localisation,analysis of protein interactions and proteinmodifications, and an opportunity for simultaneousanalysis of multiple markers (multiplexanalysis). Automated image analysis procedureswill be developed, i.e. software-based classificationof molecules and their localisation in tissuesor cells. The software will provide a rapid way toanalyse many samples as well as user-independent,unbiased data classification.Potential applicationsSecondly, the project will develop automatedimage analysis procedures to complement themolecular methods. The objective is to achievequantitative information about what molecules ormolecule complexes are present in the sampleand their tissue or sub-cellular localisation (i.e. inwhich cellular substructures).Cancer biology and diagnosis.56

Key words: cancer, biomarker, in situ analysis, technology development, proximity ligation, padlock probingROLE OF SMEsThis project is centred around three European SMEs with high future potential. The SMEsare brought together with academic scientists and one large established company, DakoDenmark, to enable the development of new efficient technical solutions for the analysis ofindividual molecules in tissues or in single cells. The results from this project are expectedto provide important new commercial opportunities for products addressing significant marketneeds, thereby allowing the participating European SMEs to build sustainable businessesat the forefront of biotechnology. To ensure that the outcome of the project will beadvantageous for the SMEs, one of them, Olink AB, has the role as project coordinator.DakoDenmark will, as a non-SME, have a role as advisor to the SMEs in matters such asproduct requirements and market needs.Scientific coordinatorBjörn EkströmAnders AlderbornOlink ABDag Hammarskjölds väg 54A751 83 Uppsala, Swedenbjorn.ekstrom@olink.comanders.alderborn@olink.comwww.olink.comPartnersMats GullbergOlink ABUppsala, Swedenwww.olink.comUlf LandegrenEwert BengtssonUppsala UniversityUppsala, Swedenwww.uu.seHenrik WintherDako Denmark A/SGlostrup, Denmarkwww.dako.comAnders LarssonImmunsystem I.M.S. ABUppsala, Swedenwww.immunsystem.comNiels FogedVisiopharm A/SHørsholm, Denmarkwww.visiopharm.comOlli KallioniemiVTT Technical ResearchCentre of FinlandTurku, Finlandwww.vtt.fiJohn BartlettThe University of EdinburghEdinburgh, United Kingdomwww.ed.ac.ukAnton RaapHans van DamLeiden University Medical CenterLeiden, The Netherlandswww.umc.nl| Microscopic examination of tissue sections.57

ACRONYMContract number: LSHP-CT-2006-037651 |EC contribution: € 2 400 000 | Duration: 36 monthsEPIVACStarting date: 1 January 2007SUMMARYMore than 40 million people are currentlyinfected with HIV1, mostly coming fromdeveloping countries resulting in an urgentneed for effective and affordable treatmentof HIV1 infections. The main objectiveof the project is to develop an efficientgenetic vaccine candidate for therapeuticand preventative use against HIV/AIDS.The vaccine planned should be capable ofinducing cell-mediated and humoralimmunity against the virus and virallyinfected cells in different phases of theviral life-cycle.DNA vaccines could fulfil these requirementsif rendered more efficient. To thisend, a combination of complementarytechnologies by four SMEs will be used.The novel DNA vaccination technologywill combine:• the restricted expression of the multiepitope/multivalentHIV antigens inspecific cells of the epidermis;• a micro-needle array-based injectiondevice for reproducible and efficientdelivery into the epidermis;• EPI-GTU® technology that allowsstrong and long-term expression usingsegregation/partitioning function ofthe Bovine papillomavirus type 1;• Plasmo-VLP® technology that allows anexpression of the immunogens withinand onto virus-like-particles;• the adjuvant effect of different cytokines.The step-by-step combination of thesetechnologies will be evaluated at the laboratoriesof the three academic partners byusing state of the art methods. The initialevaluation of vaccine efficacy will be performedon mice and pigs and will be ultimatelyvalidated in Cynomolgus monkeys.EPIVAC aims to conduct its preclinicaldevelopment up to the GMP productionphase. Testing of numerous vector batcheswill be aimed towards having enoughsuitable material ready for evaluation inclinical trials.Development of a multi-step Improved EpidermisSpecific Vaccine Candidate against HIV/AIDSBackgroundThe Human Immunodeficiency Virus (HIV) induceschronic infection in patients, eventually leading todeterioration of the immune system and the onsetof immune deficiency. HIV induces significant cellmediatedand humoral immune responses, whichconsiderably reduce viral titre after initial burst ofthe HIV1 replication and spread in the body. Thesenaturally induced immune responses only partiallycontrol HIV spread and in fact there are no clearlydocumented cases of true clearance of the viralinfection. Nevertheless, it is possible that the triggeringof additional immune responses, notablythrough the presentation of modified HIV antigens,could generate different types of immuneresponses that could contribute towards bettercontrol of the infection and thus improve clinicalevolution and reduce viral transmissibility.The quality and intensity of the humoral or cellularimmune responses required for efficaciouspreventative or therapeutic vaccinations vary,depending on the target infectious agents.Preventative vaccines against acute viral infectionsoften rely on strong neutralising antibodyresponses, while therapeutic vaccines againstchronic infectious diseases often rely on cytotoxicresponses capable of eliminating infected cells.Most antiviral vaccines in current use are basedon homologous inactivated or attenuated viralparticles, i.e. attenuated measles virus formeasles vaccination. This establishes that packagingantigens in/onto particles is one of the mostefficient ways of triggering efficient antiviralimmune responses. Some of the most promisingnew vaccines have been designed and developedin the field of DNA vaccination. DNA vaccines arelow in cost, stable and easy to produce, whilstoffering the possibility to combine several antigenswhen required. However, it appears thatDNA vaccination, typically induces cellular immunity,but rarely or inefficiently neutralising antibodiesthat often play a major role in protectionagainst viruses ( 1 ).Based on this knowledge, the EPIVAC Project proposesthe concept of combining the advantages ofvarious vaccines by engineering them into singlevectors, i.e. by designing plasmids that harbour thegenetic code necessary for the production of recombinantviral particles, which further target the skinas a preferential site for genetic immunisation.AimEPIVAC aims to generate a multi-step, improved,efficient and affordable DNA-based preventativeand therapeutic vaccine against HIV.The first goal of EPIVAC is the development ofa reliable, reproducible and robust delivery system.This will include micro-needle arrays andan injection device for the controlled delivery ofthe GTU®-based vector system and for cell-typespecificepidermal expression of the genes ofinterest in epidermal differentiating keratinocytes,Langerhans cells and melanocytes.The plasmids and genes of interest used in thesestudies will allow for the quantitative evaluationof the efficiency and kinetics of delivery of plasmidDNA into the epidermis and epidermal cells.Further, to follow the process of diffusion, degradationand intracellular up-take and onset of biologicalactivity of the delivered expression systemin specific cells of the epidermis will be assessed.The plasmids used will carry the site-specific fluorescentlabels for the monitoring of DNA deliveryinto the epidermis as well as the diffusion anddegradation of the plasmid.The second goal of the EPIVAC project will be toanalyse the effect of different HIV1 antigenexpression in different cells of the epidermis onthe nature and breadth of the induced immuneresponse.One major problem in developing an AIDS vaccineis the lack of knowledge regarding immune mechanismsfor protection against HIV1 infection andfor removing the virus from the body. Another58

Key words: vaccines, DNA Therapy, epidermal genetic vaccination, HIV infection and AIDSROLE OF SMEsEPIVAC comprises four SMEs among the seven partners, including the coordinator FITBiotech Plc., SILEX Microsystems, ESTLA Ltd. and EPIXIS s.a.FIT Biotech will contribute its GTU® (Gene Transport Unit) platform technology and the applicationsbased on it, including novel vectors, self-replicating vectors for DNA immunisationagainst HIV, AIRE (immunological mechanisms) and DNMT3L (immune diseases, new genes).SILEX will bring to the table extensive expertise from the development and production ofMicro-Electro-Mechanical-System (MEMS) components. SILEX personnel and the fullyequipped MEMS production facility provide an excellent environment for quick prototyping,development and production of microneedles that will be used in this project. The productionof microneedles is an area of specific manufacturing expertise based on previous workfor various diagnostic and drug delivery applications.ESTLA Ltd. develops, produces and supplies accessories for research organisations (optics,fine mechanics, special instruments for biophysics), special lasers (excimer, dye, coppervapour) and laser-based systems for science, medicine, industry and entertainment. Thecompany will contribute to the EPIVAC project through studies of the injection process andvaccine distribution by optical methods, and by the design and fabrication of the specialisedinstruments needed for injections with microneedle chips.EPIXIS s.a. is dedicated to the development of preventive and therapeutic vaccines againstinfectious diseases. The company’s proprietary pseudotyped virus-like particle (VLPs) havethe unique property to express the pseudotyped viral envelops in their native conformation,and can likewise efficiently induce broadly neutralising antibodies. EPIXIS will contribute toEPIVAC with pseudotyped VLPs produced in vivo by vaccination with ‘plasmo-VLPs’.Scientific coordinatorIoana StanescuFIT Biotech PlcBiokatu 8, 33520Tampere, Finlandioana.stanescu@fitbiotech.comwww.fitbiotech.comPartnersHenrik HellqvistSilex Microsystems ABSwedenwww.silexmicrosystems.comEvgeny BerikEstla Ltd.Tartu, Estoniawww.estla.comCharlotte DalbaEPIXIS S.A.Paris, Francewww.epixis.comDavid KlatzmannUniversity of Pierre and Marie CurieParis, Francewww.upmc.frMart UstavTartu University Institute of TechnologyTartu, Estoniawww.tuit.ut.eeRoger Le GrandFrench Atomic Energy CommissionParis, Francewww.cea.frgoal of this project is to contribute towards theidentification of some immune correlates of protectionduring the evaluation of vaccine efficacy innon-human primates. The induced immuneresponse triggered by the vaccination will be characterisedqualitatively and quantitatively towardsevery viral target protein. The immunised animalswill be challenged after immunisations with thehybrid SHIV, and analysed for control, clearanceand protection.Expected results• New devices and modalities for DNA delivery tothe epidermis.Potential applications• Epidermal genetic vaccinations; Improved treatmentof HIV infection and AIDS by using nano -technology.• Improved standards for vaccination in large animals,notably by using swines that are not oftenused in vaccine development and which couldbecome interesting alternatives to the use ofnon-human primates for challenge experiments.References(1) Tuteja et al., 1999.• Generate improved DNA-based vaccines combiningthe advantages of GTU vectors for longtermexpression and plasmo-VLP vectors for thepresentation of antigens onto VLPs.• Generation of new proprietary HIV antigensbased on the EPIVAC optimised vector.59

ACRONYMContract number: LSHB-CT-2007-037283 | EC contribution: € 1 887 160 | Duration: 36 monthsStarting date: 1 February 2007EURO-PHARMACO-GENESUMMARYThe project outlines the development ofa novel Gene Pharmaceutics prototypethrough translational research. This canbe accomplished by the combined effortsof three research-intensive biotech companies,together with two academicgroups, representing state-of-the-art skillsand proprietary technologies in complementaryareas. These include nucleic acidanalogue chemistry, short interfering RNA(siRNA) technology, gene transfer andgene therapy, as well as imaging instrumentmanufacturing, and methods for selfassemblingsupramolecular complexes.This will lead to the design of new selfassemblingGene Pharmaceutics and bringthem to the clinical grade stage.The aim is to develop plasmid and siRNAbaseddrugs that target the liver, since thisorgan is affected in many disorders involvinga genetic component. Three diseaseshave been selected for this purpose,namely hepatitis B and C infections andan inherited form of bleeding disorder,haemophilia A (Factor VIII deficiency).Moreover, many aspects of this platformtechnology are likely to be applicable toessentially any liver disorder and may alsobe transferable to other organ systems.Fully developed, this technology will resultin new, safer and more rational drugs.Gene Pharmaceutics technology is basedupon the addition of functional entities tonucleic acids. The schematic representation(Fig. 1) shows three different functionalentities (blue squares, orangecircles and red triangles, or different greyshades,when printed in black and white)linked to peptide-nucleic-acid (PNA)anchors, which are glued onto the plasmidthrough hybridisation to PNA anchoringsequences (green, yellow and light blueregions, or different grey-shades, whenprinted in black and white) in the plasmid.Other nucleic acid analogues, such asLNA, or derivatives thereof, can also beused as anchors. The marked sequence inthe lower portion of the plasmid representsthe transferred gene. This could bea reporter gene, a therapeutic gene, suchas the one encoding Factor VIII, which isdefective in haemophilia A, or a short hairpinRNA expression cassette, in which theshRNA is directed against a component ofhepatitis B or C virus.Design of targeted Gene Pharmaceuticsusing self-assembling functional entitiesBackgroundDuring the last years, developments in genomicshave enabled an unprecedented acquisition ofnew knowledge with relevance for human disease.In parallel, the biotech industry hasinvented novel ways of generating drugs in orderto meet the demands from the healthcare sector.The development of new pharmaceutics in thefield of genomics and biotechnology is likely to besuccessful, provided that there is an optimal integrationof multidisciplinary efforts from both academiaand industry. This is a major challenge,since new concepts need to be explored and combinedinto commercially viable innovations. Thedevelopment of a drug from the lab bench toa clinical grade product is very costly, involvingmany translational steps and often in excess ofone hundred million euros. Only major pharmaceuticalcompanies have the financial resourcesto accomplish this task. This means that small andmedium sized enterprises (SMEs) need to developnovel drug concepts to a stage where the proof ofprinciple can be evaluated by the big pharmaceuticals,in order to bring the therapy to the clinic.AimThe project has the following objectives:• generation of new forms of DNA-binding syntheticcompounds, which will serve as geneticglues;• enhancing linking chemistry for biologically activeentities coupled to DNA binding compounds;• optimising the assembly of Gene Pharmaceuticsby in vivo experimental studies;• developing standard operating proceduresfor the manufacturing and assembly of GenePharmaceutics according to good manufacturingprocedures.Expected resultsThe project combines research with technologicalimplementation in the development of new GenePharmaceutics. Obtaining pharmacologically satisfactorygene drug delivery systems has thepotential to impact positively on a range of bothcommon and rare healthcare burdens withinEurope and beyond. Strategies targeting hepatitisB and C, and haemophilia are presented in thecurrent proposal. The expected result of the proposalwould thus be efficient and productiveprogress in the development of clinically-potentand cost-effective pharmacological formulationsof gene-based medicines.The market for gene drugs is potentially verylarge, although it is dependent upon the developmentof safe and pharmaceutically acceptable formulationsand protocols. This project, through theexpertise of the partners, aims to prove that thistechnology possesses the appropriate propertiesfor successful application.Potential applicationsThe potential applications of the drug-deliverytechnology proposed here are much broaderand could include cancer, vaccine approaches toinfectious disease, arthritic disorders, tissueengineering, and various inherited syndromeswhich, while less common, nevertheless imposehuge burdens on patients, their families andhealthcare providers. The success of this proposalwill create a new pharmaceutical platform anddemonstrate its potential for treatment, whichwould have a strong impact on public health andrelated expenses.60

Key words: gene therapy, hepatitis, haemophilia A, siRNA, PNA, nucleic acid analoguesROLE OF SMEsOf the five participants to this project, two are academic and three are SMEs. The academicresearch lab from Karolinska, in addition to coordinate, will perform assembly and biologicaltesting of the tool kit for gene transfer. These tools can be described as novel selfassemblingsupramolecular complexes. While the academic research lab in Denmark willconcentrate onnew chemistry, in particular on novel nucleotide analogue chemistry andnucleic acid functionalisation, especially based on the locked-nucleic-acid (LNA) platformtechnology.The key role of the SMEs is highlighted below: Eurogentec focuses on advanced, peptidebasedsynthesis, development of optimised coupling procedures for peptides and nucleicacid analogues. The company is an SME based in Belgium.Biospace provides state-of-the-art imaging solutions for monitoring of the biological effectsof Gene Pharmaceutics. It is an SME based in France.Avaris concentrates on development of novel pharmaceutics, in particular providing translationalresearch which brings non-viral gene transfer systems from the research lab benchto the clinic. It is an SME based in Sweden.The strength of this consortium is in the diversity and complementarity among partners,combining basic research with the applications to human health.Scientific coordinatorC. I. Edvard SmithClinical Research CenterDepartment of Laboratory MedicineKarolinska Institutet at NovumHälsovägen 7SE-141 57 Huddinge, Swedenedvard.smith@ki.seWebsite: www.ki.sePartnersJesper WengelUniversity of Southern DenmarkDepartment of Physics and ChemistryOdense M, Denmarkwww.sdu.dkDaniel MarechalIvo RudloffEUROGENTEC S.A.Seraing, Belgiumwww.eurogentec.com/eu-home.htmlSerge MaitrejeanBIOSPACE S.A.Paris, FranceMats LakeAVARIS ABc/o Karolinska InnovationsStockholm, Swedenwww.avaris.se| Fig. 1 Schematic representation of technology. | Fig. 2 Interaction and complementarity among partners. The arrowsindicate reciprocal relationships, i.e. partners connected will provideknow-how, experience or products bi-directionally.61

ACRONYMContract number: LSHB-CT-2006-037168 |EC contribution: € 2 173 492 | Duration: 36 monthsStarting date: 1 October 2006EXERAwww.altaweb.eu/exeraSUMMARYThe objective of the EXERA project is todevelop novel 3D in vitro models of mousetissues from five major organs for the pharmaco-toxicologicalanalysis of EstrogenReceptors-Interacting Compounds (ER-ICs):liver, skin and bone (non reproductive systems),ovary and testis (male and femalereproductive systems).This objective will be pursued througha work programme which allies an integratedscientific approach between innovativetechnologies such as the 3D-culturedevice, known as ‘Rotary Cell CultureSystem’ (RCCS Technology adapted to theneeds of this project), established transgenicmouse lines (estrogen-reportermice, here called MOUSE-1) and genomicplatforms for ER-ICs characterisation.The strategy is planned around five mainpoints including, besides the mentionedtechnologies, multiple cell cultures qualitycontrols, immortalisation control, cell bankingand the use of specific markers of estrogenicaction and cell differentiation/health,in order to obtain estrogen -responsive 3Dculturesof well differentiated mouse cells.The corresponding work programme willbe ensured by an important involvementof the whole partnership and by a highdegree of coordination between 6 privateand 3 public institutions.Development of 3D in vitro modelsof estrogen-reporter mouse tissues for thepharmaco-toxicological analysis of EstrogenReceptors-Interacting Compounds (ER-ICs)BackgroundIndustries from different fields (Pharmaceuticals,Chemicals, Cosmetics, Foods and Toxicologicals)need reliable, fast and economic in vitro models,which are alternative to animal testing and canprovide predictive data on the actions of NR-ICsand in particular ER-ICs (Estrogen ReceptorsInteracting compounds).The need for appropriate in vitro models whichcan reproduce features and reactivity of specificmammalian target tissue/organs to ER-ICs is thusbecoming an imperative research priority. The scientifically,economically, socially and ethically relevantstakes are therefore considerable.The tissue- and organ-specific in vitro modelswhich have been built so far have several seriouslimitations:• Most of the available cell lines of mammalianorigin are derived from tumours or have a transformedphenotype. Their functional and structuralfeatures do not mirror the original tissue.• When mammalian-derived in vitro models areavailable, they consist of primary cell cultures orof isolated tissue slices: their in vitro survival islimited (time-course and dose- response studiesare very difficult). Moreover, if of humanorigin, they have the disadvantage of dependingon regular supply from available clinicalsources.• Conventional cell cultures often do not expresssuitable easy-to-assay quantifiable markers orthey need transfection procedures that increasevariability of the data.• The systems used for the in vitro and in vivoanalysis of NR-ICs (mainly estrogens and androgens)are generally composed of cells derivedfrom reproductive tissues. The recent knowledgeof the widespread distribution of nuclearreceptors(in particular steroid receptors) in allthe tissues of the organism and their involvementin several diseases, makes the availablesystems inadequate to assess the effects ofNR-ICs on the whole physiology (Villa R, 2004).• The available models do not easily provide informationon the effects of compounds at differentdevelopmental stages.AimEXERA’s original approach is based upon powerfulevidences:Use of the transgenic MOUSE-1: This estrogenreportermouse model represents a new strategythat allows studying estrogen receptors-mediatedgene regulation in vivo and in derived invitro systems. The numerous studies performedon this animal model in several laboratorieshave demonstrated its reliability and suitabilityto the study of molecules acting through estrogenreceptors.• 2-Dimensional culture conditions may be notoptimal for tissue-like organisation and cellularfunctions (e.g. polarised cells of a parenchymaltissue, which normally require complex cellularinteractions, and cannot behave physiologicallywhen adhering to solid substrates, as in thecase of conventional culture conditions).3D cultures: Cell-cell and extracellular matrixcellinteractions play a fundamental role inmaintaining the function of numerous organsystems. Hence, tissue engineering representsa good way to overcome limits of monolayer culturesand to maintain tissue-like architectureand functionality.62

Key words: ?? estrogen receptors, endocrine disruptors, estrogenic drugs, transgenic estrogen-reporter mice,in vitro assays, 3D-cultures, in vivo imagingROLE OF SMEsIndustrial participation is important (some 70 % of the EU contribution will go to SMEs) anddiversified. It is composed of 5 SMEs and one industry. One SME (ALTA S.r.l.) will be involvedin this project for administrative management. The fact that SMEs from different but complementaryfields take part in this consortium, not only implements the recommendation of the6th FP, but represent an added value since it ensures the strong commitment of the participantsto the success of the study and will guarantee the future exploitation of the project’sresults ensuring the eventual transition from discovery to the market.Specific role description:BIOSERV: Establishment of Sertoli, Leydig, peritubular and corresponding Granulosa celllines from tissue isolates of the estrogen reporter model ERE-Luc.Development of fully functional micro test systems in which cells are maintained in chipbased micro-culture environment.CELLON: Cellon will provide the 3D cell culture systems, Rotary Cell Culture Systems (RCCS).Cellon will benefit from the new application of this technology to pharmaco-toxicologicaltesting of hormonal chemicals and will promote the diffusion and applications of the RCCSin Europe and worldwide.HORMOS MEDICAL: Hormos operates in the project as an implementation and validationarena, to provide the consortium with data on different compounds with varying SERM andNR related activity in different tissues. Hormos can adapt the cellular systems ‘in house’ andvalidate the cell lines under development with selected compounds, which have known tissueselectivity and different pharmacological estrogen profiles in tissues eg. bone, uterus,breast and liver, ovaries.| Optical imaging on the estrogen reporter mouseERE-Tk-Luc. The mouse was exposed for 6 hoursto 5 μg/kg of 17ß-estradiol.DNAVISION: The main task of DNAVision is to produce gene expression profiling (by DNAmicroarrays) of the cell systems generated by the other partners of the consortium andcompare the data to the in vivo situation (from tissues of the ERE-Luc mouse).BioUetikon Ltd.: BioUetikon will provide the technical expertise to manufacture and qualitycontrol cryopreserved cell banks of up to twenty immortalised mouse cell lines suppliedto BioUetikon by the consortium.ALTA: Working in close contact with the Coordinator, ALTA’s specific contribution to thisproject will be:• to check the progress of the administrative work;• to co-ordinate the administrative bodies of the different participants’ institutions;• to organise technology transfer and follow IPR issues.| Cell-medium interface of Sertoli cell aggregatescultured in RCCS. Cells are strain with DAPI(Mag 40X).63

ACRONYMEXERATechniques and methodologies: The steps toreach the proposed objectives will involve severalcomplementary techniques and partnerexpertise: cell isolation, conditional immortalisation,cell banking, 3D-cultures, whole genomeexpression profiles, in vitro imaging, in vivoimaging, and application of 3D-cultures devices(RCCS Technology).Cell isolation from tissues of MOUSE-1: Reliableprotocols available inside the partnership willbe applied so as to isolate well differentiatedcells from liver, skin, bone, testis and ovariesof MOUSE-1 and establish cell cultures with ‘physiological’estrogen-dependent phenotypes forimmortalisation.Conditional Immortalisation: This step will be performedby transfection methodologies in 3D andby using suitable commercially available vectors,made inducible by specifically modified antibioticsdevoid of hormonal actions. The immortalisinggene will be switched on for cell production,and off for characterisation and testing.Constitution of a cell bank: Immortalised cell culturesthat will satisfy the following parameterswill be expanded and controlled for banking.3D-cultures adapted to grow cells with an unalteredestrogen-dependent phenotype: Estrogendependentpathways will be characterised in3D-cultures. Comparison between hormone stimulationin vitro and in vivo will be performed withthe use of the transgenic marker (luciferase) andgene expression profiles. Data on the activity ofselected ER-ICs will be produced in each specificcell line.Assessment of the 3D-culture systems for thepharmaco-toxicological characterisation of ER-ICs.Expected resultsThe corresponding work programme will beensured by the important involvement of thewhole partnership and by a high degree of coordinationbetween 6 private and 3 public institutions.The expected results that will be scientifically,socially and economically relevant are as follows:• the application/adaptation of new 3D-culturetechnologies to cell cultures devoted to thestudy of ER-ICs;• the constitution of a cell bank;• a battery of differentiated 3D cell-based systemsderived from estrogen-reporter mice forbasic and applied research (e.g. pharmacologyand toxicology), public use and industrial use.Potential applicationsThe EXERA project seeks to overcome the limitationsof conventional in vitro approaches to therisk assessment of endocrine active compounds.In addition to scientific and regulatory advances,EXERA will also promote technological innovationsby including research on the applicability ofnovel cell based methods and novel end-points tothe assessment of the estrogenic action of ER-ICs.The developed cell-based systems will becomevery useful tools in investigating tissue specificregulatory pathways and hormone-dependentphysiological processes.This project is the first attempt to apply the RCCStechnology performance to the systemic analysisof hormone-dependent pathways. This will beobtained by using different cell types in standardisedconditions. Its possible adaptations to industrialscreening procedures will be intensivelyexploited. The expected achievement is to fulfilthe need of additional practical, new and easilystandardisable end-points for all the estrogenhormone target organs.64

Scientific coordinatorDiego Di LorenzoLaboratorio di BiotecnologieOspedale Civile di BresciaP.le Spedali Civili 125123 Brescia, Italydilorenzodiego@yahoo.itwww.spedalicivili.brescia.itwww.med.unibs.itPartnersAdriana MaggiCenter of Pharmacologyand BiotechnologyUniversity of MilanMilan, ItalyKalervo VäänänenUniversity of TurkuTurku, FinlandPaul TomkinsBioserv Ltd.Athlone, IrelandRichard FryCELLON S.A.Bereldange, Luxembourgwww.cellon.lu| The RCCS (Rotating Cell Culture System) culturing liver fragments from ERE-tk-Luc mice.Mikko UnkilaHormos MedicalOy PharmacityTurku, FinlandJean-Pol DetiffeDNAVision S.A.Charleroi, Belgiumwww.dnavision.beJohn MilneBioUetikon Ltd.Dublin City UniversityDublin, IrelandAldo TagliabueALTA SRLSiena, Italywww.altaweb.eu65

ACRONYMContract number: LSHP-CT-2005-037912 |EC contribution: € 1 217 800 | Duration: 36 monthsStarting date: 1 December 2006FASTEST-TBSUMMARYIt is widely accepted that rapid, costeffectivediagnosis of high sensitivity andspecificity is a prerequisite for the preventionand control of tuberculosis (TB);a global disease in humans, killing morethan 3 million people annually. Methodsand devices currently in use do not meetthese requirements.New strategies are urgently needed forcombating the problems of TB diagnosis.First-generation detection tests usinga novel, high-speed device for quantitativemeasurement of antigens in sputumand urine of TB patients have recentlybeen developed. The device also enablessimultaneous measurement of antigensand antibodies within 20 minutes. Themain objectives of this proposal are to:• Identify novel antigens using genomicand proteomic approaches.• Purify sufficient quantities of antigensand raise antibodies.• Optimise immobilisation conditions forthe specific antigens and antibodies ondifferent Carriers.• Manufacture and evaluate different, fasttests using approximately 6 000 clinicalspecimens (sputum, saliva, serum, urine)from TB patients at study sites in Asia,Africa, America and Europe.Such tests and devices would be a majorbreakthrough in the early diagnosis andprevention of tuberculosis. The Coordi -nator (LIONEX, an SME) in co-operationwith a WHO centre, a lung hospital inGermany and additional expert scientistsfrom low-resource, TB-endemic countries(India, Turkey, Nigeria, Mexico) shall in thisproject, evaluate the clinical potential ofantigen and antibody detection using thehigh speed, cost-effective Point of Care(POC) tests, with which results can beobtained on site within 20 minutes. Finally,the project also aims to develop TB-HIVdual antibody detection POC Fast tests.Development and Clinical Evaluationof Fast Tests for Tuberculosis DiagnosisBackgroundThe current methods of diagnosis (microscopy,culture, chest x-ray, PPD, PCR) are inadequate forthe diagnosis of tuberculosis, as these are eithertoo slow, not sensitive enough or too expensive.The usual means of diagnosing TB in the majorityof developing countries where culture facilitiesare not available is by the detection of acid fastbacteria in sputum by direct microscopy. But thistest is laborious and insensitive as only 40-60 %of all adults with pulmonary TB can be identifiedby the current smear test using Ziehl-Neelsenstaining.In low-resource TB endemic countries, poor accessto high-quality microscopy services and/or paucibacillarynature of pulmonary TB in HIV positivepatients results in even lower rates of sensitivityof AFB (acid fast bacilli) detection.Thus, the two main problems concerning TB diagnosisare:• sputum microscopy, currently the most widelyused method to detect tuberculosis, which iscumbersome and insensitive, leaving manypatients undetected and;• bacterial culture, the gold standard, is more sensitive,but which takes 4-6 weeks to complete,and is too complex for most settings where TB isendemic.The HIV pandemic has led to a resurgence of TB asa major public health problem. ImmunodeficientHIV-positive patients are particularly vulnerableto TB and are even more difficult to diagnose thanthose who are diagnosed HIV negative.AimTo develop and evaluate high-speed, POC testsbased on the detection of antibodies and antigensin body fluids, e.g. whole-blood, serum, urine, sputumor saliva for the diagnosis of both pulmonaryand extra-pulmonary TB.Expected resultsThe outcome of this project will lead to new inexpensiveand fast diagnostic tests that can be performedon site without the requirement of anycomplicated or expensive instruments. The testswill provide results within 15-20 minutes and shallbe preferably non-invasive.Potential applicationsPotential applications of this project results are:• The new Fast tests shall enable accurate TBdiagnosis on the spot within 15-20 minutes.• Inexpensive TB diagnosis shall be feasible inlow-resource settings highly suitable to TBendemic countries.• Antigen detection Fast tests will have considerableadvantages over current methods especiallywhen dealing with HIV positive populations,which show reduced immune response.• Additional significant advancement shall bemade by developing dual HIV-TB tests which areurgently needed in endemic countries in Africaand Asia where HIV infection is increasing daily.The outcome of this project will lead tonew inexpensive and fast diagnostic teststhat can be performed on site without therequirement of any complicated or expensiveinstruments. The tests will provideresults within 15-20 minutes and shall bepreferably non-invasive.66

Key words: Tuberculosis, TB diagnosis, serology, antigen discovery, TB-Fast test development, clinical evaluationROLE OF SMEsThe project is coordinated by LIONEX GmbH, an SME dedicated to the prevention and controlof TB. The project’s efforts are focused towards the development of completely new andfast tests for the diagnosis of TB, which shall be of particular use in developing countrieswhere several million people are infected with TB each year. Several of the project’s partnerscome from developing countries. The coordinating SME will have a pivotal role in enhancingthe communicating with endemic countries.Scientific coordinatorMahavir SinghLIONEX Diagnostics & Therapeutics GmbHInhoffenstraße 738124 Braunschweig, Germanyinfo@lionex.dewww.lionex.dePartnersFrançoise PortalesInstitute of Tropical MedicineAntwerp, Belgiumwww.itg.beHelmut BloeckerHelmholtz Centre for InfectionResearch (previously GBF)Department of Genome AnalysisBraunschweig, Germanywww.genome.gbf.deHarald HoffmannInstitute of Microbiologyand Laboratory MedicineWHO-reference laboratory forTuberculosis and MycobacteriaMünchen-Gauting, Germanywww.asklepios.com/GautingOlcay YeginAkdeniz University Medical SchoolDepartment of Pediatric ImmunologyAntalya, Turkeywww.akdeniz.edu.trP. R. Narayan, Alamelu RajaTuberculosis Research CentreChetput, Chennai, Indiawww.trc-chennai.orgGertrud BiersackSacred Heart HospitalLantoro, AbeokutaOgun State Nigeriawww.geocities.com/sacredheartabeokutaJürgen KnoblochInstitut für TropenmedizinUniversitätsklinikum TübingenTübingen, Germanywww.med.uni-tuebingen.de/tropenmedizin/index.html© ShutterstockIris EstradaDept. of ImmunologyNational School of Biological SciencesSanto Tomas, Mexico67

ACRONYMContract number: LSHG-CT-2006-037683 |EC contribution: € 3 000 000 | Duration: 36 monthsStarting date: 1 January 2007FGENTCARDwww.fgentcard.euSUMMARYThe focus of the consortium project isto define biomarkers and novel diagnostictools for risk factors for coronaryartery disease (CAD) (glucose intolerance,insulin resistance, hypertension,dyslipidaemia and obesity), using functionalgenomic and genotyping technologiesalong with the wealth of knowledgearising from mammalian genome annotations.The consortium is preparing innovativeinfrastructure of both techniques andmaterials that provide strategic supportfor CAD quantitative genetic studies inanimal models and humans. FGENTCARDis using state of the art functionalgenomic and genetic technologies includingNMR metabonomic and automatedproteomic profiling of biofluids and organbiopsies, microarray based gene transcriptionprofiling and original technologiesfor identifying disease susceptibilityloci. Results from this research will provideresources for extension and validationof CAD biomarkers in other modelsand human cohorts, and will exemplifymultidisciplinary strategies which can beapplied to other disease areas.Functional GENomic diagnostic Toolsfor Coronary Artery DiseaseBackgroundThe completion of the genomic sequence ofmany mammalian species and progress in highthroughputgenotyping and gene expressionprofiling technologies are amongst the most significantrecent advances in biomedical science.With the growing number of cohorts for case-controlgenetic studies, these resources and toolshave a wide range of applications for localizingchromosomal regions associated with diseasesusceptibility, identifying disease causative DNAvariants and characterizing mechanisms regulatinggene expression in health and disease. A particularlyimportant application is in tackling thegenetic cause of increasingly frequent disordersin western society, including CAD, a growinghealth and societal concern in the general population.The genetic causes of CAD risk factors,which associate diabetes, hypertension, dyslipidaemiaand obesity, will be addressed throughthe definition of biomarkers derived using functionalgenomic and genotyping technologiesapplied in animal models of CAD and large cohortsof patients.AimThe general aim of FGENTCARD is to apply functionalgenomic and genotyping technologiesalong with the wealth of knowledge arising frommammalian genome annotations to definingnovel diagnostic tools for risk factors of glucoseintolerance, insulin resistance, hypertension, dyslipidaemiaand obesity, which are key pathophysiologicalelements in CAD. FGENTCARD resultsutilize the power of functional genomic technologiesto tackle these increasingly frequent andprevalent inherited diseases. The proposed studieswill ultimately generate fundamental knowledgeon the impact of functional genomics toidentify disease biomarkers and test their use fordisease prediction.Expected resultsFGENTCARD will deliver technological and analyticaltools applied to the definition of CAD biomarkersthrough genetic studies in clinicalcohorts and rodent crosses, which will be used tomap CAD susceptibility loci and genes providingtargets for gene cloning and entry points for drugdevelopment. A set of standard operation procedureswill be developed for the detection of CADbiomarkers for genetic and clinical studies inother cohorts and other disease areas. This programwill design and utilize methods for multimodalgene expression profiling and subsequentdata integration that can maximize the power ofgenetic linkage and association analyses.Potential applicationsAdvancement in knowledge, technological platformsand analytical tools will contribute to a betterunderstanding of genetic systems thatunderpin multifactorial diseases. Progress in thisarea will play a key role in providing the essentialtools for the development of strategies to identifygenes for epidemiological important disordersand targets for the generation of novel therapies.Overall, the potential wealth of informationobtained on gene expression represents novelchallenges in quantitative genetics and ultimatelysignificant advances for disease diagnosis andprevention. Knowledge of the effects of geneticvariations on metabolic processes and metabotyperegulation will have an important impact inthe field of polypharmacology.68

Key words: functional genomics, atherosclerosis, metabonomics, nuclear magnetic resonance,transcriptomics, proteomics, rat, mouseROLE OF SMEsThe project provides SMEs with original biological material and data from collections ofcase control cohorts and genetic crosses between animal models. These can be used totest their technologies in deriving disease biomarkers and CAD susceptibility genes. Animportant aspect of the research project lies in the application of a multidisciplinaryapproach, allowing SMEs, specialised in technologies designed to test a specific level ofgene expression control, to obtain data from a comprehensive screening of patterns ofgene expression regulation in health and disease, ranging from genetic polymorphism, totranscriptome, proteome and metabonome. This approach is designed to promote effortstowards research and innovation and to facilitate collaborations between SMEs andbetween academic groups and SMEs. The two SMEs involved in the project, namelyMetabometrix Ltd. and IntegraGen S.A., combine very different expertise in metabonomictechnologies (Metabometrix) and disease gene mapping (IntegraGen), which willsynergistically be applied to the chromosomal mapping of CAD biomarkers.Metabometrix is a spin-off company built on the skills of the world’s pre-eminentmetabonomics research team at Imperial College, London, and experienced scientistsfrom the UK and US pharmaceutical industries. The group’s portfolio of intellectual andtechnical advances is unique and underpins a substantial lead in the field. The companyhas a proprietary platform of metabonomics technologies for generating, classifying andinterpreting metabolic information from biological fluids and tissues.Methods that IntregraGen has developed for the purpose of genome-wide linkage studiesare particularly well adapted to the research of the genes predisposing to CAD pathophysiologicalcomponents, namely late onset multifactorial diseases. The techniques will beproperly used for the identification of the genes predisposing individuals to CAD andrelated phenotypes. The company will be in the best possible position to estimate therelevance of the results obtained and implement the pertinent molecular diagnostic tests.In combination, the two SMEs play crucial and synergetic roles in the FGENTCARD project.Scientific coordinatorDominique GauguierUniversity of OxfordThe Wellcome Trust Centrefor Human GeneticsRoosevelt Drive Oxford OX3 7BNUnited Kingdomgdomi@well.ox.ac.ukwww.well.ox.ac.uk/~gdomiPartnersPierre ZallouaAmerican University of Beirut,Department of Internal MedicineFaculty of MedicineBeirut, LebanonMark LathropCentre National de GenotypageEvry, FranceJeremy K NicholsonImperial CollegeChemical and Molecular Systems BiologyLondon, United KingdomUlla Grove SidelmannNovoNordisk A/SMalov, DenmarkJorg HagerIntegraGen S.A.Evry, Francewww.integragen.comFrank BonnerMetabometrix Ltd.London, United Kingdomwww.metabometrix.com| The consortium utilisesmodern functional genomicand genetic technologies tomap etiological biomarkersof coronary artery disease inanimal models and humans.69

ACRONYMContract number: LSHB-CT-2006-037661 | EC contribution: € 2 793 724 |Duration: 36 monthsGLYFDISwww.glyfdis.orgStarting date: 1 November 2006SUMMARYDeveloping effective tools to screen forcancer is an important endeavor and thereis much research taking place to developthese tools. GLYFDIS project’s objective isto develop methods for earlier diagnosticand effective disease screening of stomachand pancreatic cancer that will lead to bettertreatment outcomes. Early diagnosis ofcancer is of far greater prognostic importancethan any attempts to treat the diseasein its late stages. Even in cases wherethe eventual outcome cannot be changed,treatment is simpler and quality of lifeimproved for those cases where earlydiagnosis is achieved. For this purpose,GLYFDIS proposed a method of a simplenoninvasive blood testing. Accuratemonitoring of a cancerous state followingdiagnosis can significantly contributeto prognosis determination and on-lineevaluation of therapeutic regimens.The most widespread and diverse posttranslationalmodification is glycosylation.The location and variation of glycans placethem in a position to mediate cellularand intracellular signalling events, aswell as participate in different biologicalprocesses including pathology states suchas cancer. Therefore, the project proposesto use analyses of glycans for identifyingnovel biomarkers that can be used forthe diagnostics and monitoring of cancer.Glycans in Body Fluids- Potentialfor Disease DiagnosticsBackgroundCancer is a significant burden on individuals, familiesand society. The economic impact of cancer issubstantial. In 2002, the overall cost of cancer, aspublished by the National Cancer Institute, was172 billion US dollars. This does not account forthe psychological toll that it takes on individualsand families.Early detection and diagnosis of cancer is basedon the observation that treatment is more effectivewhen the disease is detected earlier in itsnatural history, prior to the development of symptomsthan in an advanced stage. Diagnosis of cancerin the early stages of the disease influencesmany aspects of life. It can significantly decreasecancer-associated morbidity and mortality and torelieve the burden from patients, their familiesand the society. Accurate monitoring of a cancerousstate following diagnosis can significantlycontribute to prognosis determination and on-lineevaluation of therapeutic regimens. Developingeffective tools to screen for cancer is an importantendeavour and there is much research takingplace to develop these tools. The goal is to detectthe cancer when it is localised to the organ of originwithout invasion of surrounding tissues ordistant organs.The GLYFDIS project will make use of glycans.Their diversity, compared to genome or proteome,makes the glycans ideal for diagnosis and monitoringof cancer. Cancer-associated changes in theglycome of the tumoural tissue are very frequent.Currently one of the main obstacles is the lack ofsufficient technology. Glycome-analysis technologiestoday fall behind the rapidly developinggenome- and proteome-analysing technologies.The group hopes to identify biomarkers that canbe used to develop a non-invasive method for theearly diagnosis of stomach and pancreatic cancerbased on glycan analysis.AimGLYFDIS’ main objectives are:• To optimise high-throughput methods of glycananalysis for the diagnosis of stomach andpancreatic cancer by the analysis of glycansin blood.• Identifying cancer associated glyco-markers inserum samples of stomach and pancreaticcancer patients.• Developing and validating protocols for lectinbasedmicroarrays intended for large scalescreening of cancer associated glyco-markersin serum samples.Expected results• To identify biomarkers using glycomic and proteomicmethods together with computer basedalgorithms.• To develop a non-invasive, modest, diagnostickit that will identify specific markers for cancerin the blood.• Constructing a website and a glycome bio-bankintegrating GLYFDIS results and serving as basisfor a continuously growing public glycome databank.• Dissemination of the information to the scientificcommunity and community at large.Potential applicationsThe project will generate knowledge relevant fornon-invasive diagnosis of cancerous states withthe effort in developing a standard protocol fordiagnosis of serum samples.70

Key words: diagnostics, glycome, blood, glycan, mass spectrometry, disease markersROLE OF SMEsRNTechRNTech is an SME specialising in early stage diagnosis of digestive tract cancers with specialfocus on colorectal and pancreatic cancer. The company operates a dedicated biobankof biological samples selected from patients that have undergone surgery for the removal ofdigestive tract solid tumour.RNTech’s role in GLYFDIS has three facets:• providing biological samples collected from pancreatic and stomach cancer patients andhealthy control subjects for the discovery and validation phases of the project;• contributing to the project database by providing genomics data on pancreatic cancerpatients as well as clinical data on all selected patients and healthy subjects and participatingin the bio-statistical and bio-informatics treatment of such data and researchresults;• providing with its network of clinical oncologists and cancer biology specialists to thevalidation of identified potential biomarkers.As any other partner, RNTech will also contribute to the management and the disseminationplan of the project.ProcogniaProcognia has developed a lectin-array based technology for rapid analysis of glycosylationprofiles of intact glycoproteins. The array contains 25-30 well-characterized lectins (carbohydratebinding proteins) with overlapping specificities. The binding of a glycoprotein to thearray results in a characteristic fingerprint that is highly sensitive to changes in the protein’sglycan composition. The large number of lectins, each with its specific recognition pattern,ensures high sensitivity to changes in the glycosylation pattern. Automatic algorithms wereconstructed for deconvoluting these signals into a glycan profile output. The major advantagesof this technology in comparison to traditional methods of glycoanalysis are its shortanalysis times, the relatively low protein amount needed for analysis, the possibility toanalyse multiple samples in parallel, and the relatively low costs compared to the classicalanalysis methods (HPLC/MS).Scientific coordinatorAngel PorgadorBen-Gurion University of the NegevBeer-Sheva, Israelangel@bgu.ac.ilwww.bgu.ac.ilPartnersRakefet RosenfeldProcognia Ltd.Ashdod, Israelwww.procognia.comPauline RuddNIBRTDublin, Irelandwww.nibrt.ieJasna Peter-KatalinicMuenster UniversityMuenster, Germanywww.uni-muenster.de/enJulien TaiebRNTech Diagnostics SPRLCharleroi-Gosselies, Belgiumwww.rntech.comA highly sophisticated, automated platform (GlycoScope) was first developed for use in thebiopharmaceutical industry for the analysis of recombinant glycoprotein drugs. By tailoringalgorithms for various protein families, this product provides accurate, quantitativeglycoanalysis for single proteins.In addition, Procognia is developing a line of products for the life science and academicresearch market. The products are a line of off-the-shelf kits for glycoanalysis, distributedby QIAGEN. The first product, Qproteome GlycoArray, launched in 2006, provides a rapidand simple tool for glycoanalysis of glycoproteins. This kit can be used without sophisticatedequipment, and generic interpretation algorithms provide semi-quantitative glycoanalysisfor purified glycoproteins.| Vision of MALDI-TOF-MS. © Danny Machlys, BGU.The second product will be launched in 2007 for analysis of global glycosylation patterns ofmembrane protein extracts. The kit is intended for analysing global changes in glycosylationpatterns in extracts of cell membrane proteins of cultured mammalian cells, with theaim of enabling characterisation of glycosylation-related biological effects.As a partner in GLYFDIS, Procognia will optimise the existing technology for analysis ofglobal glycosylation pattern to allow the characterisation of complex protein mixtures inserum from healthy donors and donors with pancreatic or stomach cancer.71

ACRONYMHI-CAMwww.hi-cam.orgContract number: LSHC-CT-2006-037737 | EC contribution: € 1 715 000 | Duration: 36 monthsStarting date: 1 March 2007SUMMARYThe purpose of the project is the developmentof a compact and high-resolutionAnger camera to be used in clinical andresearch environments and which allowsearlier and more reliable diagnosis andtherapy planning of cancer diseases inspecific applications where high overallspatial resolution (less than 3 mm) andsystem compactness (less than 10x10 cm 2field of view) are required.The gamma camera is based on the wellestablishedAnger architecture, wherea collimator acts as a mechanical sieve forincoming gamma photons, a continuousscintillator uses the energy of each selectivelypassed gamma photon to generatevisible photons, and an array of photodetectorsemits electric signals in responseto the absorption of the visible photons.The improvement of performances isbased on the use of a particular type ofphotodetector, the Silicon Drift Detector(SDD), which has recently demonstratedits ability to provide better performancwith respect to the commonly usedphotomultiplier tubes.The camera is intended for use both single-handedlyfor planar scintigraphic studiesand inserted in an annular holder(gantry) of small diameter for SPECT imaging.Thanks to its compactness and highspatial resolution, it offers potential applicationsin early diagnosis of cancer diseasesaffecting areas of the human bodywhich can be hardly imaged with the largeand heavy imaging heads and gantries ofcommercial Anger cameras. The camerato be developed in the present projectalso offers promising perspectives of integrationat the system level with MRIinstrumentation, thanks to the relativeinsensitivity of the SDD photodetectorsto large magnetic fields.The research activity will be organised asfollows: the first two years of the threeyearproject will be dedicated to thedevelopment of the SDD-based Angercamera, while the third year will be dedicatedto the experimentation of the camerain selected imaging applicationsrelated to cancer diagnosis and research.Development of a high-resolution Anger camerafor diagnosis and staging of cancer diseasesbased on state of the art detector technologyBackgroundThe state-of-the-art in the field is represented bya range of commercial systems, usually havinglarge field detectors (~ 40x50 cm 2 ). These systemsare best exploited while performing wholebodySPECT studies since their large, heavyPMT-based detector heads and bulky gantriespresent difficulties in operating close to thepatient’s skin for dedicated studies of specific,small tissues such as in parathyroid imaging,brain scanning or investigation of kidney cancerin infants. In a realistic clinical setting, at animaging distance usually rather greater than20 cm, the overall effective spatial resolution istypically 10-16 mm (7-10 mm for brain studies).When a single detector head is used for dedicatedscintigraphic studies of small organs, permittinga closer imaging distance, the overalleffective spatial resolution is limited by both theintrinsic spatial resolution of the system and thecollimator.AimThe aim of the project is therefore the developmentof a new compact and high position resolution(< 1 mm) gamma camera based on the newSDD photodetector technology. The first technologicalobjective is the development of anextended array of SDDs with large cell size (1 cm 2 ),characterised by high detection efficiency to thescintillation light and low electronic noise. Thelow noise level is a result of specialised advancedsemiconductor processing, as well as of the integrationof an on-chip JFET in the detector chip,which allows us to fully exploit the intrinsic lowcapacitance of the SDD, by the minimisation ofparasitic capacitances of the connection betweendetector and electronics.The other key technological objectives addressedby the project are:• the realisation of a high-resolution collimator.The aim is to obtain a parallel hole collimatorwhose spatial resolution equals ~2 mm at animaging distance of 5 cm with a sensitivity kepthigher than 20cpm/uCi. Pinhole collimators willbe also realised;• a very compact geometry of the detection module,based on a thin substrate where the SDDsarray and VLSI readout circuits will be assembled,and a single CsI(Tl) crystal (potentiallysubstituted by the more recently introducedLaBr3:Ce) will be coupled to the photodetectorarray;• the introduction of a thermoelectric system toattain moderate cooling (~ -20 °C) during operationof the gamma camera;• the development of dedicated VLSI electronicsfor amplification and filtering of the detector signals,followed by processing electronics basedon FPGA for the event reconstruction;• the design of a compact assembly of the completeAnger Camera. The compactness of theassembly will allow ease of positioning of theinstrument close to the patient’s body surface;• the realisation of image-reconstruction algorithmsand user interface software running ona common personal computer.Expected results• Development of large-areas low-noise SiliconDrift Detectors.• Development of high-resolution collimators.• Development of a high-resolution and compactAnger Camera based on state-of-the-art technologies.• Improved diagnostic capabilities thanks to theuse of the camera.Potential applications• Improved possibility to implement an effectivetherapy with higher capability to detect as smallas possible concentrations of tumour cells.• Effective imaging on reduced volume of thebiological tissues: less than 10 x 10 cm 2 area ofthe planar view (in scintigraphic investigations72

Key words: technological sciences, health sciences, physical sciences, medical imagingROLE OF SMEsTwo SMEs, L’accessorio Nucleare S.R.L. and Nuclear Field Holland B.V., are involved withkey technical aspects of the development of the HICAM gamma camera.L’ACN is a company currently operating in the market of instrumentation for nuclear medicineand will be particularly involved with the development of the gamma camera instrumentation,taking as a start-point the gamma-ray detector developed by the other partners.Adapting the technology currently employed to the results of the present project, L’ACN willbe ready to release a commercial system within a very short time for planar scintigraphyapplications.The HI-CAM project will also produce a potential development and market impact for theNuclear Field Holland (NUFI) company, which is particularly interested in launching a veryhigh resolution (VHR) collimator, similar to the one developed within HI-CAM, onto theworld market for use in diagnostic medical imaging. With the potential to create an intrinsicresolution of 1 mm, which is the aim of the HI-CAM project, the goal of NUFI is to createa 0.5 mm hole collimator which would suit the resolution of the HI-CAM camera. In doing so,the project will develop the next generation commercial, low cost collimators, giving OEMcompanies the possibility to move in this direction and begin redesigning their systems.with one single imaging head); less than 10 cmtotal extent on the coronal plane of the patient’sbody being imaged by the acquired scans (afterappropriate rotation of the camera/s on theannular holder in the tomographic arrangement).• Measurements on anatomical sites of the targetwhich usually lead to severe space constraintsduring acquisition of the scan.• Improved use of imaging instrumentation inthose conditions where the patient’s age, conditionor physical disabilities (e.g. patient onwheelchair) prevent an effective use of largedetector heads and gantries without compromisingpatient comfort.• Brain tumours.• Thyroid cancer, particularly differentiated carcinomas,with 99mTc-perthecnetate.• Parathyroid cancer with 99mTc-sestamibi forpreoperative localisation of parathyroid adenomaswith the aim of surgical planning inMIP interventions (minimally invasive parathyroidectomy).• Breast cancer with 99mTc-labelled lipophiliccations (SestaMIBI or tetrofosmin). The mostpromising application of the proposed systemconcern its use in preoperative or postoperativesites.In addition, the project offers innovativeapproaches to the diagnosis of tumours in infantsand children.Scientific coordinatorCarlo FioriniPolitecnico di MilanoVia Golgi 4020133 Milano, Italycarlo.fiorini@polimi.itwww.elet.polimi.itPartnersCarla FinocchiaroCF consulting FinanziamentiUnione europea srlMilano, Italywww.cf-consulting.itLeonardo PepeL’accessorio Nucleare S.R.L. (L’ACN)Cerro Maggiore (MI), Italywww.acn.itPieter van MullekomNuclear Fields International B.V.Vortum Mullem, The Netherlandswww.nuclearfields.comLothar StrüderMax-Planck-Gesellschaft zur Foerderungder Wissenschaften eVMünich, Germanywww.mpg.deBrian HuttonUniversity College LondonLondon, United Kingdomwww.uclh.nhs.ukUgo GuerraOspedali Riuniti di BergamoBergamo, Italywww.ospedaliriuniti.bergamo.itIgnasi CarrióInstitut de Recerca de l’Hospitalde la Santa Creu i Sant PauBarcelona, Spainwww.santpau.esGiovanni LucignaniUniversità degli Studi di MilanoMilano, Italywww.unimi.it| Principle scheme of the Anger camerabased on Silicon Drift Detectors technologydeveloped in HICAM.73

ACRONYMContract number: LSHC-CT-2007-037642 | EC contribution: € 3 635 200 | Duration: 36 monthsStarting date: 1 March 2007HighReXwww.sectra.se/medical/mammography/highrexSUMMARYBreast cancer is currently the most commoncause of death from cancer forwomen below seventy years of age andcurrently over 100 million Europeanwomen are screened every year for earlydetection through mammography. Theobjective of the proposal is to increasethe efficiency in detection and diagnosisof breast cancer and thus to decrease themortality in breast cancer. To achieve this,we will develop novel imaging methodsbased on recent results in the researchfields of nanotechnology, x-ray optics,detector technology and integratedelectronics. The new modality will bedesigned by leading European industryand SMEs in these areas and develop theonly commercially available Europeandetector platform for digital mammographytoday into a leading technology platformfor tomorrow. The novel method willprovide significantly increased contrastand spatial resolution compared to currentstate-of-the art breast imagingthrough elimination of noise from electronicsas well as from overlapping tissueand by way of utilizing the signal moreefficiently through fast single photoncounting integrated circuits. To makesure that the project targets the rightissues in breast imaging, experiencedmammography doctors from severalEuropean breast imaging centres areinvolved in the project and they will alsotest and evaluate the new imaging systemand compare it to current state-of-artmammography as well as ultrasound andMR imaging of the breast. The clinical trialswill involve an enriched populationof symptomatic women and the potentialimpact on European screening forand diagnosis of breast cancer will beestimated from the results.High Resolution X-Ray Imaging for ImprovedDetection and Diagnosis of Breast CancerBackgroundThe incidence of breast cancer currently increasesin all European countries and according to theEuropean Breast Cancer Network (EBCN), everyyear 50 000 women are diagnosed with breastcancer. Around 40 % of these women will die fromthe disease, making it the second most commoncause of death for women between the age of 20and 70. The most efficient weapon against breastcancer is currently early detection through mammographyscreening. An early detection makesthe subsequent therapy more successful and alsomitigates bi-effects and facilitates breast conservingsurgery in contrary to mastectomy. Thereis currently scientific evidence for a decrease ofmortality between 30 and 40 % in the screenedpopulation.Currently, film is the most common image receptorin mammography, but this is now beingreplaced by digital mammography.In mammography screening 70-90 % of the cancersare detected. The undetected cancers aremainly in women with dense breasts where thecontrast resolution of state-of-the-art equipmentis limited by overlapping tissue. Recent resultsfrom the so called ACRIN trial show that this challengecan to some extent be met with the adventof digital mammography. The improvements are,however, modest and the problem remains. Whatmakes the problem worse is that the risk forbreast cancer is almost a factor three higher forwomen with dense breasts.One way of solving the problem would be toincrease the radiation dose to increase contrastresolution. However, in dense breasts, this wouldalso increase the noise caused by overlying tissue.Moreover, the radiation dose in mammographyis a growing concern, and increasing theradiation dose would mean an increased risk forradiation induced cancers. This is particularly truefor women below the age of 50 who on averagehave much denser breasts and who, because oftheir age, are significantly more radiation sensitivecompared to older women. Due to the limi -tations of the current technology, in many EUcountries breast cancer screening is presentlyonly offered to women older than 50.AimThe HighRex project intends to solve the currentdilemma in mammography by increasing theimage quality in terms of contrast and spatial resolutionwhile lowering the radiation dose. This willbe achieved by using results from fundamentalresearch in nano-technology, x-ray optics anddetector technology obtained during the lastyears. The currently only European detector platformcommercially available for digital mammographywill be drastically improved and developedinto a detector system for the next generationbreast imaging equipment.Expected resultsAn increase in breast cancer detection rate inscreening of just 1 % in Europe would mean thatan amount of cases in the order of 500 otherwiseundetected cases would be diagnosed annually,with a potential of 100 to 300 lives saved. It may,however, be expected that the increase in detectionrate is significantly higher than 1 %, maybeeven exceeding 10 %.Potential applicationsCompetitiveness of the Highrex European technologyplatform will manifest itself stronger inthe second generation of mammography and theproposed project will be able to deliver a standardfor 3D mammography that will be unsurpassedfor quite some time. reason to believethat the photon counting advantages in mammographywould also be beneficial in other imagingapplications such as CT and chest x-rayimaging, and this project has the potential to providethe example needed for the technology tospread also to those areas.74

Key words: mammography, breast imaging, photon counting, tomosynthesis, contrast mammography, breast cancer, dual-energyROLE OF SMEsThe three participating SMEs, Detection Technology (DEETEE), Silex Microsystems AB(SILEX), and Artinis Medical Systems (ARTINIS) will be heavily involved in the design andassembly of every crucial part of the proof-of-principle prototypes. DEETEE will be responsiblefor designing the required application specific circuits as well as the X-ray sensors;SILEX will design the X-ray optics while ARTINIS will design phantoms for evaluation ofthe prototypes. If the proposed research is successful, the proof-of-principle prototypeswill be developed into real products and the participating SMEs will be in an excellentposition to take part in volume production as well as in continuous development of theproduct. The competitiveness of the SMEs will further be strengthened through theincreased capacities developed within the project, as well as through the internationalcontacts created and a network that will facilitate problem solving in the future and forma basis for other cooperation projects. The know-how gained in the project is likely to besufficiently generic to have the possibility of being applied also in other areas, e.g. indeveloping imaging modalities for other examinations than mammography.Scientific coordinatorMats DanielssonSectra Mamea ABKistagången 2SE-164 40 Kista, SwedenMats.Danielsson@sectra.sewww.sectra.com/medicalPartnersMikko JuntunenDetection Technology Inc.Ii, Finlandwww.deetee.comEdvard KälvestenSilex Microsystems ABJärfälla, Swedenwww.silexmicrosystems.com/pagesRoeland van der BurghtArtinis Medical Systems B.V.Zetten, The Netherlandswww.artinis.comMatthew WallisAddenbrooke’s HospitalUniversity of CambridgeCambridge, United KingdomKenneth YoungRoyal Surrey County Hospital NHS TrustGuildford, United KingdomWalter HeindelMünster UniversitätMünster, GermanyUlrich BickCharité Universitätsmedizin BerlinHumboldt UniversityBerlin, GermanyBrigitte SéradourAssociation pour la Rechercheet le Dépistage des Cancers du SeinMarseille, FranceNico KarssemeijerRadboud UniversityNijmegen, The Netherlands| Vision of clinical application for breastcancer detection with 3D photon countingtomosynthesis based on research in theHighrex project.Ruben van EngenStichting Landelijk ReferentieCentrum voor BevolkingsonderzoekNijmegen, The NetherlandsKarin LeiflandCapio Diagnostics Radiology SwedenStockholm, SwedenUlf StrandAvalon Product DevelopmentHelsingborg, Sweden75

ACRONYMContract number: LSHP-CT-2007-037760 | EC contribution: € 1 103 505 | Duration: 36 monthsStarting date: 1 April 2007HIVResInhSUMMARYHIV-1 can develop multidrug resistance inpatients receiving various combinationchemotherapies. This is one of main problemsin anti-HIV/AIDS chemotherapy. Toidentify compounds active against HIV-1drug-resistant strains, project partnersplan to synthesise and investigate thestructure, conformation and selectedphysicochemical and biological propertiesof a range of new and known, modified2’, 3’-dideoxynucleoside analogues.Compounds of this type should act ascompetitive drug-resistant reverse transcriptase(RT-Res) inhibitors. Slow releasingforms of these compounds (prodrugs)will also be prepared. Drug-resistantreverse transcriptases will be obtainedfrom engineered HIV-1 drug-resistantmutants, as well as by recombinant techniques.Interactions of synthesized compoundswith the wild type HIV-1 RT, aswell as with HIV-1-Res RT, will be investigatedand potent inhibitors will be subjectedto antiviral activity determinationsin cell cultures and in vitro cytotoxicity.Structure-activity relationships will beperformed and selected RT inhibitors willbe subjected to determination of completecross-resistant profiles in laboratoryand clinical HIV-1 strains fromdocumented clinical context of resistance.Investigation of in vitro viral escape willalso be determined. Long-term antiretroviraltherapy often results in toxicadverse events attributable to mitochondrialdamage due to the inhibition of DNApolymerase γ synthesis and the reductionof cellular energy production.Preparation and Identification of New HIVReverse Transcriptase Inhibitors Targeted AgainstHIV Strains Resistant to anti-HIV/AIDS drugsBackgroundHuman immunodeficiency virus (HIV) encodes foran RNA-dependent DNA polymerase (reversetranscriptase, RT), but not the specific enzymesrequired for the phosphorylation of 2’,3’-dideoxypyrymidineand purine nucleosides. To exertantiviral activity, these analogues must undergoa three-step phosphorylation by host cell kinasesand/or be metabolised by other enzymes. Their5’-triphosphates act as RT competitive inhibitorsand/or DNA terminators. Since RT is essential toHIV replication, the development of RT inhibitorsis a key strategy in the fight against AIDS.However, drug resistance emerges rapidly withthese nucleoside-based inhibitors (NRTIs).At present, the emergence of HIV-1 variants resistantto standard drugs is one of the major obstaclesto chemotherapy of HIV-1 infection. HIV-1 candevelop multidrug resistance in patients receivingvarious combination chemotherapies. Thereforethe development of novel compounds especiallymodified 2’,3’-dideoxynucleosides, which areactive against wild-type as well as multidrugresistantvariants, is urgently needed.AimThe general aim of this project is to identify andprepare and identify new potential drugs from theclass of new modified 2’,3’-dideoxynucleosides,active against HIV-1 drug-resistant laboratory andclinical strains.Expected resultsTo obtain new modified 2’,3’-dideoxynucleosidesand their phosphates, highly active drugs againstdrug-resistant HIV strains, and to detect theirphysico-chemical and biological properties. Resultswill be disseminated through patenting.Potential applicationsAfter obtaining positive biological results,patents and publications will be submitted toa pharmaceutical firm (SME) for further investigationsin animals and in the clinic, allowing potentialoutlicensing of the above-mentioned drugs.The toxicity of the new drugs will be evaluatedby determining the inhibitory properties(IC 50 ) and insertion and exonucle olyticremoval of new nucleoside analogues byDNA polymerase γ. Finally, selected activecompounds with low in vitro cytotoxicity willbe subjected to in vivo (in mice and/or rats)pharmaco-toxicological investigations.76

Key words: chronic diseases, virology, anti-HIV and AIDS drugsROLE OF SMEsThis project comprises one SME, InPheno AG, which plays a key scientific role in the project.Researchers at InPheno have a solid background in pre-clinical profiling of anti-HIV drugs.InPheno will mainly contribute to the determination of a complete cross resistance profileof new HIV inhibitors in laboratory strains and variants from clinical context, as well asinvestigating whether the new inhibitors provoke viral escape in vitro. InPheno expertise iscentred around preclinical profiling of HIV resistance in diagnostics and drug discovery,which will provide an important contribution to the critical mass of the project.Scientific coordinatorTadeusz KulikowskiInstytut Biochemii iBiofizyki PAN5a Pawinskiego Street02-106 Warsaw, Polandtk@ibb.waw.plwww.ibb.waw.plPartnersKazimierz KitaInstytut Przemyslu OrganicznegoOddzia w PszczyniePszczyna, Polandwww.ipo.pszczyna.plMarek FiglerowiczInstytut Chemii Bioorganicznej PANPoznan, Polandwww.ibch.poznan.plPatricia Laquel-RobertUMR 5097 CNRS/Université Bordeaux 2Bordeaux, Francewww.cnrs.frAndrzej PiasekInstytut Medycyny Doswiadczalneji Klinicznej im. M. Mossakowskiego PASWarsaw, Polandwww.cmdik.pan.plFrancois HamyIn Pheno AGBasel, Switzerlandwww.inpheno.comKazimierz KitaInstytut Przemyslu OrganicznegoOddzial w PszczyniePszczyna, Polandwww.ipo.pszczyna.pl© Shutterstock77

ACRONYMContract number: LSHP-CT-2007-037301 | EC contribution: € 2 250 000 | Duration: 36 monthsStarting date: 1 January 2007HIVSTOPSUMMARYThe Acquired Immunodeficiency Syndrome(AIDS) caused by infection with the humanimmunodeficiency virus type 1 (HIV-1) isa pandemic continuing to grow at analarming rate, despite the availability ofhighly active anti-retroviral chemotherapy(HAART). The World Health Organisation(WHO) and European Union (EU) thereforelaunched a co-ordinated action program tocombat poverty-related communicablediseases, including AIDS.In this project a novel therapy for thetreatment of individuals infected withHIV-1 is to be developed. This therapyinvolves the application of RNA interference(RNAi) to prevent productive infectionof new cells with HIV-1 and thereforeeventually cure infection. An SV40-basedvector will be used to transfer the therapeuticanti-HIV-1 sequence to T-cells ofHIV-1 infected individuals in order toresult in long-lasting improvements oftheir condition. SV40 vectors are intrinsicallysafe, transfecting both non-dividingand dividing cells. In order to use thistherapy in developing countries it isessential to keep the costs and complexitylow. A producer cell line will thereforebe generated in order to produce viralvector particles at high titres and focuson a single-administration, long-lastingtherapeutic molecular vaccination.The safety and efficacy of the developedtherapeutic vaccine will be tested in vitroand subsequently in vivo using mouseand simian challenge models.Development of an Effective RNAInterference-Based Anti-HIV-1 TherapyUsing an SV40-Derived VectorBackgroundHAART can be effective; however, resistant viralstrains do emerge. Eventually, these resistantvariants can cause AIDS in treatment-resistantpatients. A novel therapy that involves the applicationof RNA interference (RNAi) to prevent productiveinfection of new cells with HIV-1 and thuseventually cure infection is the aim of this project.So far, RNAi-based inhibition of HIV-1 replicationhas been accomplished through the introductionof virus-specific, synthetic short double-strandedRNAs. These are short interfering RNAs or DNAconstructs encoding short hairpin RNAs. However,their use as therapeutic antiviral against HIV-1 islimited because of the rapid emergence of virusescape variants.In order to solve this durability problem, DNA constructsencoding virus-specific long hairpin RNAs(lhRNAs) were developed. It was demonstratedrecently that expression of such lhRNAs in targetcells provides durable, sequence-specific andbroad-spectrum inhibition of HIV-1 replication.AimTo develop a novel therapy for the treatment ofindividuals infected with HIV-1. This therapyinvolves the application of RNA interference(RNAi) to prevent productive infection of new cellswith HIV-1 and so eventually cure infection.An SV40-based vector will be used, and the costsand complexity will be kept low. Therefore a producercell line will be generated, to produce viralvector particles at high titres and focus ona single-administration, long-lasting therapeuticmolecular vaccination.Expected results• Proof of safety and efficacy of the developedtherapeutic vaccine tested in vitro and subsequentlyin vivo using mouse and simian immunodeficiencyvirus (SIV)/Cynomolgus macaquemodels.• A producer cell line to produce viral vector particlesat high titres.Potential applicationsTherapeutic anti-HIV-1 Vaccine.78

Key words: therapeutic molecular vaccination, HIV-1, AIDS, SV40-Vector and RNA interferenceROLE OF SMEsThe SME involved in this project, Viruvation B.V., will be responsible for the co-ordinationof the project. Viruvation is a young biotechnology company which focuses on RNAi-basedantiviral strategies and will be responsible for the development of SV40 production technology.The company will further contribute with know-how on virology and proprietarytechnology of importance for the project’s core tasks.Scientific coordinatorGerrit-Jan van HolstViruvation B.V.Wassenaarseweg 72, PO box 10482302 BA Leiden, The Netherlandsgerritjan.vanholst@viruvation.comwww.viruvation.comPartnersBen BerkhoutAcademisch Medisch Centrum (AMC)Amsterdam, The Netherlandswww.amc.nl.Puri FortesFundación para la InvestigaciónMédica Aplicada (FIMA)Pamplona, Spainwww.cima.esNeil AlmondNational Institute for BiologicalStandards and Control (NIBSC)Potters Bar (Hertfordshire), United Kingdomwww.nibsc.ac.uk© Shutterstock79

ACRONYMContract number: LSHB-CT-2006-037319 |EC contribution: € 2 467 314 | Duration: 36 monthsIBDchipStarting date: 1 December 2006SUMMARYThe IBDchip Project will develop an easyto use DNA array and accompanying innovativechip reading device. The IBDchipwill be a non-invasive tool with thecapacity for the simultaneous analysis ofaround 100 relevant mutations to predictthe clinical evolution, the risk of developingIBD-related complications, and thelikelihood of responding to certain drugsfor each IBD patient.Usefulness of a new DNA array (IBDchip) to predictclinical course, development of complications andresponse to therapy in patients with inflammatorybowel disease (IBD)BackgroundInflammatory bowel disease (IBD) includes Crohndisease (CD) and ulcerative colitis (UC). Both areincreasingly common, chronic illnesses, currentlyaffecting nearly 1 million patients in Europe. CDand UC affect patients early in life, seriouslyimpairing their quality of life and resulting in enormouspersonal, social, and economic costs.There is evidence suggesting that genetic factorsplay a key role in IBD pathogenesis, pointingtowards a polygenic mode of inheritance for CDand UC. However, to date studies have onlyaddressed the influence of single mutations onIBD, resulting in a poor prediction of clinical courseor response to therapy in individual patients.AimThe main aim of this project is to provide doctors,for the first time, with a non-invasive, predictivetool to optimise treatment in IBD patients, thusresulting in better clinical outcomes and improvedcost-effectiveness of treatment.Expected results• A fully validated innovative prototype IBDchipwhich will give doctors vastly improved capacitiesto make more accurate individualised predictionsof clinical outcomes of IBD and choosethe optimum and most cost effective therapy foreach patient.• A clear understanding of the pathways to clinicalservice, ethical and legal issues, and costeffectivenessof the IBDchip, which will resultin maximum uptake of the IBDchip in routineclinical practice.• The results for the academic partners will benew knowledge derived from the researchundertaken in the project and published ina range of leading academic publications.Potential applicationsThe IBDchip will have very wide application acrossthe EU and beyond. The team has the workingobjective of the IDBchip being used for 15 % ofboth UC and CD patients (a total of approximately320 000 people) within three years of the endof the project (i.e. in 2011). These illnesses areincreasing and the project team expects that theIBDchip and new reader will be embedded asa routine part of treatment over the coming decade.It is also probable the IBDchip project R&Dprocesses and the resulting technologies can beadapted to address problems in the predictionand treatment of other polygenic inflammatoryconditions such as rheumatoid arthritis. The teamintends to use the consortium and its work overthe next three years as the foundation for futureprojects to explore other potential applications ofthe technology.• A new DNA array reader which will be faster andone fifth of the price of existing machines tooptimise the reading of the IBDchip and helpmake it ubiquitous.80

Key words: inflammatory bowel disease, IBD, Crohn’s disease, ulcerative colitis, genetic factors, DNA array, scanner,pathways to clinical serviceROLE OF SMEsProgenika Biopharma S.A., one of the two SMEs involved in the project, has been the mainproject driver, having originated the idea, identified and engaged the partners and will performtasks that use a major part of the EC contribution to the budget. Building on developmentwork done for their existing products, Progenika will use this project to validate newtechnology and knowledge and create a prototype IBDchip that has been tested in clinicaluse and, therefore, is close to final commercialisation. The innovative prototype chip willgive Progenika a clear advantage over competitors in becoming first to market with theirnew knowledge intensive product.Innopsys is the second SME involved in the project and will develop a slide reader to becommercialised alongside the IBDchip, which will be smaller and much cheaper than existingmachines and will take the company into a new market place (the reading of DNA arrays)while reinforcing their scientific and technological capacity for future innovations.Scientific coordinatorMiquel SansGastroenterology DepartmentHospital Clínic/IDIBAPSBarcelona, Spainmsans@clinic.ub.eswww.idibaps.ub.eduPartnersMarta ArtiedaProgenika Biopharma S.A.Derio, Spainwww.progenika.comStéphane Le BrunInnopsys S.A.Carbonne, Francewww.innopsys.frDerek JewellUniversity of OxfordNuffield Department of Medicineand Oxford GKPRadcliffe InfirmaryOxford, United Kingdomwww.ndm.ox.ac.ukwww.oxfordgkp.orgSeverine VermeireThe University Hospital in LeuvenLeuven, Belgiumwww.kuleuven.beSalvador PeñaThe Laboratory of ImmunogenicsDepartment of PathologyVU University Medical CenterAmsterdam, The Netherlandswww.vumc.nlStefan SchreiberUniversity Hospital Schleswig-HolsteinThe Institute for ClinicalMolecular Biology (ICMB)Kiel, Germanywww.uk-sh.deMilan LukasThe University Hospital in PraguePrague, Czech Republicwww.cuni.czSilvio DaneseIstituto Clinico HumanitasRozzanoMilan, Italywww.humanitas.it81

ACRONYMContract number: LSHM-CT-2006-037400 | EC contribution: € 2 500 000 |Duration: 36 monthsStarting date: 1 January 2007IMMUNATHSUMMARYThe immune system has a major role in atherosclerosisand its innate and adaptivearms jointly and separately co-determineatherosclerotic disease initiation and progression.The search for approaches tomodulate the inflammatory response inatherosclerotic disease is still in its infancy.Inflammatory diseases like rheumatoidarthritis (RA) have much longer been recognizedas immune disorders and henceare much ahead in development of therapeuticstargeting inflammation. A multidisciplinaryapproach will stimulate thediscovery of immune modulating compoundsto treat atherosclerotic disease.Thereto, the current project joins forces ofthree SMEs owning unique proprietarycomplementary technology together withfour academic groups, which are activelyinvolved in the field of cardiovascular diseaseand immune modulation. Researchgroups’ work is dedicated to SMEs todevelop new and test pre-existing leadcompounds that modulate the innate oradaptive immune response and subsequentatherosclerotic disease. In addition,diagnostic markers will be exploited thatreflect the severity of atherosclerotic diseasebased on innate receptor ligands andresponsiveness, focused on TLR and NODreceptors.In work packages (WP) 1 and 2, targets forintervention that have been discoveredusing an integrated genomics or proteomicsapproach, will be validated andantagonists constructed using both smallmolecule and antibody technology. WP 1will focus on innate receptor signalling,WP 2 will address the therapeutic anddiagnostic value of TLR ligands andresponsiveness. In WP 3 and 4, the propertiesof therapeutic lead compounds anddiagnostic modalities that are based onmodification of the innate and adaptiveimmune response will be assessed usingstate of the art in vitro and animal modelsystems. This STREP will significantlyadvance the position of three SMEs basedon a multidisciplinary approach, and willpromote therapy and diagnosis for a diseasewith high socio-economic impact.Translating innate immune receptor functioninto diagnostic and therapeutic applicationsfor atherosclerosisBackgroundAtherosclerotic cardiovascular disease remainsas number one killer of the aging population inWestern Society and numbers of cardiovascularevents are strongly increasing in developingcountries. Worldwide about 17 million deaths arecaused by this inflammatory disease and thecosts for health care and loss of productivityexceeds $ 169 billion Euro a year in Europe.Fortunately, increasing knowledge on the mechanismsof atherosclerotic disease resulted in preventivestrategies and a subsequent decrease inrate of mortality in industrialized countries since1950. However, the increasing prevalence of typeII Diabetes in developed and developing countriesdeserves careful consideration since thiswill surely influence morbidity and mortality ratesdue to cardiovascular disease. Improvement ofour understanding of the mechanisms that leadto atherosclerotic disease has resulted in innovativemodalities that may help diagnose, preventand treat this life threatening disease.We now know that atherosclerosis is an inflammatorydisease and that the body’s immune systemplays a central role in the initiation andprogression of atherosclerotic lesion development.The recent insights in how the immune systemrecognizes endogenous and exogenousligands and how ligation of innate immune receptorsresults in a local inflammatory response, hasopened exciting new therapeutic avenues whichwe would like to implement. Atherosclerosisbears many similarities to other inflammatory diseaseslike rheumatoid arthritis or Crohn disease.Experimental studies revealed that such diseasesmay be treated by different approaches in humans:blockade of innate immunity (anti-TNFalpha) andalso by immunisation in mouse models. In atheroscleroticmice, it has been shown that thevaccination approach may also be applied toatherosclerotic disease. A successful vaccinationstrategy to prevent adverse outcomes dueto atherosclerotic disease will have enormousimpact on healthcare.AimGeneral project objective: to develop and validatetherapeutic approaches that modulate the innateand adaptive immunological responses in atheroscleroticdisease.This general objective can be specified accordingto 4 Work packages:WP 1 – Receptors. To identify targets for interventionand test antagonizing compounds in the signallingcascade of the innate receptors, TLR andNOD, to inhibit atherosclerotic lesion development.WP 2 – Ligands. To identify endogenous ligandsfor TLR and NOD that are involved in atherogenesis and assess diagnostic value of ligandexpression and receptor responsiveness followingligation.WP 3 – Innate Immunity. To inhibit atheroscleroticlesion progression by leading compounds, targetingTLR ligation or signalling and TNFalpha thathave been developed and licensed by participatingSMEs.WP 4 – Adaptive immunity. To inhibit atheroscleroticlesion progression by immunisation targetinglipoproteins that have been shown to induce a vascularinflammatory response and plaque formation.82

Key words: Atherosclerosis, immune system, toll like receptor, vaccinationROLE OF SMEsThree SMEs will participate in this consortium: OPSONA (Dublin), Bio-Invent (Lund) andAlloksys (Utrecht). All three companies have specific expertise that does not overlap: productionof TLR agonists/antagonists, immune-therapy based on passive immunisation andToll Like receptor ligand recognition, respectively. These companies will provide tools andcompounds that will be used in experimental models in order to examine applicability totreat atherosclerotic disease. In addition, the academic institutes will search for new ligandsand proteins that play a role in TLR signalling in atherosclerotic disease. The SMEs willthen try to develop antagonising therapies to prevent or stabilise atherosclerotic disease.These will be evaluated in experimental models in the participating academic centres.Expected resultsIt is expected to detect:• molecules/proteins that serve as a therapeuticaltarget in atherosclerotic disease;• targets that may serve as surrogate endpointsfor adverse cardiovascular events in clinical trialsor as a prognostic marker for clinical eventsdue to atherosclerotic disease;• therapeutic interventions to prevent initiation orprogression of atherosclerotic disease by:– antagonising receptors,– antagonising ligands,– altering receptor response,– immunisation.Potential applications• Therapeutical interventions based on immunomodulation that may prevent initiation of andcomplications by pre-existent atheroscleroticdisease.• Prognostic measures that may help diagnosingthe patients prone to develop acute myocardialinfarction.Medium TNF10 ng/ml TNF + Remicade Sups + RemicadeSups IL-1 10 ng/ml IL-1 + IL-1 Ra Sups + IL -1 RaScientific coordinatorGerard PasterkampUniversity Medical Center UtrechtExperimental CardiologyRoom G02-5123Heidelberglaan 1003584CX UtrechtThe Netherlandsg.pasterkamp@umcutrecht.nlwww.vascularbiology.nlProject managerArnold HeijkampInteruniversity CardiologyInstitute of The NetherlandsPostbox 192583501 DG UtrechtThe Netherlandsarnold.heijkamp@icin.knaw.nlwww.icin.knaw.nlPartnersMark HeffernanChrisopher LocherOPSONA Therapeutics Ltd.Dublin, Irelandwww.opsona.comMarc FeldmannClaudia MonacoKennedy Reserach InstituteImperial CollegeLondon, United KingdomR. CarlssonBo JanssonBioinvent International ABLund, Swedenwww.bioinvent.comJ NilssonHarry BjorkbackaUniversity of LundLund, SwedenG. HanssonZhong-Qun YanKarolinska InstituteStockholm, SwedenJon Daniel LamanErasmus UniversityRotterdam, The Netherlands| Monaco C. et al, 2007 (unpublished data).Ruud BrandsAlloksys Lifescience B.V.Utrecht, The Netherlandswww.alloksys.eu/php/index.phpGerard PasterkampDominique de KleijnUtrecht University Medical CentreUtrecht, The Netherlands83

ACRONYMContract number: LSHC-CT-2006-037489 | EC contribution: € 3 000 000 |Duration: 36 monthsStarting date: 1 October 2006Immuno-PDTwww.immunopdt.netSUMMARYPhotodynamic therapy of cancer, i.e. thegeneration of reactive oxygen species inthe tumour environment which followsthe irradiation of suitable photosensitizingmolecules, is an attractive modalityfor the selective ablation of inoperablesuperficial neoplastic lesions. This Proj -ect puts together a network of academicresearch groups and companies for thedevelopment of antibody-based targetedphotodynamic therapy modalities. Theplanned research activity starts with thesynthesis of novel photosensitizing moleculessuitable for conjugation to antibodies,and with the identification ofnovel human monoclonal antibodies,capable of a selective targeting of thetumour neovasculature for immuno-PDTapplications. Following an extensive invitro characterisation of the most promisingantibody-photosensitizer conjugates,the therapeutic potential of thebest conjugates will be tested in rodentmodels of cancer, paving the way forfuture clinical applications.Immunophotodynamic therapyof cancer: concepts and applicationsBackgroundCancer chemotherapy is generally accompaniedby severe side effects, mainly due to unspecificcytotoxicity of classic antineoplastic treatments.Photodynamic Therapy contributes to a significantefficacy in the treatment of neoplasticand abnormal tissues, using a combination ofphotosensitizer, such as porphyrin, chlorin, bacteriochlorin or phthalocyanine derivatives, andtissue-penetrating visible laser light. Laser lightpromotes the photosensitizer into its excitedstate. The photosensitizer, in turn, interacts withmolecular oxygen and returns to its ground state,resulting in the generation of the highly localisedcytotoxic agent, singlet oxygen, which ultimatelyaffords tumour destruction.PDT is a modality of cancer treatment that causescytotoxic action only locally in the region of exposureto laser light with a specific wavelengthmatching the absorption profile of the photosensitizer,thus leading to very site specific toxicity.The targeted delivery of photosensitizers to suitableneoplastic sites is likely to increase the scopeand the efficacy of PDT therapy still further. Theantibody-mediated targeted delivery of photosensitizersto the tumour neo-vasculature mediates arapid occlusion of blood vessels, thus deprivingtumour cells of oxygen and nutrients and triggeringan avalanche of tumour cell deaths. As anadditional benefit, lower doses of photosensitizercan be administered, thus reducing problems ofskin photosensitivity.AimThe present project has as objectives the synthesisand conjugation of novel infrared photosensitizersto the most promising antibodies againstvascular tumour antigens obtained by humanantibody technology, the immunohistochemicalcharacterisation, the biodistribution and imagingtargeting in vivo, in order to select the best antibody-photosensitizerconjugates to be taken forwardinto clinical trials as a final objective.In detail, the objectives are:• the synthesis of novel infrared photosensitizerswith sufficient water solubility (i.e., not sticky tounwanted cells and tissues), which absorb inthe near-infrared light spectrum and which efficientlygenerate singlet oxygen and/or otherreactive oxygen species;• screening of phage display libraries to find themost suitable antibodies for the project;• investigation of a novel method for the conjugationof the antibody and photosensitizer molecules.The project proposes to investigate thecoupling of photosensitizers to antibodies,based on the non-covalent but stable interactionof photosensitizing molecules with specificantibody fragments or suitable single domainbinders;• evaluation of the conjugates in vitro and in vivo.The project’s novel PDT agents will be extensivelytested in vitro, in order to ascertainwhether non-covalently bound photosensitizerscan retain singlet oxygen production activityupon irradiation.The agents will be tested in rodent models of cancerand, if successful, will open novel therapeuticopportunities for the selective treatment of superficialtumours in accessible body cavities.Expected resultsMost importantly, there is a reasonable expectationof a medical benefit for cancer patients stemmingboth directly and indirectly from this Project:• directly, since immuno-PDT procedures promiseto be invaluable for the selective ablation ofinoperable superficial neoplastic lesions, suchas certain head and neck, gastrointestinal, urogenitaland gynecological tumours;• indirectly, since the knowledge generated bythe validation of novel antibodies for vasculartargeting applications is likely to have an impactin other forms of immunotherapy, including theuse of full IgGs and antibody-cytokine fusionsfor cancer therapy.84

Key words: photodynamic therapy, antibody-photosensitizer conjugates, tumour neovasculatureROLE OF SMEsImmuno-PDT has put together a network of academic research groups and companies forthe development of antibody-based targeted photodynamic therapy modalities. The threeSMEs – Philogen, Photobiotics and Trojantec – are crucial partners in Immuno-PDT andshare 52 % of the budget.Philogen (Italy) will produce antibodies against vascular tumour antigens by humanantibody technology, with the final aim of selecting the best antibody-photosensitiserconjugates to be taken forward into clinical trials.Photobiotics (UK) will contribute with the synthesis of novel photosensitizing molecules,suitable for conjugation to antibodies. The wide range of immuno-conjugates made will havediffering physico-chemical properties, which may lead to different internalisation rates.Trojantec (Cyprus) will use low levels of cell permeating peptides (antennapedia) co-coupled toantibody fragments to enhance cellular delivery. This technology will be used to supplementphotosensitiser delivery to tumour cells, by facilitating photosensitiser delivery to tumour cellssurrounding the targeted vasculature.The collaborations will establish the feasibility and biomedical potential of a novel class oftargeted PDT applications, and will provide invaluable information about their anti-cancerpotential for selective destruction of tumour neo-vasculature. The three SMEs will ensurethat all necessary expertise and resources are in place, to assist translational activities suchas patent filing, Material Transfer Agreements, licensing deals, GMP manufacture activitiesand clinical development.Scientific coordinatorChiara FalcianiReinerio GonzalezPhilogen S.p.A.Siena, Italychiara.falciani@philogen.itreinerio.gonzalez@philogen.itwww.philogen.itPartnersRoss BoyleUniversity of HullHull, United KingdomGokhan YahiogluPhotobiotics Ltd.London, United Kingdomwww.photobiotics.comLuciano ZardiCentro Biotecnologie AvanzateGenova, Italywww.biotecnologie.itDario NeriSwiss Federal Institute of TechnologyZurich, Switzerlandwww.pharma.ethz.ch/people/neridPeter VajkoczyUniversity of HeidelbergHeidelberg, Germanywww.uni-heidelberg.de/index_e.htmlPotential applicationsWhen considering immuno-PDT applications inoncology in a strict sense, the potential market isdirectly determined by the incidence of inoperablesuperficial neoplastic lesions, such as certainhead and neck, gastrointestinal, urogenital andgynecological tumours, which would benefit froma PDT-based ablation.In a broader sense, discoveries in terms of newtumour targets, new antibodies, new couplingmethodologies, and new photosensitizers willbenefit several areas of biomedical development,including non-oncological indications such aspotentially-blinding angiogenesis-related oculardisorders (such as age-related macular degeneration,diabetic retinopathy, etc.).Mahendra DeonarainImperial College LondonLondon, United Kingdomwww3.imperial.ac.ukChristina KousparouTrojantecNicosia, Cypruswww.trojantec.com85

ACRONYMINDABIPContract number: LSHM-CT-2006-037050 | EC contribution: € 1 600 000 | Duration: 36 monthsStarting date: 1 December 2006SUMMARYThe INDABIP project aims to identifybiomarkers for the early diagnostics ofParkinson disease. Biomarkers are anytype of biological molecules that arepresent in people suffering a specific disease,even when the symptoms are mild,but that are not present in people freefrom the disease or suffering from otherdiseases. The identification of the earlyindications of the development of a neurodegenerativedisease is the basis forpreventive treatment strategies, whichaim to control the disease at early stagesrather than when irreparable neurologicaldamage has been caused.Innovative diagnostic approachesfor biomarkers in Parkinson diseaseBackgroundParkinson disease (PD), a specific type ofa group of neurodegenerative disorders calledsynucleinopathies, is the second most commonneurodegenerative disorder worldwide. Manyneuro degenerative disorders are preceded bya pre-symptomatic phase, probably lasting years,during which degeneration and death of neuronsoccurs before any clinical symptoms appear. Onemajor challenge of clinical research is to improveearly detection of these diseases by developingtools to move diagnosis backward in the neurodegenerationtemporal course. Thus, the centralobjective of this INDABIP proposal is the identificationof molecular markers that hallmark theonset of a cellular dysfunction in the brain areasinvolved in PD, and that enable to identify at-riskgroups, both for disease onset and progressionduring the pre-clinical period.AimWhile biomarkers can take many forms, the IND-ABIP project aims to identify relevant proteins,mRNA, miRNAs, differentially matured RNAs andmethylated DNA, whose analysis can be transformedin diagnostic tests. The brain damage inParkinson disease and other neurodegenerativediseases is progressive and, by opening a windowfor therapeutic treatment and prevention, the earlydetection of biomarkers may help to identify individualsthat have started to develop the disease.While most biomarkers are mere reporters of thedisease state, others may actually be key factors inthe processes that lead to the onset and developmentof the disease. The second aim of the INDABIPproject is therefore to identify these key factors andto evaluate their potential as drug targets.To study the development and evaluate potentialtargets and therapies for Parkinson disease, biologicalmodels are needed, in which the eventsthat occur in the patient are mimetized. A target isany molecular entity (transcript, protein, …) thatcan be interfered with to interrupt the chain ofevents leading to the onset or development of thedisease. We will develop novel in vitro models forParkinson disease based on cell cultures for thedevelopment of a high throughput screening platform,and use these for in vitro target validationexperiments.Finally, we will initiate a screen for potential drugsinteracting with selected molecular targets.Expected resultsThe INDABIP project aims to deliver an early diagnosticassay for Parkinson disease validated inthree independent laboratories. We will workclosely together with Parkinson disease PatientsOrganizations to discuss and promote the possiblefuture implantation of this diagnostic assay inthe national health systems.Potential applicationsEarly diagnostics becomes really helpful whenappropriate treatments become available thatcan prevent the further development of the incipientdisease. The INDABIP project will thereforedevelop the tools to screen for drugs that can preventthe further development of Parkinson diseaseand initiate the process of drug development.86

Key words: Parkinson disease, diagnostics, drug target identificationROLE OF SMEsINDABIP is a SME driven and SME coordinated project. Two companies with complementaryinterests will receive about 50 % of the project financing: Oryzon Genomics, a biotechcompany based in Barcelona (Spain) and Genfit, a biopharmaceutical company located inLille (France). Oryzon Genomics contributes to the Project with experience in DNA chiptechnologies and bioinformatics applied to the discovery of biomarkers in neurodegenerativeand oncological diseases. Oryzon Genomics will perform analysis of gene expression,splicing and methylation analysis in the project. Genfit has solid knowledge in thefield of gene regulation. The Company has gained a solid experience in the analysis of thefamily of transcription factors known as ‘nuclear receptors’ and has developed innovativestrategies to screen for drug candidates that target and modulate these receptors. Genfitwill also bring its experience in animal models to the project. Both companies believe inthe power of the symbiosis between academic and SME partners and are determined toadd a long term product-oriented vision to the project.Scientific coordinatorTamara MaesC. S. O. Oryzon genomicsOryzon genomics S.A.Parc Cintífic de BarcelonaJosé Samitier 1-508028 Barcelona, Spaintmaes@oryzon.comwww.oryzon.comPartnersSakina Sayah-JeanneGenfit S.A.Lille, Francewww.genfit.comIsidro FerrerFundació Privada Institut d’InvestigacióBiomèdica de BellvitgeBellvitge, SpainPDDLBDHans KretschmarLudwig-Maximilians-University of MunichZentrum für Neuropathologieund PrionforschungMünich, GermanyIrina AlafuzoffKuopio UniversityDepartment of Neurologyand NeuroscienceKuopio, FinlandRegis BordetDepartment of PharmacologyFaculty of Medicine, UL2leUniversity HospitalLille, FranceLewy bodies: optical and e.m.| LEWY BODIESSpherical intracytoplasmic inclusions withconcentric eosinophilic core and peripheralunique or multilayered narrow, pale-stained,hallo. Diameter ranging from 8 to 30 μm.May bwe unique or multiple. The core iscomposed of densely packed filaments andgranular material. The hallo is formed byradially-arranged 7-20 nm intermediatefilaments associated with granular electrondensecoating material and vesicular structures.87

ACRONYMContract number: LSHP-CT-2006-036871 |EC contribution: € 2 000 000 | Duration: 36 monthsStarting date: 1 January 2007INNOVACSUMMARYThe INNOVAC project comprises sevenpartners, three of whom are SMEs. Theconsortium will develop three platformtechnologies that will be used for noveland highly innovative methods for vaccinationagainst two of the most importantpoverty-related diseases, namely tuberculosis(TB) and malaria. An importantaspect to this project is the inclusion ofa vaccine-producing SME, Vabiotech,from a developing country. The threeR&D platforms are:• bacterial spores. Robust and heat-stablebioparticles with proven efficacy asmucosal vaccines;• intracellular & Invasive bacteria includingE. coli strains and Mycobacteriumbovis (rBCG);• S-layer protein conjugates and S-layerprotein coated liposomes.INNOVAC will focus on discovery activitiesincluding proof-of-principle studiesto show Ag expression, testing of vaccinesin vitro as well as challenge experimentsin vivo. The project will test andevaluate highly innovative strategies forvaccination using recombinant systems,some in their infancy and others at a moreadvanced stage of development. Thisproject will include construction of vaccinevehicles, their evaluation in animalmodels, challenge experiments andfinally safety tests, where appropriate, inorder to take potential vaccines to thestage of clinical evaluation. Inclusion ofa partner SME from Vietnam will enabletechnology transfer to disease-endemiccountries.Highly innovative strategies for vaccinationto poverty related diseasesBackgroundThe partners have a background in vaccinedevelopment (Cutting; Cobra Biomanufacturing &Nano-S), vaccine manufacture (Vabiotech), malaria(Heussler) and tuberculosis (Manganelli andDelogu). They have formed a collaborative groupingthrough which they will exploit novel intellectualproperty (IP) with the aim of demonstratingproof of principle and commercial feasibility.AimThe aim of this project will be to develop new andnovel vaccines that could be developed for vaccinationagainst malaria and/or TB. Proof-ofprinciplethat can enhance the value of existing IPwill be the primary aim. The technologies underdevelopment are particularly novel and includeheat-stable bacterial spores for antigen deliveryas well as bacterial systems that can deliver antigensinside the host cell (intracellular delivery).Malaria and TB are of concern to both developingand developed countries. One of the partners inthe project, Vabiotech, is a commercial partnerwith a long history in vaccine production froma developing country, namely Vietnam. It isexpected that this company will facilitate thedevelopment of novel vaccine technology fordeveloping countries.Expected resultsIt is not expected that a ‘ready-to-go’ vaccine willbe developed during the lifetime of this project.The aims are more realistic, namely the validationof one or possibly more of the platform technologiesin development. In principle, the projectmay generate encouraging results with one ormore vaccine candidates against either malariaor TB. This could lead to preclinical studies andlong-term clinical studies, in collaboration withindustrial partners.Potential applicationsHeat stable vaccines are of particular interest todeveloping countries enabling more stable androbust products. Invasive delivery systems, ifvalidated, could be efficient at targeting andpreventing infection of not only Plasmodiumand M. tuberculosis but also other intracellularpathogens.88

Key words: Bacillus, bacterial spores, spore vaccines, heat-stable vaccines, 2 nd generation vaccines, mucosal vaccines,oral vaccines, edible vaccines, malaria, tuberculosis, nanobiotechnology, S-layers, M. bovis, M. tuberculosisROLE OF SMEsThe INNOVAC consortium carries 2 SMEs, Nano-S, and Cobra that have IP rights to novel vaccinationstrategies, vectors and strains. A further SME is Vabiotech in Hanoi, Vietnam, whowill collaborate with the European partners. Its inclusion is important to introducing andtransferring technology rights to disease-endemic countries.Cobra, will manage pilot scale production of spore vaccines. This will include the design andproduction of GM spores that are unable to proliferate; GMP production methods for sporeproduction and optimised methods for large scale production.Nano-S will be responsible for optimisation of S-layer vesicles for mucosal immunization.Scientific coordinatorSimon M. CuttingSchool of Biological SciencesRoyal Holloway University of LondonEgham, Surrey,TW20 0EX, United Kingdoms.cutting@rhul.ac.ukwww.rhul.ac.ukPartnersRocky CranenburghCobra Biomanufacturing plcKeele (Staffordshire), United Kingdomwww.cobrabio.comAlexander MatisNano S Biotechnologie GmbHVienna, Austriawww.nano-s.comRiccardo ManganelliDepartment of HistologyMicrobiology andMedical BiotechnologiesUniversity of PadovaPadova, Italywww.unipd.itGiovanni DeloguIstituto di MicrobiologicaFacolta’ di Medicina e Chirurgia “A. Gemelli”Universita Cattolica del Sacro CuoreRoma, Italywww.unicatt.itVolker HeusslerBernhard Nocht Institutefor Tropical MedicineDepartment of MolecularParasitologyHamburg, Germanywww.bni-hamburg.de© ShutterstockNguyen Thu VanVabiotechNational Institute ofHygiene & EpidemiologyHanoi, Vietnamwww.vabiotechvn.com89

ACRONYMContract number: LSHM-CT-2006-037965 | EC contribution: € 1 299 697 | Duration: 36 monthsStarting date: 1 November 2006INTELLIMAZEwww.intellimaze.orgSUMMARYBehavioural change is the most sensitive biologicalend-point signalling any alteration inthe organism of a mouse. However, largescalebio-assays of behaviour face limitations:outdated technology, need for spaceand specialised manpower, lack of standardisation,and increasing legal demands on animalhusbandry. This has limited the use ofbehavioural methods to specialised laboratories,also limiting the market.In order to advance scientific progress andexpand the market, 2 SMEs and 1 academicpartner will combine their existing expertiseand products for behavioural phenotypingto generate a compact modularsystem, INTELLIMAZE, based on a recentlydeveloped technology of in-cage testing ofmicrochipped mice, INTELLICAGE. This systemshould fit into a single small mouseroom, where it will:• assess home cage activity and learning oftransponder-tagged mice living in socialgroups;• automatically analyse social behaviour;• guide individual mice to a battery of traditionallyused tests;• show ongoing learning on-line to a supervisorworking in his office;• analyse data according to expert knowledge-basedrules;• provide a web-based analysis of resultsfor user groups.The bottleneck of such technological developmentis functional validation and comparisonwith traditional tests. Three reputedacademic partners will use the novel technologyfor:• generating new mouse models of depression;• profiling malfunctions of specific brain systems;and• monitoring the effects of age-dependentneurodegeneration in existing and newmouse models. Finally, an SME partner inneed of efficient behavioural phenotypingwill validate the novel systems for drug discoveryand development.It is expected that the availability of simplified,rapid and thorough behavioural testingof mice without need for specialised personnelwill open new and much larger marketsfor the SMEs. Moreover, significantscientific discoveries in the fields of drugdevelopment, psychopharmacology, neurodegeneration,neural plasticity and repair,and genetic engineering are predicted.High-throughput, fully automated and cost-effectivebehavioural phenotyping of normal, clinical andgenetic mouse modelsBackgroundToo many mice. During the past 15 years, molecularbiology and ENU mutagenesis programmeshave led to an explosion of mouse models, manyof them needing behavioural characterisation.Behavioural characterisation (‘phenotyping’) oflaboratory animals is an established tool in neurobiologyand neuropharmacology, but may findmuch wider application in drug development, ecotoxicologyand other fields of biomedicine dealingwith changes in body physiology. However, thereis no appropriate technology to deal with the largenumber of mice. High-throughput behaviouralphenotyping (HTBP) would be needed, either formass screening of mice, or, equally importantly,for the application of numerous tests to selectedsamples.Simplistic technology. Traditionally, animals aresubjected manually to a battery of tests designedfor demonstrating changes in spatial or fearrelatedmemory, motivation, exploration or learningabilities, thought to reflect the operation ofspecific brain system. In addition, tests have beendesigned to model processes observed in humandiseases of the CNS. Thus, every laboratory specialisingin behavioural analysis must maintain anexpensive collection of test set-ups, all of thembeing conducted with single mice.Economic limits. A standardised preliminary behaviouralscreen of a knockout mouse requires testingof about 100 mice in 4-6 different tests, equallingthree person-months; a more detailed characterisationrequires up to 6 person-months, even whenusing highly standardised procedures and automateddata analysis. Thus, the main obstacles forhigh-throughput behavioural phenotyping arecosts in terms of space, salaries and expertise.Hidden problems in mouse testing. Traditionalbehavioural characterisation of mice faces a numberof problems well known to experts but rarelydiscussed publicly:• mice are far less cooperative than rats and otherlaboratory animals;• there is limited knowledge about the behaviouralbiology of mice;• species-pecific functions of structures in themouse brain are poorly known;• the development of clinical mouse models forpsychopathology faces problems in recognisinghow a behavioural impairment relevant to thehuman disorder would manifest itself in a mouse;• all these problems are compounded by the lackof standardisation and comparability of testresults.Animal welfare. For behavioural testing, mice areoften kept isolated over prolonged periods. Yet,mice are social animals and isolation in an impoverishedenvironment can cause many physiologicaland neurochemical changes producing confoundedresults. Moreover, European legislation islikely to ban animal housing under isolated conditions.This calls for social in-cage alternatives inbehavioural testing.AimThis SME project allies three SME’s and four academicpartners for developing and validatinga compact, economic and fully automated modularplatform, INTELLIMAZE, that will permit bothhigh-throughput and detailed behavioural characterisationof current and future mouse modelsin biomedicine. In accordance with legislativetrends in Europe, the system will operate withmice living in social groups in a home cage.The technical development will be done by twoSMEs (NewBehavior, and Frank Buschmann Inter -national) and one academic partner (Laboratoryof Systemogenesis at the Anokhin Institute ofNormal Physiology of the Russian Medical Academyof Science).The commercial objective is to obtain a significantmarket share of the developing market of automatedtest systems, expand the present market toinclude new categories of customers, and to tailorsuch systems for small biotech SMEs in need ofbehavioural characterisation.90

Key words: mouse phenotyping, testing apparatus, high-throughput testing, transponder technology, automation,Alzheimer’s disease, depression, anxiety, brain lesions, neurology, transgenic miceROLE OF SMEsThree SMEs, sharing 45% of the project budget, are key players of the project. NewBehavioracts as coordinator and is responsible for the development of hard- and software for novelautomated systems evolving from current products centred on automated assessment ofbehaviour and learning in home cage systems. Frank Buschmann International adds complementaryexpertise in construction of behavioural apparatus of single animal testing, togetherwith expertise derived from its products in web-based management of experimental protocolsand mouse colony supervision. Thus, the resulting INTELLICAGE and INTELLIMAZE system willnot only operate in a single laboratory but can be used for parallel multi-user testing inEuropean projects and large pharmaceutical companies. Finally, the company Evotec, actingas a validating user, brings its experience in industrial drug development and testing. This willensure that the developed systems do comply with both the needs of academic research laboratoriesand those of pharmaceutical and biotech companies. It is anticipated that thisapproach will substantially enlarge the market for behavioural testing systems for mice.The joint scientific objectives of the academicpartners are validation of this novel technologyand inter-laboratory standardisation. Accordingto their expertise, they will also implement thenovel technology specifically for:• in-depth behavioural profiling of brain lesions inmice, focussing on hippocampus, striatum andprefrontal (University of Zurich);• development of novel behavioural paradigmsfor mouse models of anxiety and depression(Istituto Superiore di Sanita in Rome);• monitoring the progress of brain malfunction inmouse models of Alzheimer’s disease and prematureageing (EVOTEC Hamburg and NEUROTECat Karolinska Institute Stockholm).Expected resultsWhat is proposed here is almost a dream for mousebehavioural biologists: a fully automated behaviouraltest system for mice inside a home cage, andoutside in traditional test arenas, working withoutsupervision, and outputting data in familiar formatand ready for statistics. Scientifically, it will permitto conduct almost all those studies that shouldhave been done but were never realised. Moreover,cross-laboratory standardisation is achieved withminimal efforts, and animal welfare guaranteed.Commercially, it will certainly penetrate the market,and has the potential of opening new markets inbiotechnology and pharmaceutical industry havingbeen hesitant in using costly behavioural assessment.Finally, as the products combine state-of-thearttechnology with expert behavioural knowledge,it will offer a sustainable perspective for the SMEs,providing a technological edge over the US, andkeeping production competence in Europe.Potential applicationsIt is expected that these systems will be employedby the pharmaceutical industry, by small biotechcompanies producing and testing their own com -pounds, by companies offering phenotypingservices for mice, and by academic behaviouralresearch laboratories.Scientific coordinatorHans-Peter LippNewBehavior AGHardurmstrasse 76CH-8005 Zürich, Switzerlandhp.lipp@newbehavior.comProject managerToni Lippt.lipp@newbehavior.comwww.newbehavior.comPartnersFrank BuschmannFrank Buschmann International GmbHBochum, Germanywww.fbiscience.comEnrico AllevaIstituto Superiore di SanitàDipartimento di BiologiaCellulare e NeuroscienzeRoma, ItalyAbdul MohammedKarolinska InstituteDepartment of NeurobiologyHealth Care Sciences and Society (Neurotec)Karolinska University HospitalStockholm, SwedenDavid P. WolferUniversity of ZürichInstitute of AnatomyDivision of Functional NeuroanatomyZürich, SwitzerlandKonstatin AnokhinRussian Academy of Medical ScienceAnokhin Institute of Normal PhysiologyDepartment of SystemogenesisMoscow, RussiaAntje WilluweitEVOTEC Neurosciences GmbHIn vivo Pharmacology GroupHamburg, Germany| Assessing learning abilities of individualtransponder-tagged mice in an automatedhome-cage (INTELLICAGE). Each cage house upto 16 mice and contains 4 operant conditioningunits allowing for assessment of spatial,temporal and operant learning abilities.91

ACRONYMContract number: LSHB-CT-2007-037636 | EC contribution: € 2 701 611 | Duration: 36 monthsStarting date: 1 January 2007InVitroHearter-projects.gf.liu.se/~invitroheartSUMMARYInvitroheart seeks to establish stable celllines that reliably reflect human cardiomyocyteproperties through the developmentof models derived from humanembryonic stem (hES) cells. Its aim is todeliver reliable in vitro models that couldbe used by the pharmaceutical industryto replace experimental animals in:• investigations on pharmacological toxicityand safety of compounds in the drugdiscovery and development processes;• the testing of toxic effects of chemicalsaccording to the new system of the Com -munity on the Registration, Evaluationand Authorisation of Chemicals (REACH).The Invitroheart consortium is composedof nine participants and four of them areSMEs. The SMEs contribution is crucial tothe project as regards the generation ofcells and assay technologies, and asexperts in life science and micro-sensortechnologies, they are the key providersof state-of-the-art technology.Reducing Animal Experimentation in Drug Testingby Human Cardiomyocyte In Vitro Models Derivedfrom Embryonic Stem CellsBackgroundIn the pharmaceutical industry, reliable in vitrocell models would contribute to replace currenttechniques with animal experimentation in theselection and optimisation of lead compoundsand in documentation of a selected drug candidatebefore it enters clinical phases. In the toxicitytesting of chemical substances, replacement ofanimal testing methods can be attained as well.The means to accomplish the objective, in additionto new stable hES cell derived cardiomyocytes,are as follows:• state of the art methods for electrophysiologicalcardiac cell monitoring;• optical micro-sensor monitoring in micro-cultivationsystems for in vitro screening;• a multi-micro-bioreactor platform for highthroughputscreening of drugs and chemicals.Invitroheart will carry out comparative studies ofcardiomyocytes derived from hES cells withestablished in vitro models in order to validate thenew models and methods. The outcome of theproject is new efficient in vitro pre-validationmodels which will significantly reduce the use ofanimal experimentation for cardiotoxicity testingby 60-80 %. Furthermore, it will strengthen thepossibility for the participating SMEs to marketnew potential products in the areas of in vitroassay methods and in vitro compound screening.Studies of toxicity and safety pharmacology ingeneral, and cardiotoxicity in particular, are keyactivities throughout the drug discovery programsin the pharmaceutical industry. Such activities areinitiated to detect detrimental compound effects.For example, electrophysiological changes such asQT prolongation, which leads to delayed ventricularrepolarisation and cardiac arrhythmia, areinduced by a vast range of chemical entities formultiple therapeutic areas. Unintended QT effectsof new drugs are the most common cause of drugwithdrawal from the market and delays in or lackof regulatory approval for marketing.Clinical cardiotoxic effects are defined as symptomsof clinical heart failure, and subclinical cardiotoxiceffects such as cardiac abnormalitiesdetected in asymptomatic persons by means ofvarious methods. One of the problems is the availabilityof preclinical models able to screen rapidlya large library of substances and to providerational bases for clinical trials. A significant bottleneckin the development of novel assays hasbeen the lack of research purposes. Animal modelshave been invaluable for risk assessment ofcompound safety; however, critical limitationsremain in these models for robust prediction ofcertain toxic outcomes in humans.AimThe overall aim of the project can be summarisedas follows:• to replace animals with human cell culture systemsin preclinical pharmaceutical developmentand chemical substance toxicity testing;• to support the predictability of the drug discoveryand development process of cardiovascularpharmaceuticals by allowing more reliable andrelevant testing in the preclinical phase andhinder weak lead candidates to enter clinicalphases with innovative human cardiomyocytecell systems;• to deliver an in vitro testing system with adjacentmethodology pertinent for validation inGLP/SOPs environment for cardiac safety;• to deliver in vitro testing systems with adjacentmethodology pertinent for chemical substancetoxicity testing within REACH;• ultimate aim: to reduce or even totally abolishthe use of animals in drug and chemical substancetesting, refine the model system underconsideration and to replace the animal modelscurrently used.Specific technology related objectives:• to establish relevant hES cell derived cardiomyocytescultures that allow a more predictable preclinicallead testing program to be carried out;92

Key words: embryonic stem cells, cardiomyocyte, animal experimentation, safety assessment, in vitro models,cardiac toxicity, electrophysiology, QT prolongation, optical sensor, high-throughput screening, bioassaysROLE OF SMEsOut of nine partners in Invitroheart, four are SMEs (Cellartis, Multi Channel Systems,Pharmacelsus and PreSens) and their share of the requested funding from the Commissionamounts to 59 %. They provide state of the art expertise in key research activities.In particular:Cellartis brings to the project a strong expertise in the field on hES cells. They will establishappropriate protocols for the production and characterisation of cardiac cells, for qualitycontrol of these cells according to GMP-standards, and for development of innovative cellpreservation methods. They will provide to partners well characterised human cardiomyocytesfor the planned research. A future goal is to investigate in detail differentiationprocesses and to provide large quantities of cardiomyocytes to customers.Multi Channel Systems (MCS) provides functional electrophysiological monitoring duringthe development of the hES cell derived cardiomyocytes. Furthermore, MCS will developa hardware platform optimised for cardiomyocyte electrophysiology screening, includingdevelopment of software to automate the data acquisition and analysis. Also, a prototype ofan integrated automated screening system will be manufactured. MCS provides access tothe worldwide distribution network to market the complete assay.Pharmacelsus will design and build new in vitro assay systems for hES cell derived cardiomyocytesin order to support predictive in vitro models of the consortium. Furthermore,Pharamacelsus will provide its scientific experience of a broad range of in vitro models forpharmaceutical testing and will integrate consortium knowledge in statistical validationinto the developed new assay systems. Pharmacelsus’ excellent in-house facilities foranalysis (Fluorimetry, Spectroscopy, HPLC, LC-MS/MS) will support partners to carry outspecific assay testing with the different systems developed.PreSens will integrate chemical optical sensors for pH and oxygen measurements in theassay technologies developed, adapt existing sensors and develop new sensors accordingto the special demands of the new methods. PreSens will integrate optoelectronicinstruments based on its sensor technology and will deliver these to the partners of theconsortium. Furthermore, it will investigate the implementation of fluorescence intensitymeasurements in the existing instruments and will give support in data interpretation.Scientific coordinatorCarl-Fredrik MandeniusLinköping University, IFM, SE-581 83Linköping, Swedencfm@ifm.liu.sewww2.ifm.liu.se/biotech/Project managerMagnus Fredrikssonmagfred@ifm.liu.sePartnersPeter SartipyCellartis ABGöteborg, Swedenwww.cellartis.comThomas MeyerMulti Channel Systems GmbHReutlingen, Germanywww.multichannelsystems.comChristine Batzl-HartmannPharmacelsus GmbHSaarbrücken, Germanywww.pharmacelsus.comChristian KrausePreSens GmbHRegensburg, Germanywww.presens.deMorten LaursenLundbeck A/SDept. of Safety PharmacologyValby, Denmarkwww.lundbeck.comA. LindahlGöteborg UniversityDept. of Clinical Chemistry/Transfusion MedicineGöteborg, Swedenwww.biomedicine.gu.se/avdelningar/avdelning_4• to develop a real-time sensor based in vitromodel for short-term studies of cardiac sideeffectsthat mimics the function and complexityof the cardiomyocyte tissue in vivo;• to develop a real-time sensor based in vitromodel for long-term studies of cardiac sideeffectsthat mimics the function and complexityof the cardiomyocyte tissue in vivo;• to establish a versatile cell lab platform basedon the developed cell lines and cultivated inadvanced miniaturised bioreactor systems withnon-invasive measurement techniques for invitro testing of cardiotoxicity.Expected resultsSuccessful results of the project will, if adopted bythe European pharmaceutical community, lead to:• the preservation of significant numbers ofexperimental animals;• reduced work carried out during pharmaceuticaldrug discovery and development in thepreclinical and early clinic phases;• improved predictability of quality of lead candidatesincreases the chances for passing theentire clinical trials process;• reduced total development time of leads;• attainment of better quality and safety in documentationfiled to regulatory bodies.Elmar HeinzleSaarland UniversityDept. of Biochemical EngineeringSaarbrücken, Germanywww.uni-saarland.deSusanne BremerECVAM (European Centre forthe Validation of Alternative Methods)Joint Research CenterInstitute for Health andConsumer ProtectionIspra, Italyecvam.jrc.it/index.htm93

ACRONYMLIGHTSwww.lights-EU.orgContract number: LSHC-CT-2006- 037852 | EC contribution: € 1 902 150 | Duration: 36 monthsStarting date: 1 October 2006SUMMARYOvarian cancer is the fifth most commoncause of death from cancer in women. Thestandard first-line treatment is a combinationof paclitaxel and carboplatin (DDP) orcarboplatin alone. In the case of progressivedisease or drug resistance treatmentwith platinum, either alone or in combination,especially investigational compoundsshould be used. The mechanismsbehind acquired resistance to cDDP andits derivatives are not clear yet, althoughit is evident that the process is multifactorial,including enhanced DNA repair. In thehuman ovarian carcinoma cell line A2780,a 3-fold-DDP-resistance was associatedwith cross-resistance to the thymidylatesynthase (TS) inhibitor 5-fluorouracil andto methotrexate, a 2.5-fold increase in TS,and an increase in the intracellular poolsof the TS cofactor 5, 10-methylentetrahydrofolateand of tetrahydrofolate. The ultimategoal of LIGHTS is to directly halttumour progression and the developmentof drug resistance upon treatment withplatinum derived drugs, by inhibiting theprotein regulatory function of monomericTS through small molecule cellular perturbation.The scientific and technologicalobjectives will be to design small-ligandlibraries to bind to the TS monomer (dimerinterface) and thereby disrupt TS. Thestrategy will include systems pathwayanalysis, protein SH-labelling to identifylow-affinity ligands, peptide mimic design& synthesis, and filtering for ADME properties.The multidisciplinary approach willbe carried out by a consortium integratingMolecular modelling, Chemistry, Chemoin -formatics, Structural Biology and Pharma -cology, and will apply the knowledgebeing created by genomics and otherfields of basic research to the problem ofdiscovery of anticancer agents. The consortiumconsists of six groups from fivedifferent countries, including three SMEs.Small ligands to interfere with Thymidylatesynthase dimer formation as new tools fordevelopment of anticancer agents againstovarian carcinomaBackgroundOvarian cancer is the fifth most common cause ofdeath from cancer and the most common cause ofdeath from gynecologic cancer in women of allages in the Western world. Single-agent carboplatin(cDDP) has been considered a reasonableoption for first-line chemotherapy for ovarian cancer.However, the occurrence of resistant cell populationsin the tumour, limiting the usefulness ofthe platinum drug represents a growing problem.Resistant cells often became refractory to the initiallyused drugs and extremely difficult to eradicate.Therefore the use of drug combinations isnecessary. The combination of cDDP and antifolatessuch as azidothymidine (AZT), a deoxythymidineanalogue, or more recently pemetrexed(Alimta), which inhibits three enzymes in the denovo purine and pyrimidine pathways, has beenshown to synergistically affect the growth ofhuman ovarian carcinoma cells resistant to DDP.Due to the role played by the enzymes of DNAsynthesis and repair in the occurrence of cDDPresistance,it seems of great priority to developclinical reagents designed to limit the intracellularlevel of TS protein, which is associated withclinical resistance, thus sensitising even resistantcells to the effects of anticancer drugs. Theultimate aim of LIGHTS is to directly halt thetumour progression and interfere with the developmentof drug resistance upon treatment withplatinum derived drugs by inhibiting the proteinregulatory function of TS through small moleculecellular perturbation.AimThe project is clearly oriented to directly halt theprogression of ovarian cancer and interfere withthe development of drug resistance upon treatmentwith platinum-derived drugs by inhibiting theprotein regulatory function of monomeric TS. Theintermediate objectives are based on employingnovel medicinal chemistry strategies to identifypotential drug candidates with new mechanisms ofaction. LIGHTS specifically addresses early phasemedicinal chemistry issues that can critically influencethe time schedule for obtaining an investigationaldrug candidate. Nevertheless it is alsoexpected as a byproduct of the project that potentialdrug candidate(s) with high quality in vitroactivity profile can be obtained ready for in vivopharmacology profiling.In particular LIGHTS objectives are:• derivation of small-ligand libraries with ligandsdesign to bind to the Thymidylate synthasemonomer/monomer interface affecting dimerformation and TS- TSmRNA interactions;• validation of the integrated, multidisciplinarydrug design strategy necessary to achieveobjective 1, which poses a highly challengingdesign problem. The strategy including proteincysteine SH-labelling to identify low-affinityligands, peptide mimetic design, and filteringfor ADME properties;• identification of small-ligands identified ina chemical-biology approach as effective perturbingagents to investigate the mechanismof resistance against a panel of cis-platinumresistant ovarian carcinoma cell lines;• provide potential drug candidate(s) with newmechanism of action for further development assafer therapeutic agent(s) for the treatment ofovarian carcinoma.Expected resultsThe project provides the integration of differentscientific areas that are culturally well separated intomore established medical approaches to impacthealth determinant in ovarian cancer disease.It supports the discovery of new potential anticancerdrugs with non-cross resistance profiles;the new potential drug candidate will be ready toenter the pharmacological phase. If the new identifiedmolecules will be moderately/very active withgood bioavailability in vitro against ovarian cancer,these products will be very interesting to largerpharmacompany and could provide a successfultechnological transfer outcome.94

Key words: ovarian cancer, thymidylate synthase, drug resistance, drug discovery, protein-protein interactionROLE OF SMEsOut of the 6 partners, three are SMEs, highly committed to the project research objectivesand outcome. In fact, the involvement of the SME Naxospharma, Molecular Discovery andEML provide expertise in discovery and synthetic chemistry support, lead development,intellectual property issues, searching for out-licensing and/or co-operative opportunitiesfor the inventive aspects of the project.In particular:EML Research will contribute by setting up and simulating biochemical network models forthe cycles involving TS, protein design, protein structure-based ligand and peptide design,ligand optimisation, and mechanistic studies of effects of ligands on TS dimerisation andRNA binding.Naxospharma encompasses discovery and synthetic chemistry support, lead development,intellectual property issues, searching for out-licensing and/or co-operative opportunitiesfor the inventive aspects of LIGHTS.Molecular Discovery will provide high quality software tools and chemoinformatics proceduresaimed at the prediction of the physicochemical profiling of the investigated compoundswith potential anti-tumour activity. This data is crucial for the discovery planningand flow-chart LIGHTS. IT procedures, models building and applications will be the maintask of Molecular Discovery. The software will be developed and implemented by introducingthe data obtained by the other partners in LIGHTS. Particular focus will be givento ADMEtox profiles.Scientific coordinatorCosti Maria PaolaInstitution, University of Modenaand Reggio Emilia, ItalyVia Campi 18341100 Modena, Italycostimp@unimore.itcdm.unimo.it/home/dipfarm/costi.mariapaolaPartnersRebecca WadeEML Research GmbHHeidelberg, Germanywww.eml-r.org/english/index.phpPaolo LombardiInstitution, Naxospharma srlCesate (MI), Italywww.naxospharma.comHannu MyllykallioInstitut de Génétique et MicrobiologieUniversité Paris-SudOrsay, Francewww.igmors.u-psud.fr/MYLLYKALLIO/MYLLYKALLIO-eng.htmMassimo BaroniMolecular Discovery Ltd.Ponte San Giovanni (PG), Italywww.moldiscovery.comRobert StroudUCSF-Genentech Hall, UCSFSan Francisco, USAmsg.ucsf.edu/stroudThe proposed research could provide the technicaldevelopments and innovation, which could havea large impact on Biotech industry. The selection ofthe participating SME partners guarantees that thenew knowledge (methods, potential drug(s) candidate(s))might be transformed into new technologyand new products.Potential applicationsThe proposed research could lead to technicaldevelopments and innovation, which could havea large impact on Biotech industry. The selectionof the participating SME partners guaranteesthat the new knowledge (methods, potentialdrug(s) candidate(s)) might be transformed intonew technology and new products. The consortium,in addition to its contribution to the project’sbasic research by providing a suitablediscovery chemistry programme, will be responsiblefor further development of the selectedpromising new chemical entities comprisingintellectual property protection, chemical andpharmaceutical development.| Detail of the X-ray source of the European Synchrotron Radiation Facility (ESRF), Grenoble, France.95

ACRONYMContract number: LSHB-CT-2006-037499 |EC contribution: € 2 933 291 | Duration: 36 monthsliintopwww.liintop.cnr.itStarting date: 1 January 2007SUMMARYThe main aim of the project is to optimiseand provide established protocols andexperimental in vitro models for testingintestinal and liver absorption, metabolismand toxicity of molecules of pharmacologicalinterest. The added value of theproject, with respect to the existingexperimental approaches in this field, isto provide optimised sequential procedures,easily amenable to validationstudies for screening and testing of newdrugs, possibly by miniaturised andautomated technology. A consortium of15 participants includes seven companies,out of which six are SMEs. Thedirect participation of SMEs in theresearch activities will assure that thoseprocedures will meet the requirements ofindustrial application.The project is, therefore, articulated indifferent approaches, which will integrateat various levels. A first basic approachwill be the optimisation of in vitro liverand intestinal models for their use intransport and toxicity of structurallydiverse reference drugs chosen with thehelp of a steering committee of relevantstakeholders. A parallel approach willdeal with the identification of the transportand metabolic pathways and possiblecytotoxic effects of these drugs, inorder to develop appropriate monitoringprocedures. New advanced technologies(genomics, proteomics, metabolomics)will be used in order to develop highthroughput models related to the specificarea of intestine-liver absorption andbiotransformation. Each approach willtake care of the reliability of the protocolsused and of the relevance of the wholeprocedure to the in vitro/in vivo extrapolationof drug effects. To this end, a unit incharge of computer-based studies willsupport and pilot the project throughout.Optimisation of liver and intestine in vitro modelsfor pharmacokinetics and pharmacodynamics studiesBackgroundIn Europe, three Directives regulate the testingof chemicals: Council Directive 67/548/EEC andits subsequent amendments; Council Directive88/379/EEC and subsequent amendments, andCouncil Directive 76/769/EEC. Moreover, theCouncil Regulation No. 793/93 on the evaluationand control of risk of existing substances alsodeals with the same topic. The main new aspect isthat a distinction has been made between the newsubstances notified since 1981, and those notifiedbefore then. For the latter (about 100 000), it hasbeen estimated that insufficient data are availableconcerning their safety. Thus, the White Paper proposesa harmonisation of testing requirements fornew and existing substances, by introducing a newsystem for the Registration, Evaluation and Authori -sation of new and existing Chemical Substances(REACH) (COM-2001/88 Final; COM-2003/644).This implies, on the one hand, a cumbersome planof testing, and on the other hand, the use ofa huge number of animals. The European Centrefor Validation of Alternative Methods (ECVAM)has already addressed the possibility of usingalternative methods, according to the 3Rs model,in order to reduce this number, or at least the animalsuffering associated with certain kind of tests.The EU has addressed this issue in the directive86/609. The use of non-validated alternatives hasalso been suggested based on the ‘weight of evidence’,i.e. widely used and well consolidated procedures.This project may well contribute to thoseaspects, by providing new procedures submittedto optimisation.A successful outcome of the project, in fact, willhave a strong and diversified impact on social andeconomic issues. The main effect will be related tothe expanded use of in vitro systems, meetingexisting expectations from the public at large andfrom industrial enterprises. In vitro systems complywith the request of reducing animal experiments,thus satisfying a widely shared ethical concern. Onthe other hand, they offer economic advantages interms of reduced time consumption and lower costsin safety assessment of novel drugs.AimThe main aim of the project is to optimise and provideestablished protocols and experimental invitro models for testing intestinal and liverabsorption, metabolism and toxicity of moleculesof pharmacological interest. Moreover, from a scientificpoint of view, the project representsa unique effort to link, by an in vitro approach, differentsystems (i.e. gastrointestinal tract andliver) and pathways involved in vivo in the absorptionand metabolism of orally ingested substances.This kind of approach is important forfurther development of tests for chronic exposurein which the interrelation between differentorgans is a key factor and where at present nearlyno in vitro data are available. Such integratedmodels will be developed to the point of enteringpre-validation procedures to be submitted toregulatory boards.Expected results• To provide standardised cellular models ofhuman hepatocytes and enterocytes reliablefor prediction of drug absorption, metabolismand toxicity. Sequential procedures, easilyamenable to validation studies, possibly byminiaturised and automated technology will bedeveloped.• To obtain on these models a database concerningin vitro absorption, metabolism and toxicityof selected drugs including the characterisationof the regulation of relevant genes.96

Key words: in vitro human hepatic and intestinal models, metabolism, absorption pharmacokinetic and pharmacodynamics,in silico modellingROLE OF SMEsAmong the 15 consortium participants, seven are industrial companies, namely six SMEsplus a large company, NV Organon. This project presents a strong contribution from hightechSMEs, like Biopredic International, Advancell, Siena Biotech that will convey into theproject leading and innovative core technologies and services. Their direct participation inthe research activities (particularly on transporters and metabolites identification) willassure that the optimised sequential procedures, for screening and testing of new drugs willmeet the requirements of industrial application.This proposal addresses an issue of great relevance in the drug discovery process, i.e.absorption and entero-hepatic bio-disposition of drugs, which presently still relies onin vivo experimentation. The development of integrated in vitro predictive tools capable ofaddressing these issues, possibly sustained by miniaturised and automated technology,will have a positive outcome in competitiveness and success of pharmaceutical industry,since decisions taken on partially characterised compounds (or with questionable humanrelevance) may lead to great economic losses at later stages.| In vitro intestinal cells, immunostained witha thight junctions marker.• To develop prediction mathematical models ofpharmacokinetics and pharmacodynamics basedon the available in vivo data and on the in vitrodata from the cellular models used in the project.Best case scenario:• to transfer the best hepatocyte and enterocytemodels and relevant testing procedures to theindustrial setting for high throughput applicationsin the development of new drugs;• establishing the relevance of the proposed invitro models to human in vivo situation.Potential applicationsOptimised sequential procedures and referencestandards concerning in vitro models of hepatocytesand enterocytes, easily amenable tovalidation studies will allow a new molecule ofpharmacological activity to be tested for:• potential toxicity at the level of the intestinalmucosal barrier;• intestinal absorption;• metabolic modification in the intestinal cells;• absorption and metabolism in the hepatocytes;• hepatotoxicity;• optimal pharmacokinetic behaviour.Scientific coordinatorFlavia ZuccoCNR, Istituto di Neurobiologia e Medicina MolecolareVia del Fosso di Fiorano 6400143 Roma, Italyf.zucco@inmm.cnr.itwww.cnr.it/sitocnr/home.htmlPartnersPascale AnderleEnte Ospedaliero Cantonale/IstitutoOncologico Svizzera Italiana (EOC/IOSI)Bellinzona, Switserlandwww.eoc.ch/Jose V. CastellDep.de Bioquímica Fac. Medicina/Centro de InvestigacionHospital Universitario La FeValencia, Spainwww.fundacionlafe.org/indexE.htmChristophe ChesneBIOPREDIC InternationalRennes, Francewww.biopredic.comAndrè GuillouzoINSERM U62OFaculté de Pharmacie, Université de Rennes 1Rennes, Francewww.inserm.fr/en/home.htmlJouni HirvonenFaculty of Pharmacy, University of HelsinkiHelsinki, Finlandwww.helsinki.fi/university/index.htmlBrian HoustonSchool of Pharmacy and Pharmaceutical SciencesUniversity of ManchesterManchester, United Kingdomwww.manchester.ac.ukMaria Laura ScarinoIstituto Nazionale di Ricercaper gli Alimenti e la Nutrizione (INRAN)Roma, Italywww.inran.itVera RogiersVrije Universiteit BrusselDept. ToxicologyBrussels, Belgiumwww.vub.ac.be/english/index.phpJouko UusitaloNovamass Analytical Ltd.Oulu, Finlandwww.novamass.netSjeng HorbachNV OrganonDepartment of PharmacologyOss, The Netherlandswww.organon.com/authfiles/index.aspDr. Karen Rowland -YeoSimcyp Limited Blades Enterprise CentreSheffield, United Kingdomwww.simcyp.comUgo ZanelliSienaBiotech SpADrug Profiling – MetabolismSiena, Italywww.sienabiotech.com/index/index.jspMyriam FabreAdvancellBarcelona, Spainwww.advancell.net/index.htmlPeter KrajcsiSOLVOBudaörs, Hungarywww.solvo.hu97

ACRONYMMagRSAwww.MagRSA.orgContract number: LSHM-CT-2006-037957 | EC contribution: € 2 095 800 | Duration: 36 monthsStarting date: 1 October 2006SUMMARYMethicillin-resistant Staphylococcus aureus(MRSA), a virulent organism resistantto many drugs, is responsible for mostnosocomial and community-acquiredinfections. It can cause life-threateningdisease, and treatment options are limited.Effective diagnostics is a strategic keyelement in the campaign against thespread of MRSA, allowing better infectionsurveillance and control measures as wellas more efficient patient treatment and/orisolation options. The MagRSA projectaims at the development of a new diagnosticsplatform that will provide a fast,simple and accurate identification of MRSAfrom clinical samples.Fully Automated and Integrated MicrofluidicPlatform for Real-Time Molecular Diagnosisof Methicillin-Resistant Staphylococcus AureusBackgroundMethicillin-resistant Staphylococcus aureus (MRSA),an organism resistant to many drugs, is seen withincreasing frequency in hospitals and long-termcare facilities. It can cause life-threatening disease,and treatment options are limited. MRSA infectionsare indeed associated with a 40% mortality whenfound in the blood of patients suffering fromsevere staphylococcal infection. According to theWorld Health Organization (WHO), resistance ofStaphylococcus aureus (Staph A) to methicillin, itsusual antibiotic, increased from 2% in 1975 to 60%today and no new antibiotic is expected on the marketfor many years. Whereas MRSA is considered asa nosocomial pathogen, recent reports showed anincreasing number of outbreaks in the community,despite the absence of known risk factors (priorhospitalisation, antibiotic use or household contactsfrom the healthcare system). Indeed, a relativelylarge spread of MRSA strains within the gaycommunity was recently reported in severalEuropean countries and the United States. Suchatypical MRSA is known to produce a potent toxincausing severe skin infections and necrotisingpneumonia in both immunocompromised andimmunocompetent individuals.AimThe MagRSA project aims at the development ofa new diagnostics platform that will provide a fast,simple, automated and accurate identification ofMRSA from clinical samples.The diagnostic protocol that is proposed relies ona new and clinically validated procedure that consistsof a direct one-step enrichment of MRSApresent in either nasal or inguinal swabs, followedby DNA extraction of immunocaptured bacteriaand their identification by multiplex sequenceamplification, using real-time quantitative PCR.This protocol will be implemented with a simple‘hands-off’ system based on:• novel strategies for the integration of full operationsrequired for the entire nucleic acid analysischain in a microfluidic platform; and• advanced microfluidic magnetic nanoparticlesmanipulation technology allowing efficient captureand extraction of target bacteria andnucleic acids. The separate steps of samplepreparation, signal amplification by multiplexPCR, and simultaneous detection of multiplegenes, will be performed as one single stepusing a ready-to-use disposable fluidic chip.With such critical health issues, an early detectionof MRSA carriers is crucial for infection controlstrategies but also to take appropriate therapeuticdecisions, avoiding non-appropriate utilisation oflast barrier antimicrobial agents. Strategies to fightMRSA transmission are indeed well-documented,and can efficiently reduce subsequent colonisationand infection. However, for cost issues and betterpatient management, these strategies need to befocused on patients with confirmed MRSA anddefined resistance phenotype.In light of the above, this project aims to providehospitals and care units with a fast, easy andautomated test for the rapid diagnostic of MRSA.Moreover, the simplicity of the proposed technologyconcept, integrating cost effective and widelyavailable components, allows for the provision oflow cost systems, a prerequisite condition for thelarge adoption of molecular tests by hospitals.98

Key words: magnetic nanoparticles, microfluidics, quantitative PCR, antimicrobial resistance, MRSA, molecular diagnosticsROLE OF SMEsThe MagRSA project Consortium is composed of 6 partners, among which are 3 high-techSMEs with complementary expertise. Ademtech is an established company with largeexpertise in magnetic nanoparticles manufacturing for in vitro diagnostics and life sciencesapplications; Spinomix is a start-up company specialized in the development of fullyautomated and miniaturized solutions based on a proprietary magnetic nanoparticleshandling technology – termed MagPhase – in a micro fluidic environment. The technologyoffers cost-efficient, rapid, automated and compact sample handling systems formultitude of applications in life-science and in vitro diagnostics (IVD) market; and TATAA isa leading service provider in tailor-made real-time quantitative PCR (RT-qPCR) geneexpression analysis in Europe.The project presents therefore a strong contribution from high-tech SMEs with leadingand innovative core technologies and services. With complementary competencies andcore activities, all SMEs expect from this project to expand further their technologies andactivities portfolio. Moreover, these SMEs consider the project as a technological andcommercial opportunity that may open large market perspectives to their existing coretechnology and products.In addition another SME, a young Swiss company called SCIPROM, takes care of the projectmanagement.Expected resultsThe MagRSA project measurable and quantifiableobjectives can be classified in three categories:• new molecular diagnostics protocol allowingefficient and reliable MRSA diagnostics andgenotyping;• new assay reagents including magnetic nanoparticlesfor sample preparation and quantitativePCR (Q-PCR) related reagents;• fully automated systems, mainly based onadvanced microfluidics and nanoparticles handlingtechnologies, for MRSA diagnostics andgenotyping.Scientific coordinatorJacques SchrenzelGeneva University HospitalsDivision of Infectious Diseases – GenomicResearch LabRue Micheli-du-Crest 24CH-1211 Geneva, Switzerlandjacques.schrenzel@genomic.chwww.genomic.chProject managerKirsten LeufgenSCIPROMrue du Centre, 70CH-1025 St-Sulpice, Switzerlandinfo@sciprom.chwww.sciprom.chPartnersAmar RidaSpinomix S.A.Lausanne, Switzerlandwww.spinomix.comamar.rida@spinomix.comNeven ZoricTATAA Biocenter ABGöteborg, Swedenwww.tataa.comneven.zoric@tataa.comFelix von StettenDepartment of Microsystems EngineeringFaculty of Applied SciencesLaboratory for MEMS ApplicationsFreiburg, Germanywww.imtek.defelix.von.stetten@imtek.uni-freiburg.deManuel GaboyardADEMTECH S.A.Pessac, Francewww.ademtech.comgaboyard@ademtech.comPotential applicationsThe MagRSA project will address the unmet needfor new diagnostics tools for management andcontrol of antimicrobial resistance in generaland Methicillin-resistant Staphylococcus aureus(MRSA) in particular. Moreover, MagRSA projectwill provide a diagnostics platform with potentialapplications in molecular diagnostics as themost growing segment within the global in vitrodiagnostics market.| Staphylococci growing on agar plates (yellowcolonies are Staphylococcus aureus, and whiteones are Staphylococcus epidermidis).99

ACRONYMContract number: LSHC-CT-2006-037555 |EC contribution: € 2 500 000 | Duration: 48 monthsStarting date: 1 January 2007MAMMIevalin12.ific.uv.es/ep_mammiSUMMARYThe proposed project focuses on thedevelopment of a PET prototype dedicatedto the examination of breast cancer,using a gamma ray sensor based onan innovative design and the new generationof photo-detectors and scintillatingcrystals. The innovative features of thePEMT (Positron Emission Mammo Tomo -graphy) system proposed will implya high resolution (pushed to the physicallimit), higher sensitivity and lower costs.It includes integrated analogue and digitalelectronics through the design of anASIC chip. The main application will beearly breast cancer diagnosis and evaluationof chemotherapy response. Newradio-tracer molecules will be searchedfor the detection and visualisation ofthe pharmacokinetics of breast tumours,more specific than glucose (FDG) forbreast cancer, and based on human aminoand fatty acids. Phase I Clinical trials willbe performed with the new radio-tracers.A clinical multi-centric validation will beperformed for the PEMT prototypes.Mammography with molecular imagingBackgroundBreast cancer is the most common non-skin cancerand the leading cause of cancer death inwomen. The best condition for successful breastcancer treatment is early detection. Some studiesindicate that early breast cancer detectionhas reduced the disease mortality by about29 %. The ability to define the extent of disease,to monitor response, and to predict tumourbehaviour in patients with breast cancer aretherefore important public health problems.Conventional methods for breast cancer imaginglike X-ray mammography, ultra-sound andMagnetic Resonance Imaging (MRI) produce morphologicand structural images, show lesions(like micro-calcifications), but not cancers. On thecontrary, imaging methods based on MolecularImaging show functional images, metabolism.This implies that they are much more sensitiveand hence these devices can be used to detectand locate malign tumours at an early stage. Forinstance, PET (Positron Emission Tomography) isa powerful tool for non-invasive molecular imagingdiagnostic based on gamma ray (emitted byan isotope compound, previously administeredto the patient) detection.Expected resultsMAMMI proposes a new PET device specificallydesigned for breast cancer diagnosis and evaluationof therapy response. The dedicated breastcancer PET camera will improve the position resolutionof current whole-body PET cameras (about5mm) and will push it to the physical limit (slightlybelow 1mm).The new detector design will also have the abilityof detecting the depth of interaction of the gammaray interactions within the crystal with a resolutionbetter than 3mm. This is an essential featuresince it allows for an improvement of the finalimage resolution by almost eliminating the parallaxerror present in current PET detectors. This isessential in the case of breast examination sincethe detector cameras are placed close to thebody, to increase the sensitivity.The advantages of the new generation of photodetectors(silicon photo-multipliers), such astheir compactness, will be explored. The designof the electronics, including an ASIC, will allow anacquisition rate capability of the order of 1 MHz,with minimum dead time, to cope with the highersensitivity.Aim• Design and development of a dedicated low costPET camera prototype for breast examinationwith an intrinsic resolution of less than 1 mm,high sensitivity, and tomographic 3D reconstruction.• Study of new and more specific radio-pharmaceuticalsfor breast cancer detection and therapymonitoring (FLT, FAS, etc.). Perform phase Iclinical trials of the radio-tracers.• Clinical multi-centric validation of the new PEMTprototype.Moreover MAMMI will develop and study morespecific than FDG radio-tracers for breast cancerdiagnostic and therapy monitoring, based onhuman amino acids (such as FLT) and fatty acids(such as FAS).Potential applicationsThe main application will be early breast cancerdiagnosis and evaluation of chemotherapyresponse. New radio-tracer molecules will besearched for the detection and visualisation of thepharmacokinetics of breast tumours, more specificthan glucose (FDG) for breast cancer, andbased on human amino and fatty acids.100

Key words: PEMT, PET mammography, molecular imaging, breast cancer diagnosis, chemotherapyROLE OF SMEsEach of the three SMEs participating in MAMMI, namely General Equipment for MedicalImaging S.L. (GEM-Imaging), DIGI UTOPIKA Ltd. (DUT) and Ray Therapy Imaging AB (C-RAD),brings specific expertise into this consortium, complementing and strengthening the overallgroup. GEM-Imaging has experience in the construction of gamma ray detectors and istherefore crucial to the overall project. It will not only help constructing the prototype, butalso be instrumental in the eventual exploitation at the end of the project. For this purpose,GEM-Imaging has already conducted a market research study and set up a preliminarybusiness plan. C-RAD is involved in the manufacturing of associated electronic parts andplays an important role in the building of the prototype. DUT has extensive experience withsoftware development, and bring this knowledge to bear on the project for tailor-madesoftware solutions essential for the operation of the final machine.Scientific coordinatorJose M a BenllochConsejo Superior de Investigaciones científicasIFIC- Instituto de Física CorpuscularEdificio Institutos de Investigación46071 Valencia, Spainbenlloch@ific.uv.esific.uv.esPartnersSibylle ZieglerKlinikum Rechts der Isarder Technischen Universität MünchenMunich, Germanyportal.mytum.de/navigation_viewAngels BernabeuGeneral Equipment forMedical Imaging, S. L.Paterna, Spainwww.gem-imaging.comJohann HauerFrauhnofer-Institut fürIntegrierte Schaltungen (IIS)Erlangen, Germanywww.iis.fraunhofer.dePedro BrancoDIGI-UTOPIKA Ltd.Lourinhã, Portugalwww.utopika.net/utopika/ENNorberg GunnarC-Rad Imaging ABFrösön, Swedenwww.c-rad.seAnders BrahmeKarolinska InstitutetStockholm, Swedenki.se© ShutterstockRenato A. Valdês OlmosNetherlands Cancer InstituteAmsterdam, The Netherlandswww.nki.nl101

ACRONYMContract number: LSHE-CT-2006-037899 |EC contribution: € 2 914 000 | Duration: 36 monthsStarting date: 1 January 2007MANASPwww.manasp.orgSUMMARY• The goal of the project is to developnew treatment strategies for InvasiveAspergillosis (IA) which has become themajor infectious complication of treatinghaematological malignancies with intensivechemotherapy or haematopoieticstem cell transplantation (HSCT).Development of novel management strategiesfor invasive aspergillosis• Ineffective host immune responsesfacilitate fungal invasion of the pulmonarysystem and other vital organsleading to death. In order to redressthis immunological imbalance, it is proposedthat new immunotherapeuticstrategies are developed, which willaugment current antifungal treatmentsand reduce morbidity and mortality.• Facilitated by recent publication of theA. fumigatus (the principal pathogen ofthe genus) genome sequence the projectwill exploit new knowledge and techniquesin genomics and post-genomics.The project will identify the immunologicallyimportant fungal molecules todesign immunotherapies based on vaccinesusing fungus-primed innate immunecells, monoclonal antibodies or adoptivetransfer of specific T lymphocyte clones.• The project will also generate newnucleic acid based diagnostic tests toinform when and how immunotherapycan be optimally applied.The outcomes will have strong commercialapplications which will be deliveredby three leading European SMEs withinthe consortium.BackgroundOver the past decade, invasive aspergillosis (IA)has emerged as the most serious life-threateninginfectious complication of intensive remissioninductionchemotherapy and allogeneic HSCT inpatients with a variety of haematological malignancies.Aspergillus fumigatus is the most commonlyisolated species from cases of IA and is the focus ofproject research although it is believed that theintended outcomes will act as a paradigm for managementof IA due to less common species such asA flavus and the emerging A terreus. Despite thelimited improvements that have been made withpreventative strategies and the developmentof new antifungal drugs, IA has an incidence of10-30% and is still associated with high mortalityrates as high as 90 % in some surveys. T lymphocytesprovide a critical secondary defense againstthis and other fungal pathogens. Therefore,Aspergillus-specific T-cell immunity, transferredthrough the infusion of ex vivo-generated, donorderived,Aspergillus-specific T-cells might be beneficialfor recipients of allogeneic HSCT.There are only raw data regarding immunotherapyof patients with invasive fungal infection, and minimaldata relating to IA. This might be due, at leastin part, to the complex antigenic properties ofA. fumigatus, which have been less well characterisedcompared to viruses such as CMV or EBV.Only a minority of the hundreds of (glyco)proteinsof A. fumigatus reported in the literature havebeen characterised at either a molecular and/orbiochemical level.The diagnosis of IA is a particular challenge.Conventional microbiological methods fail to detectmost cases so that current diagnostic categoriesare based on a combination of clinical, imaging,and histopathological (often post-mortem) criteria.There have been some advances with non-culturetechniques based on PCR based amplification offungal DNA or detection of Aspergillus antigens inblood samples. However, these have not beenvalidated as tools for identifying patients at risk orfor monitoring responses to treatment by determinationof fungal loads.AimThe overall goal of this project is to develop moreeffective management strategies for IA with thefollowing aims:• development of immunotherapeutic strategies forInvasive Aspergillosis. This will be achieved byidentifying the T-cell clones that react with specificAspergillus targets and evaluating their efficacyfor prevention and treatment of IA. Successwill be measured by characterisation of the generatedT-cells, and demonstration of their functionalproperties against Aspergillus;• development of improved diagnostic tests for IAwith commercial potential. This will be achievedby identifying appropriate nucleic acid targets,extraction and amplification protocols and demonstratingtheir sensitivity and specificity in clinicalsamples;• validation of a dendritic cell based vaccineimmunotherapy strategy in animal model to generateprotective immunity against Aspergillus;• use of genomic and proteomic techniques to identifynew Aspergillus targets that interact with thehost’s immune system.Expected results• Identification of different pattern recognitionreceptors in response to A. fumigatus and theirrole in activating DCs.• Identification of PAMPs of A. fumigatus usefulfor immunotherapy strategies.• Identification of murine DC subsets capable ofinducing antifungal Th responses.• Adoptive transfer of manipulated DC into micesuffering from IA.• Characterisation of Aspergillus-specific T-cellresponse in healthy individuals.• Identification of a protective T-cell response inpatients surviving IA.• Development of a clinical protocol under currentcGMP-conditions for treatment of patients with IA.• Modulation of Aspergillus-specific immuneresponse by transduced T-cells.• Preparation of a bank of monoclonal antibodiesagainst A. fumigatus.102

Key words: immunotherapy, vaccine, antigens, T cells, dendritic cells, A. fumigatus, PCR diagnostics, monoclonal antibodies,GMP-conditions, aspergillosis, transplantationROLE OF SMEsMANASP focuses on the commercialisation of assays for molecular diagnosis and immunetherapy of invasive aspergillosis. Three out of nine partners from the consortium are SMEs,while one Work Package leader comes from an SME. Translational strategies for commercialexploitation of the results exist, including an IPR Advisory Committee.Cepheid AB, who acquired the diagnostic company Sangtec in 2007, already producesmolecular diagnostic kits for the detection of viral infections. They have 11 years of experiencewithin the field of molecular diagnosis and are certified according to ISO-9001/2000.Their activities comprise research and development, manufacturing and the sale ofCE-labelled PCR-based molecular diagnostics. Cepheid has many patents relevant to MANASP,including a non-exclusive worldwide PCR license, a non-exclusive license for real-time PCR andalso a non-exclusive worldwide UDG sterilisation license. Currently, they are working on theoptimisation of different fungal PCR assays and on automated fungal DNA extraction.MAT Biotech is a private biotech company founded in 1999. The company has two activities,namely the development of therapeutics and an antibody high throughput screening platform.With the former, the company focuses on the development of antibody therapies totreat haematological cancers. MAT’s product portfolio comprises a 90Y-anti-ferritin polyclonal(Ferritarg) antibody to treat refractory Hodgkin’s disease, and a 90Y-AMB8LK monoclonalantibody-radioisotope product to treat refractory Hodgkin’s disease, liver cancer, andpancreas cancer, which is in advanced pre-clinical trials. Currently, they perform screeningassays to identify reactive monoclonal antibodies against A. fumigatus.Miltenyi Biotec GmbH is a leading, international biotech company in the field of magneticcell separation (MACS®technology). Miltenyi Biotec develops, produces and sells worldwidemagnetic cell separation reagents and equipment for biomedical research and clinicalapplications, particularly in the fields of haematology and immunology. The CliniMACS®system is an automated cell selection device. It is approved for clinical stem cell graft engineeringusing CD34 and CD133 selection and permits large-scale cell isolation of other cellularproducts such as dendritic cell precursors, NK cells and T-cell subsets. In addition,pioneering technologies are made available, such as MACSiBead particles for activationand expansion of T-cells, or the Cytokine Secretion Assay for isolation of cytokine-secretingcells, e.g. antigen-specific T-cells. Reagents and tools for the GMP-grade generation of dendriticcells and T cells for immune therapy against invasive aspergillosis are also available.Scientific coordinatorHermann EinseleUniversity of WuerzburgMedizinische Klinik IIKlinikstrasse 6 – 897070 Wuerzburg, Germanyeinsele_h@klinik.uni-wuerzburg.deProject managerJuergen Loefflerloeffler_j@klinik.uni-wuerzburg.dePartnersBirger JanssenCepheid ABBromma, Swedenwww.sangtec.comTom RogersTrinity CollegeDepartment of Clinical MicrobiologyDublin, IrelandJean Paul LatgéInstitute PasteurUnité AspergillusParis, FranceLuigina RomaniUniversity of PerugiaDepartment of ExperimentalMedicine and Biochemical ScienceMicrobiology SectionPerugia, ItalyJean KadoucheMonoclonal Antibody Therapeutics (MAT)Evry, Francewww.matbiopharma.frAxel BrakhageLeibniz Institute for Natural ProductResearch and Infection BiologyJena, Germany• Selection of the most efficient antibodies by invitro and in vivo analysis.• Development of an assay to detect AspergillusDNA with high specificity.• Development of an assay to detect AspergillusRNA with high sensitivity.• Clinical evaluation to confirm sensitivity in detectingAspergillus infection using standardised definitionsproduced by International consensus andcomparison to different well established assays.• Commercialisation of the assay into an affordableand rapid diagnostic test.Potential applications• Surveillance of patients being treated for haematologicalmalignancies by chemotherapy or HSCTusing DNA/RNA based molecular diagnostics.This will generate greater ascertainment of possibleand probable cases of IA and earlier therapeuticintervention leading to improved survival rates.• Incorporation of these diagnostic tests into internationallyaccepted EORTC/MSG criteria for clinicalapplication in categorising cases of IA tofacilitate research trials of new antifungal agentsor other novel therapies.• Development of immunotherapeutic strategiesbased on demonstrated efficacy against Aspergillusin vitro and in animal models. This will eitherbe through adoptive transfer of donor T-cells, oradministration of monoclonal antibodies targetedagainst immunologically relevant Aspergillusantigens/epitopes.• Wider application of this technology to the treatmentof other groups of patients (outside theHaematological Malignancy field).Georg RauserMiltenyi Biotec GmbHBergisch Gladbach, Germanywww.miltenyibiotec.com/en/default.aspxJean-Marie FrançoisInstitut National des Sciences AppliquéesDépartement de Génie Biochimiqueet AlimentaireToulouse, France103

ACRONYMContract number: LSHG-CT-2006-037226 |EC contribution: € 1 999 962 | Duration: 36 monthsStarting date: 1 October 2006MEGATOOLSwww.cellectis.com/megatoolsSUMMARYThe MEGATOOL project aims to developa large number of new sequence-specificendonucleases to recognise and targetalmost any possible DNA sequence inany living cell or organism, as well as tooptimise homologous recombination, toprovide scientists with a powerful toolto undertake functional genomics.New tools for Functional Genomics basedon homologous recombination induced bydouble-strand break and specific meganucleasesBackgroundThe genome sequence programmes have contributeda huge amount of information, and createdmany possibilities. An exhaustive catalogueof genes is now available for many organisms,but the real meaning of this information remainsto be deciphered. Thus, the success of functionalgenomics definitively lies in the development ofnovel tools breaking through the practical limits itsuffers today. Meganucleases-induced recombinationcould provide a practical alternative to currentapproaches.Meganucleases are, by definition, sequencespecificendonucleases with large (→ 14 bp)recognition sites. However, the inactivation ormodification of any and all known genes, orgenomic sequence, depends on the availability ofMeganucleases that cleave within or in the vicinityof each gene sequences. This issue would beaddressed if it was possible to rapidly engineerthe specificity of natural Meganucleases.AimThe first objective of the project is to provide themeans to modify a large number of sequences inrodent genomes. The second is to develop thetools to engineer a large number of rodent genes,for functional genomic purposes.Since meganuclease-induced recombination representsan extremely powerful tool for gene alteration,MEGATOOL will focus on the generation offour kinds of results:• a large collection of novel meganucleases. Thiscollection of novel proteins should greatlyenhance the repertoire of natural meganucleasesand thus allow for the targeting of a largenumber of genes in organisms whose genomehas been sequenced, with a strong focus onrodent genomes;• the means to exponentially increase this collection.The collection of novel meganucleasesshould provide a unique database of characterisedDNA binders. Structural and statisticalstudies should reveal the laws governing theseinteractions, and this data could in turn be usedin a predictive way, for the design of novelmeganucleases;• the methods, procedures and quality standardsto make these meganucleases widely usable asresearch tools;• a refined method to use these meganucleases incells. The focus will be on mouse cells for functionalgenomics, providing a direct validation.Expected results• Protein engineering: Partner 1 has establishedthe basis of a combinatorial process to assemblefunctional engineered meganucleases. It isexpected that this combinatorial strategy willprovide a functional meganuclease for mostchosen genes.• Computational biology: The FoldX algorithmcan successfully predict the effect of proteinmutation on the specificity of protein-DNArecognition specificities. Subsequent versionsof FoldX should allow for more efficient designof meganucleases combinatorial process.• Structural Biology: A continuous flow of novelstructures that will contribute to the computationalsteps is expected.• Standardisation of protein storage and use:An efficient purification and characterisationprocess for each engineered protein is expected.• Validation of the general approach: The wholeapproach should eventually be validated bythe use of engineered meganucleases on realchromosomal targets in rodent cells. A general,standard protocol for rodent cells is expected.Potential applicationsThe possibility of correcting errors in a genomethrough targeted homologous recombination ormodifying at will any DNA sequence is clearlyenormously attractive to the scientific community.104

Key words: functional genomics, genome engineering, protein engineering, meganucleases,gene targeting, computational biologyROLE OF SMEsThe project involves two SMEs (Cellectis S.A. and Fermentas UAB) and two academic laboratories(CRG and CNIO).Cellectis S.A. is a SME biotech company leading the field of genome engineering. Its uniquetechnology and strong intellectual property are centered on homologous recombinationinduced by double-strand breaks using meganucleases and its applications. Its aim is todevelop new tools for functional genomics, gene therapy and genome modification.Cellectis has entered into more than 40 deals with industrial partners using living strains ororganisms in their processes. It is also pursuing applications of its technologies to humantherapy. Cellectis has developed specific skills in the field of genome engineering and proteinengineering. One of the great achievements of the company lies in a High-ThroughputScreening platform. Using cell-based functional assays for the identification of novelendonucleases, this platform has delivered hundreds of novel meganucleases. MEGATOOLSwill allow a broad dissemination of Cellectis’ genome engineering tools to the research community.As a SME demonstrating very strong innovative activity, Cellectis is at the crossroadof the upstream research that feed the project and of downstream development steps. Assuch, Cellectis has a pivotal role in the development of novel products and process withinMEGATOOLS. Cellectis will use its High-Throughput Screening platform to deliver custommeganucleases cleaving sequences in the mouse genome. Cellectis will also contribute itsexpertise in the field of genome engineering and, more specifically, in gene targeting andknock-out rodent genes with a panel of novel meganucleases, thereby validating the generalapproach and refining the methods for using these novel tools for functional genomics.Scientific coordinatorFrédéric PâquesCELLECTIS S A102 Route de Noisy92 235 Romainville CedexFrancepaques@cellectis.comwww.cellectis.comPartnersCentro Nacional de InvestigacionesOncologicas (CNIO)Structural Biology – MacromolecularCristolography GroupMadrid, Spainwww.cnio.es/ingCentro de Regulacio GenomicaSystem Biology LaboratoryBarcelona, Spainwww.crg.esFermentas UABVilnius, Lithuaniawww.fermentas.comFermentas UAB, an ISO09001, ISO140001 certified company, is a world leading SME biotechcompany in the discovery, manufacturing and marketing of quality molecular biologicalsand in the providing of services to the international research community. Fermentas hasstrong expertise in nucleases and in their production, implementation and enzymology. Thecompany’s product range consists of approximately 400 different molecular biology products,of which 200 are nucleases. Products under the Fermentas brand name are marketedvia a distributor network covering 74 countries in Europe, North and South America, Asia,Australia and Africa. The key commercial target for Fermentas in MEGATOOLS is to produceand to make meganucleases developed during the project available to the research community.Meganucleases, like other restriction enzymes, perform site-specific cleavage ofdouble-stranded DNA. In fact, these rare-cutting enzymes could be used in many in vitroapplications where restriction enzymes are commonly used. Meganucleases should conformto all quality requirements that are applicable to traditional restriction enzymes. Theprimary function of the SME in the MEGATOOLS project is to test whether mutant meganucleasescreated during the project can be used as molecular tools for the rearrangement ofDNA molecules not only in vivo, but also in vitro. After receiving meganuclease mutants,Fermentas will follow the traditional implementation route of restriction enzymes, includingpreliminary evaluation of properties in crude cell extracts, purification, quality controls,basic enzymology studies and stability tests. These studies will show if and how thesemutant enzymes could be used as analytical tools.Although it is clearly valuable to understand howgenomic information is translated into function,rational modification of the DNA sequence of anorganism has been limited by the time consumingprocess it requires, despite the development ofnew tools for the construction of targeting vectors.Thus, the possibility of having new tools that willallow targeting of any DNA sequence for insertion,deletion or repair could introduce a new revolutionin the field of functional genomics and couldalso bring a new paradigm and a new momentumto human gene therapy.105

ACRONYMContract number: LSHM-CT-2007-037831 | EC contribution: € 2 374 689 | Duration: 36 monthsStarting date: 1 January 2007MEMORIESSUMMARYAlzheimer’s disease (AD) is a progressivebrain disorder that gradually destroysa person’s memory and ability to learn,reason, make judgments, communicateand carry out daily activities. The diseaseis the major kind of dementia affectingelderly people, and the percentage ofpatients is going to increase exponentiallyover the next few years. Currently, noaetiology and cure has been found. Onemajor hurdle in drug screening and targetdiscovery in AD is the lack of a suitableanimal model, as these fail to fully reproducethe characteristics of the disease.The MEMORIES project aims to developnew mouse models based on deficit ofneurotrophic signalling, potentially usefulfor developing new therapeutic tools.Development, characterisation and validation ofnew and original models for Alzheimer’s DiseaseBackgroundAlzheimer’s disease (AD) is a neurological disorderand is the most common form of dementia inlater life. It is estimated that, by 2050, the numberof people aged 80 years or older will approach370 million worldwide and that 50 % of thoseaged 85 years and older will be affected by AD.AD is clinically characterised by short-term memoryloss and cognitive dementia, associated withlanguage and behavioural impairments. Thepathological hallmarks of AD include the presenceof extracellular amyloid plaques, intracellularneurofibrillary tangles (NFT), neurodegenerationand cell loss. One severely affected region of theAD brain is the basal forebrain (which includes thenucleus basalis of Meynert, the medial septumand the diagonal band of Broca), a group ofcholinergic neurons that are connected to areas ofthe neocortex and hippocampus and that areimportant for learning, memory and attention.The complex degeneration in AD has been fertileground for the formulation of hypotheses on thepathogenesis of the disorder. Methodologicaladvances allowedshedding light on alterations ofthe various neurotransmitter systems in the ADbrain. The discovery of the degeneration in thebasal forebrain, in the context of experimental evidencefor the role of acetylcholine in memory, haveled to the development of a symptomatic therapyfor AD, based on enhanced acetylcholine availabilitydetermined by cholinesterase inhibitors.Recently, memantine, an uncompetitive antagonistof the N-methyl-D-aspartate receptor, wasapproved for the treatment of moderate-to-severeAD. These agents can benefit some AD patients fora limited period of time. However, due to the extensiveand multifocal nature of AD degeneration, theeffects of these neurotransmitter modulators aremodest and the need of a truly disease-modifyingdrug persists. Although there have been significantadvances in understanding the biology and subsequentdiagnosis of AD, such research has not beentranslated into a disease-modifying treatment.One limit in translating basic research findingsinto therapeutical agents is the lack of suitableanimal models fully reproducing the AD neurodegeneration.Having animal models reduces therisk, and thus the cost, of developing drugs.In the past decade, AD research has been fundamentallyinfluenced by the development of geneticallymodified animal models of amyloid-driven ortau-driven neurodegeneration. These in vivo models– exploited on the basis of early-onset diseasedetermined by rare, inherited mutations – areimportant in understanding the involvement of amyloidor tau in the onset of the disease, but failed toreproduce the hallmarks of the AD pathology fully.One other potential pitfall in these transgenicmice is that these models might not be applicableto sporadic AD. Indeed sporadic forms of AD,which account for more than 95 % of the populationafflicted by AD, are multifactorial diseases,the progression of which is influenced by genderand epigenetic factors (such as neuroinflammation,growth factor deficits, autoimmunity/autotoxicity).The use of animal models derived fromthe genetic forms of AD to screen drugs, insteadof more appropriate animal models, revealed thelimitations of their use for sporadic AD. Indeed,the vaccine approach seemed to work well inmice, but brain inflammation in a few patientstriggered an abrupt halt to the clinical trial.AimThe MEMORIES hypothesis-driven project gatherstogether eight partners from five different countriestowards the aim of developing, characterisingand validating new animal models that havea real potential for becoming a gold standard inthe AD field.106

Key words: Alzheimer’s disease, transgenic mouse model, neurotrophinsROLE OF SMEsThree European SMEs are partners in MEMORIES, and are based in Italy and France.These SMEs will receive approximately 35 % of the project budget. Lay Line Genomics isan integrated antibody company, focused on the therapeutic area of neurodegenerativediseases, whose mission is the discovery of drugs for Alzheimer’s and other neurologicaldiseases, leveraging on a unique antibody based technology platform. LLG has an exclusivelicence covering any use of the AD11 anti-NGF mouse model. During the MEMORIESproject, LLG will exploit the AD11 mouse model and produce new antibody based mousemodels with the aim of creating new experimental models, also useful in the developmentof new therapeutic tools for this disease. The involvement of the other two SMEswill be crucial for the standardisation of the procedures to be used in the different laboratoriesand the management of the project. Neureva conducts drug discovery and drugdevelopment for diseases of the central nervous system. Its research activity is centredon anatomical and behavioural characterisation of mouse models for CNS pathologies,the choice of mice models being driven by the availability of a large number of transgenicmice which allows alternative ways for testing molecular or cellular hypotheses. Neurevawill add competencies to standardised protocols and validate mouse models. ACIES isexpert in managing International Management projects and in optimising the financingof innovation for enterprises working in various industrial and technical sectors. Since1990, over 500 major companies, research organisations and very innovative small andmedium-sized businesses, have put their confidence in ACIES to implement financingsystems, valorise innovation or to set up and manage their International projects.ACIES’s methodology, based on the principles of Total Quality Management (TQM),allows managing multidisciplinary consortiums. ACIES will provide high quality managementservices (including knowledge) throughout the project, in accordance with theISO 10006 (guidelines for quality management in projects) standard.Scientific coordinatorAntonino CattaneoEuropean Brain research InstituteRita Levi-Montalcini FoundationVia del Fosso di Fiorano 64/6500143 Roma, Italya.cattaneo@ebri.itwww.ebri.itPartnersManuel GaviriaNeuréva Inc.Montpellier, Francewww.neureva.comThomas E. WillnowMax Delbrück CentrumFür Molekulare MedizinBerlin, GermanyLiliana MinichielloEuropean Molecular Biology LaboratoryMonterotondo, ItalyEero CastrenUniversity of HelsinkiHelsinki, FinlandDaniel ConstamSwiss Federal institute of Technology –“Daniel Constam” École PolytechniqueFédérale de LausanneLausanne, SwitzerlandDavid KoubiACIESLyon, Francewww.acies.frExpected resultsUsing a multidisciplinary approach, a panel ofmouse models will be produced and analysedfor the presence of neurodegeneration. AD11 anti-NGF, which already represent a good model forsporadic AD, will be crossed to mice in whichpro-convertases or SorLA receptors are knockedout. Additional mice will be created, expressingmutated form of pro-NGF or in which knockoutof TrkB, TrkA and NGF will be achieved.Mice will be analysed using standardised methodologyfor neuroanatomy and behavioural analysis.We anticipate that blocking differentsignalling pathways will help in ameliorating thecurrently available experimental mouse models,and will also be useful for developing new therapeutictools for this disease and strengtheningEuropean competitiveness in the war against AD.Potential applicationsThe creation of a mouse model that by fully reproducingthe hallmarks of the disease, will not onlyprovide insights into the neurobiology of the disease,but will also allow the evaluation of theresponse to drugs, especially in relation to theeffects on pathology is one of the most challengingaims of AD research.The potential medical benefits that will derive fromthe production of this mouse model are immense.The identification of protein linked to specific cellularpathways will provide the possibility todevelop new diagnostic assays and new drug targetsfor the treatment of AD. Mouse models willalso make it possible to visualise neural circuits intheir normal and abnormal states, which is likelyto have a large impact on the diagnosis of diseaseand the evaluation of the effectiveness of therapy.Anders NykjaerNeuronIcon A/SAarhus, Denmark107

ACRONYMContract number: LSHB-CT-2006-037702 | EC contribution: € 2 370 155 | Duration: 36 monthsStarting date: 1 October 2006Mimovaxwww.mimovax.euSUMMARYAlzheimer’s disease (AD) is characterisedby the abnormal accumulation of amyloidplaques in the brain. These plaquesmainly consist of the Amyloid- (A) peptidesAβ40/42 derived from the AmyloidPrecursor Protein (APP). In light of thecharacteristics of amyloid composition inpatients, Aβ peptides and its truncatedand modified derivatives are highlyattractive targets providing neo-epitopesnot present on parental APP. A MimotopebasedAD vaccine targeting truncatedforms of Aβ would therefore induce a safeantibody response exclusively reactingwith the pathological Aβ molecules butnot with parental APP and would avoidthe induction of autoreactive T-cells. Thisvaccine will be evaluated in a preclinicalAD animal model and tested in a clinicaltrial in patients. Thus, the MimoVax vaccinewill provide an innovative, safe, costeffective and efficient approach to successfullytreat AD patients and to limit thesevere personal and economic impact ofAD on patients, their families and society.Alzheimer’s disease-treatment targeting truncatedAβ 40/42 by active immunisationBackgroundAlzheimer’s disease (AD) is the most commonform of dementia in humans. According to theAlzheimer Association, there are currently 12 millionpatients worldwide with estimated socialcosts for every patient reaching € 40 000 per year.At present, no effective treatment is available tostop the progressive neuro-degeneration andassociated cognitive decline in AD patients. Alltreatment strategies applied today are focusingon the use of small molecular drugs inhibiting theactivity of Cholinesterase to alleviate diseasesymptoms. These drugs however have not provento effectively halt or revert disease progressionafter prolonged treatment.AD is characterised by the abnormal accumulationof amyloid plaques in the brain. These plaquesmainly consist of the Amyloid- (A) peptidesAβ40/42 derived from the Amyloid PrecursorProtein (APP). In humans, the majority of amyloidplaque material is formed by Aβ40/42 derivativeswhich are frequently truncated and modified. Aβpeptides are considered to be directly involved inthe pathogenesis and progression of AD.Immunotherapeutic treatment targeting Aβ ledto amyloid plaque reduction and had beneficialimpact on disease progression in animal models.However, the first phase II clinical vaccination trialin AD patients using full length Aβ42 as antigenhad to be discontinued due to severe neuroinflammatoryside effects including brain infiltrationby autoreactive T-cells.AimThe novel technology presented in the MimoVaxproject has been developed to create antigensmimicking the structure of neo-epitopes which donot contain sequences of the native Aβ peptide.A Mimotope-based AD vaccine would thereforeinduce antibody responses, exclusively reactingwith the pathological Aβ molecules but notwith parental structures like APP. Furthermore,Mimotopes do not contain potential T-cell selfepitopesand avoid induction of detrimental auto -reactive T-cells. Thus, the goal of the MimoVaxproject is the development of a safe and efficaciousAlzheimer vaccine which is predicted toavoid the development of immunological complicationsdue to autoreactive T-cells. The developmentof such innovative AD vaccines targeting Aβcould therefore be a safe treatment regimen toefficiently fight AD in patients. In addition, newdiagnostic methods will be developed in thecourse of the MimoVax project in order to monitortreatment efficacy.Expected resultsSuccessful preclinical evaluation of a MimotopebasedAD vaccine is expected to demonstratereduction of amyloid plaque load and alleviationof the pathologic hallmarks in the brain of animalmodels for AD. Additionally, Mimotope-based ADvaccines will provide means to target the solubleoligomers of Aβ which are thought to be a majorcause of the synaptic alterations and cognitivemalfunctions typical of AD.Similar to full length Aβ, truncated and modifiedAβ peptides also seem to be involved in thepathogenesis and progression of AD. They aretherefore also a suitable point of attack for noveltreatment strategies, but no relevant developmentprogramme has been started to date.Once these vaccines have proven their efficacy inreducing Alzheimer-like pathology in our animalmodels, an initial clinical trial will be initiated todemonstrate safety of the identified peptide vaccinesin patients. The development of such innovativeAD vaccines targeting Aβ could thereforebe a safe treatment regimen to efficiently fight ADin patients and successful completion of initialclinical testing will be followed by further productdevelopment.108

Key words: Alzheimer’s disease, neurodegeneration, dementia, amyloid plaque, truncated Aβ 40/42, mimotope,active immunotherapy, preclinical characterisation, animal models, clinical trialROLE OF SMEsThe project consortium is constituted by 5 SMEs and 2 academic institutions.MimoVax is coordinated by an SME, AFFiRiS GmbH, expert in the development of vaccineson the basis of peptides to treat Alzheimer’s and atherosclerosis. It is supported a dedicatedmanagement partner (Biolution Grünert & co keg) also in charge of knowledge transfer andpublic relations. JSW-Research’s competences comprise R&D and contract research as wellas the performance of clinical research complemented by histological and biochemical evaluationmethods. Its staff possesses long standing experience with a quality assurance systemand behavioural studies. piCHEM has been working in the field of peptide chemistry formore than 10 years. This enterprise puts its main stress on developing and producing peptidesfor all kinds of research purposes worldwide. EuroEspes, S.A. expertise includesregular clinical and lab evaluations of patients as well as clinical trials, preclinical pharmacologyand genetic diagnosis. Having focused on biochemical research of disorders ofthe Central Nervous System, EuroEspes has already performed more than 20 clinical trialsconcerning Alzheimer’s disease.The tight collaborations between academia and participating SMEs and the financing of theclinical trial will provide the basis for the financial exploitation of any IPR generated withinthe project by participating SMEs and academic institutions and will lead to potentialbenefit for the participating SMEs and University Institutes.Scientific coordinatorMarkus MandlerAffiris GmbHCampus Vienna BiocenterViehmarktgasse 2a1030 Vienna, Austriamarkus.mandler@affiris.comwww.affiris.comPartnersIris GrünertBiolution gruenert & co KEGVienna, Austriawww.biolution.netAntón AlvarezEUROESPES S.A.Department of NeuropharmacologyBergondoA Coruna, Spainwww.euroespes.comManfred WindischJSW – Research GmbHGraz, Austriawww.jswresearch.comFritz AndreaepiCHEM research developmentGraz, Austriawww.pichem.atPotential applicationsCurrently 12 million patients worldwide are sufferingfrom AD. This number, however, will increase upto 22 million by 2025, according to the AlzheimerAssociation. There is, however, no effective treatmentavailable to stop the progressive neurodegenerationand associated cognitive decline inhuman patients, thus creating an enormous socialproblem for all European societies as well as for therest of the western world.The novel peptide vaccine developed in theMimoVax STREP therefore aims at the potentialsubsequent use in treatment of Alzheimer’s diseasein human patients. Vaccination will be a costeffective and powerful way to reduce the economicaland psychological burden exerted by this disease.It would significantly reduce the high costsassociated with this disease, which will soonexceed US$ 4 billion annually.Richard DodelPhilipps-Universität MarburgMarburg, Germanywww.med.uni-marburg.de/d-einrichtungen/neurologieAlexander DrzezgaTechnische Universität MünchenKlinikum rechts der IsarMunich, Germanywww.nuk.med.tu-muenchen.de| Amyloid plaque staining in the brain of an AD mouseOne of the hallmarks of Alzheimer’s disease is theaccumulation of amyloid plaques in the brain. Theseamyloid plaques can be visualised on sections of thesebrains by staining with amyloid specific antibodies. Thisstaining reaction results in a red amyloid plaque (indicatedby a white arrow) surrounded by blue nuclei of surroundingcells like neurons or astrocytes. A Mimotope-based ADvaccine as described in this abstract would induce suchspecific antibody responses reacting with the pathologicalAβ molecules and could therefore be a safe treatmentregimen to efficiently fight AD in patients.109

ACRONYMContract number: LSHG-CT-2007-037291 |EC contribution: € 2 755 356 | Duration: 36 monthsStarting date: 1 April 2007MODESTSUMMARYDevices for ultra high-throughput transfectionand screening of primary cells, foruse in the study of e.g., immunological,neuronal and liver disorders shall bedeveloped. Modification of cells is a centraltopic in pharmaceutical and medicalsciences as well as in basic research. Thedominant consideration for cell manipulationis the type of cells used. Until now,most often conventional, immortal celllines, being cultured for years or evendecades in flasks, have been assigned tothis specified use, although they aremainly irrelevant in physiological andmedical respects. The optimal choicewould be primary cells, since they are distinctlycloser to the physiological situationthan cell lines. However, primary cellsuntil recently were hard or often evenimpossible to transfect by non-viral methods,and consequently, many researchersstill hesitate to adopt these cells despitetheir unquestionable advantages. Withthe advent of the nucleofection® technology,a unique method for the highlyefficient transfection of primary cellswas recently made available to the lifescience community.Modular Devices for Ultrahigh-throughputand Small-volume TransfectionBackgroundCell transfection belongs to the well establishedtechnologies in biological, medical, and pharmaceuticalresearch but delivery to relevant cellssuch as primary cells and adult stem cells is stilla major bottleneck. While conventional transfectionmethods, such as lipofection or electroporation,usually yield satisfactory results forstandard cell lines, many other cell lines as wellas most primary cells are difficult or even impossibleto transfect with these methods. Viral vectors– as alternative for DNA delivery – work wellin some cases, but are labour-intensive, not versatile,and remain connected with significantsafety issues. In consequence, most primary cellswere considered non-transfectable, representinga tremendous disadvantage in highly relevantresearch areas as primary cells most closelyresemble the situation in the living organism.Unlike cell lines, which often have been culturedfor decades, primary cells are freshly isolatedfrom the organism’s tissue, and have not gonethrough any transformations, the prerequisite forthe unlimited growth of conventional cell lines.Against this background, it goes without sayingthat the pharmaceutical industry is highly interestedin using primary cells instead of cell lines forcell-based screening campaigns in drug development.With more predictive screens – in terms ofboth the relevance of a target and the pharmacokinetics/-dynamicsof a drug compound – itbecomes much easier to take adequate decisionsas to which targets or compounds to focus forfurther development. Consequently, the use ofprimary cells in preclinical R&D will positivelyimpact attrition rates and reduce the significanttime and capital involved in developing a drug.as neuronal disorders and liver metastasis tofacilitate investigations of possible mechanismsof intervention.Expected resultsOn the basis of the Nucleofector® 96-wellShuttle® device and 96-well Nucleocuvette®plates and modules which were launched byAMAXA in 2006, the Consortium will developultrahigh-throughput devices and plates. In parallel,protocols for cultivating, differentiation,nucleofection®, and functional screens of primarycells in small volumes and with low cellsnumbers will be elaborated and, in a further step,adapted to the devices.Potential applicationsInnumerable opportunities, e.g., in discovery ofnew regulatory pathways, novel targets, andpotential drug candidates as well as clarificationof signal transduction are addressed by thedevices that shall be developed in the frame ofthis project. Researchers will make rapid stridesin the analysis of the biology of cells among othersfor the development of therapeutics, and newtypes of treatments as well as possible cures fora variety of diseases and injuries.AimThe main objectives are:• the development of devices for ultrahighthroughputnucleofection® of primary cells inmulti-well plates; and• the application of this technology to thehighly relevant area of immunological as well110

Key words: nucleofection, primary cells, hard-to-transfect cell lines, RNAi, siRNA, ultra high throughput transfection,adult stem cells, neuronal cells, apoptosis, lead, gene silencing/knockdown, screeningROLE OF SMEsSMEs play a major role in MODEST, since five of the eight partners are SMEs. Moreover, themedium-sized enterprise AMAXA acts as co-coordinator of the whole project.AMAXA is the only institution worldwide which has the necessary knowledge and experienceto adapt the technical needs of device development to the conditions used for the efficienttransfection of primary cells and hard-to-transfect cell lines. After performing anextensive market study, AMAXA is responsible for prototype building from concept for thedevices up to testing of software and hardware specifications. As co-ordinator of the project,AMAXA will ensure that the expertise brought to the table by each partner will enablethe collaboration to achieve the goal of providing powerful new tools for basic research anddrug discovery.The main emphasis of Fotec is on the development steps in injection molding of the multiwellplates. This partner will develop the production process for a micro-plate with 384 wellsand will develop a process concept for the production process of a micro-plate with1 536 wells (technical study). Together with another partner (HTP Electronics GmbH), Fotecalso designs the necessary injection moulds.AMAXA will support RNAx, Protobios and Dominion Pharmakine to establish nucleofectionprotocols and functional assays for relevant cells, in order to evaluate the devices inrespect to nucleofection of small volumes and cell numbers up to single cells, respectively.With the expertise of RNAx as a partner of MODEST, RNAi technology will become the idealbasis for a highly efficient high-throughput validation system for the definition of functionsof identified targets. RNAx has extensive experience in the development of automatedRNAi, including the adaptation of the system to various cells and cell lines, as well as in thedevelopment and adaptation of assays to the RNAx automated platform.Protobios has unique expertise in neural stem cells, nervous system development mechanismsand transcription regulation networks. The uniqueness of the input of Protobios liesin the competition advantage of the new method of creating human neural stem cells andinfluencing them to differentiate into various derivates of the nervous system. Protobiosappraises the devices for ultra-high-throughput application, by contributing large cellnumbers of hNCS.The role of Dominion Pharmakine is to identify new biomarkers related to site-specific developmentof metastasis, which may be used as prognosis indicators at the clinics, and to optimisethe selection of the most likely successful antimetastic targets among large lists ofcandidate genes, ensured by the knock-down functionality assays. Moreover, DominionPharmakine contributes to the MODEST project by providing high-quality primary cell culturesand considerable experience in cell culture techniques.Scientific coordinatorHerbert Müller-HartmannAmaxa A.G.Research & DevelopmentNattermannallee 150829 Cologne, Germanyherbert.mueller-hartmann@amaxa.comwww.amaxa.comProject managerBirgit Nelsen-SalzBirgit.nelsen-salz@amaxa.comPartnersAndrej ManteiDeutsches Rheuma ForschungszentrumBerlin Immunomodulation/DRFZ/GermanRheumatism Research Centrewww.drfz.deJörg PötzschRNAx GmbHBerlin, Germanywww.rnax.de/en/index.htmlKaia PalmProtobios Ltd.Tallinn, EstoniaHelmut LoiblFOTEC Forschungs- undTechnologietransfer GmbHWiener Neustadt, Austriawww.fotec.at/pages/indexEN.htmlJosef Anton PallanitsHTP Electonics GmbHWiener Neustadt, Austriawww.hti-ag.at/de/geschaftsfelder/kunststoff/beteiligungen/htp_electronics/Naiara Telleria GarayDominion Pharmakine S.L.Cell Biology and Culture Laboratory/Dominion PharmakineDerio, Bizkaia, Spainwww.pharmakine.comThomas SchaumannPrevas ABInstrument DevelopmentVästerås, Swedenwww.prevas.com/product development.html111

ACRONYMContract number: LSHP-CT-2006-037200 | EC contribution: € 1 505 702 | Duration: 36 monthsStarting date: 1 January 2007MUNANOVACSUMMARYThe MuNanoVac STREP project will assessa new vaccine strategy to prevent HIV-1infection based on a primo-vaccinationusing a biodegradable synthetic colloidalcarrier made of poly-lactic acid (PLA)nanoparticles covered with adsorbedantigens. The aim is to demonstrate thatPLA nanoparticles are a perfect transcutaneousor mucosal vaccine vehicle,immunogenic for both arms of immunityand adaptable to many types of antigensas well as easy and simple to produce.Such nanoparticle-based vaccine carrierswill allow targeting dentritic cells or transportingthe vaccine through skin ormucosal epithelial barriers. To amplify themucosal immune response, the projectwill investigate the potential use ofimmunomodulator molecules associatedwith the comparison of two differentimmunisation routes.Moreover, the MuNanoVac project willcontribute to advancing a promising vaccineapproach for HIV that could alsoprove versatile enough for application toother poverty-related diseases such astuberculosis. With the proposed vaccinecandidate, the project gives Europea tremendous opportunity to gain leadershipin the use of biodegradablenanoparticles for vaccine carriers.Mucosal Nano Vaccine Candidate for HIVBackgroundIn order to halt HIV infection spreading, a safe andeffective AIDS vaccine for both developing anddeveloped countries is urgently needed. Indeed,HIV is still spreading worldwide with more than65 million people infected (source: UNAIDS/WHO,2006) and the number of new infections is risingsharply in Asian countries, Eastern Europe and sub-Saharan Africa. The numerous research efforts carriedout in this domain have not yet produced anefficient anti-HIV vaccine.Many infectious diseases for which no vaccine isavailable suffer from the absence of a good candidatethat allows efficient T and B cell immuneresponses. In the case of HIV-1 mediated infection,the present postulate is that both arms of theimmune response (humoral and cellular) shouldbe stimulated by any potential vaccine candidate.Moreover, recent data on natural primary HIV-1infection establish that the spreading of the virusin the mucosa is essential for the infection to takeplace. Hence, every vaccination strategy shouldbe able to elicit a strong mucosal immunity at thepotential sites of contamination and preventspreading of HIV-1 virions.A future goal for vaccine design is therefore toincrease their efficiency by reaching the highestnumber of antigen-presenting cells (APCs) possibleand to achieve the high local concentrationsrequired, inducing a potent immune response.Thus, facilitating vaccine compounds penetrationinto immunisation sites that are rich in APCs aswell as specific migration and activation of APCsthat would benefit the efficacy of new vaccines inthe induction of protective immune response.AimCurrent research in the nanotechnology of biomaterialsis aimed at using nanosystems as vaccinecarriers able to target dendritic cells (DCs) orallow transport through skin or mucosal epithelialbarriers. Results show that not only the colloidalproperties but also the polymer composition andmacromolecular architecture, are critical in inducingan effective immune response. In this context,MuNanoVac aims to assess the proof-of-conceptof a new vaccine candidate to prevent HIV-1 infectionat portal of entry; based on a primo-vaccinationusing a biodegradable synthetic colloidalcarrier, made of PLA nanoparticles bearing anyabsorbed HIV-1 antigens on their surface.Expected resultsThe target vaccine candidates will be intensivelyevaluated and optimised to reach the best potential.The project will cover the necessary steps to achievea complete proof of concept, including preliminaryprocess development aspects. MuNanoVac willcontribute towards:• bringing new knowledge and innovative technologiesthrough the HIV vaccine discoveryprocess, and;• proposing new vaccine candidates for combatingand preventing HIV/AIDS.Additionally, the project results will be promotedas a basis for developing vaccine candidates forother poverty-related diseases. Indeed, the projectaims to establish a proof-of-concept in orderto promote the potential of PLA nanoparticlebasedcompounds as effective vaccine candidatesto support a new HIV vaccine strategy.Potential applicationsMuNanoVacs aims at an efficient vaccine strategyfor the prevention of HIV infection, with a view totreating also other poverty-related diseases.Moreover, the advanced research activities conductedin MuNanoVac will generate novel data oninnovative HIV vaccine vehicles with a view toimproving the efficacy of the proposed vaccine.This data is crucial for publishing scientific results,contributing to sharply estimating the accuracyand pertinence of such new HIV vaccine candidatesand, therefore, for accelerating vaccinedevelopment.112

Key words: vaccines, immunology and Infections, HIV/AIDS, immune response, vaccine strategy, mucosa,skin, poly (lactic acid), PLA, nanoparticle and biodegradable carrierROLE OF SMEsPHUSIS, as the project coordinator, will be in charge of securing the manufacture of selectedpoly (D, L-lactic acid) – PLA – nanoparticles, with full quality control of the materials, and forthe scaling-up of the production process – polymerisation, purification, and drying. PHUSISwill also take the lead in securing an agreement among all the parties involved, so that theprocess of PLA nanoparticles preparation can be subsequently marketed.Scientific coordinatorJacqueline HuetPHUSISEspace Randon, 58 Route du Rivet38330 Saint Ismier, Francejhuet@phusis.frwww.phusis.frProject managerBernard VerrierInstitut de Biologie et Chimie des ProtéinesUMR 5086 CNRS/UCBL7 Passage du vercors69367 Lyon Cedex 07, Franceb.verrier@ibcp.frwww.ibcp.frPartnersRobin ShattockSt George’s Hospital Medical SchoolLondon, United Kingdomwww.sgul.ac.ukTeresa GallartHospital Clínic de BarcelonaBarcelona, SpainRoger Le GrandCommissariat à l’Énergie AtomiqueParis, Francewww.cea.frMilan RaskaPalacky University in OlomoucOlomouc, Czech Republicwww.upol.czBehazine CombadiereUniversité Pierre et Marie Curie – Paris 6Paris, Francewww.upmc.fr| Uptake of Poly Lactic Acid Nanoparticles loaded with p24 HIV gag protein.by dendritic cells.Illustration by electron microscopy of sub-cellular location in endosomal compartments.Ulrike Blume-PeytaviCharité Universitätsmedizin BerlinBerlin, Germanywww.charite.de113

ACRONYMContract number: LSHM-CT-2006-037833 | EC contribution: € 2 700 000 | Duration: 36 monthsStarting date: 1 October 2006MYASTAIDwww.euromyasthenia.euSUMMARYAutoimmune Myasthenia Gravis (MG) isa rare, chronic and heterogeneous neuromusculardisease characterised by severemuscle weakness. In most patients, it isdue to auto-antibodies to the acetylcholinereceptor (AChR). The detrimental effects ofthe autoimmune attack on the muscle arenot fully understood. The current treatmentsof MG induce severe side-effectswith no permanent clinical remission. Theearly-onset patients are mostly femaleswith thymic hyperplasia, while the existingexperimental model for MG (EAMG) doesnot present thymic pathology. This projectintends to develop models to progress inknowledge, monitoring, diagnosis andtherapy of MG:• videomicroscopic models to explore themotility of lymphocytes involved inthymic remodelling in young females;• new transgenic models overexpressingthe CXCL13 chemokine in the thymus, tobetter mimic the human disease whichinvolves thymic abnormalities andincreased thymic CXCL13 expression;• mouse model of estrogen deficiency, todetermine the influence of estrogens inpredisposition and progression of MG;• humanised NOD/SCID mouse modeltrans ferred with human MG thymocytes totest therapy by human regulatory T cells;• T cell receptor-based signature, for betterclassification and monitoring of MGpatients;• rat EAMG models immunised withTorpedo AChR, to test an array of therapies(IVIg subfractions, chemokineinhibitors, regulatory cells);• rat models immunised with recombinanthuman AChR subunits, to determine thecontribution of each subunit to the pathogenicityand develop immunotherapies;• monkey models to test protective anti-AChR antibodies.Since the research teams involved in thisprogramme also participate in a large‘European MG Network” supported by theEC, interactions between the two networkswill promote efficient dissemination of theobtained knowledge.Development of models to improve managementof Myasthenia Gravis: From basic knowledge toclinical applicationBackgroundAcquired Myasthenia Gravis (MG) is a rare autoimmunedisease with a prevalence around 0.1/2000.This disease is due to autoantibodies directedagainst components of the neuromuscular junctionand leading to disabling fatigability of muscles.MG is mainly (85 % of the patients) caused byanti-acetylcholine receptor (AChR) autoantibodiesand in some patients (about 5 %) by autoantibodiesagainst a muscle-specific receptor tyrosinekinase (MuSK). The remaining population forwhich the autoimmune target is not yet identifiedis defined as double negative MG patients.If the muscle is the target organ in this disease,the thymus is clearly involved in the pathogenesisof MG with anti-AChR antibodies. Indeed, 50-60 %of the patients present a thymic hyperplasia withgerminal centres (GCs) and around 20 % of thepatients have a thymoma. The titre of anti-AChR isnot correlated with the severity of the disease butis associated with thymic abnormalities. Thehyperplastic thymus includes all the componentsof the anti-AChR response: the autoantigen(AChR), B cells producing anti-AChR antibodiesand anti-AChR autoreactive T cells. The thymus isthus clearly involved in the development of MGand thymectomy is often advised for MG patientsimproving slowly but efficiently over a few yearstheir symptoms. The other pharmacological treatmentsproposed are:• symptomatic drugs such as cholinesteraseinhibitors preventing the degradation of acetylcholine;• glucocorticoids and immunosuppressor drugswhich are used for many autoimmune diseasesand act in a global way on the immune response;• plasmapheresis or intravenous human immuno -globulins in crisis period.Although progress has been made in developingtherapies for MG, this disease is still incapacitatingand treatments are not satisfactory. Manyquestions remain unanswered: Why is there nocorrelation between the anti-AChR antibody titerand the disease severity? Which are the otherautoantigens? Why is the thymus pathologic inmost cases? Why are females predominant in theearly onset disease? What occurs in the muscleafter the autoimmune attack? And – finally – howcan therapy of MG be improved?AimMyasthenia gravis (MG) is a well-defined antibodymediateddisease, but the pathogenic mechanismsat the effector organ (the thymus) and atthe target organ (the muscle) are still puzzling. Theaims are to improve knowledge, diagnosis, monitoringand management of MG patients. The mainscientific and technological objectives of the projectare as follows:1. To improve knowledge on the mechanisms ofpathogenicity occurring in myasthenia gravis.• Mechanisms of thymus remodelling in youngpatients. This topic will be addressed bya genomic approach using cDNA microarrays anda post-genomic approach exploring the role ofchemokines previously identified as key moleculesin the development of the disease. Newtransgenic models overexpressing CXCL13 in thethymus will be established to investigate whethergerminal centers (GCs) will be generated afterinducing the disease in this animal model.• Determination of the consequences of theautoimmune attack on the muscle organisation,gene expression and function.– The transcriptome analysis of muscle biopsiesshould identify a specific signature for the differentsubgroups of patients: patients withanti-AChR antibodies or with anti-Musk antibodies,and double negative patients.– Identification of new genes and proteinsderegulated as a result of the autoimmuneattack by analysis of muscle transcriptome inMG patients, rat EAMG, and in vitro model.– Investigating the specificity and pathogenicityof each subunit domain. New in vivo modelswill be created by immunising the rodentswith each subunit ectodomain as well as theircombination to evaluate the pathogenicity ofeach subunit.114

Key words: Myasthenia gravis, rare disease, chemokines, hormones, transcriptome, thymus, muscle,diagnosis, anti-TCR antibodies, therapy, antibodies, acetylcholine receptor, regulatory cellsROLE OF SMEsThe MYASTAID consortium includes 6 SMEs which will have a key role in the development ofnew diagnostic and monitoring assays, and in the development of new therapeuticsapproaches. Therefore, MYASTAID will reinforce the SMEs scientific and technological knowledgeon the validation of innovative solutions. The highly experienced SMEs participating inthis project aim to exploit the RTD findings for commercial markets and its translation to theclinic. The following table shows the contribution and potential benefits to each of the SMEs.Scientific coordinatorSonia Berrih-AkninUniversité Paris Sud (UPS)CNRS UMR 8162 Hôpital Marie LannelongueAvenue de la Résistance 13392350 Le Plessis-Robinson, Francesonia.berrih-aknin@u-psud.frPartnersSocrates TzartosHellenic Pasteur Institute (HPI)Athens, Greece• Understanding the female predominance in theearly onset disease by analysing the transcriptomeof the human thymus in young normalmales and females and by exploring the influenceof sexual hormones on the susceptibility ofMG disease in animal models.2. To improve diagnosis and monitoring ofMyasthenias.• By developing a new diagnostic assay moreeasy and to develop a monitoring assay of theautoimmune and regulatory status.• By searching for the autoantigen in the anti-MuSK and anti-AChR negative patients by usingproteomics approach.• By analysing the complete repertoire of the T cellsand the diversity of the anti-TCR antibodies.3. To improve therapy for MG using severalapproaches all of which are based on modulationof the adverse autoimmune responseand/or activation of the muscle response to theautoimmune attack in animal models.Expected results• Identification of genes involved in MG pathogenesis.• Mechanisms of action of germinal centre developmentin the thymus.• Establishment of transgenic mice overexpressingCXCL13 in the thymus and determination ofthe role of CXCL13 in the development of thymicpathology.• Identification of genes of predisposition specificto females.• Identification of new autoimmune targets indouble negative MG patients.• Mechanisms of action of anti-TCR antibodies.• Development of new therapies for MG.Potential applicationsThis project aims to improve diagnosis and monitoring.The collaboration with 6 industrial partnersincluded in this project will help developingthe following clinical applications:A new, easier diagnostic assay for anti-AChR antibodytiters is expected to be developed.A biological diagnosis is still expected for doubleseronegative MG patients. But in that case, theresearch proposed in this project aims first toidentify this autoantigen.The use of the technology developed by one of theproject’s industrial partners to analyse the T cellrepertoire in MG patients will provide a pioneeringwork as an example for studies in other diseasestherefore increasing the existing market forimmune signatures. This technology is based ona genomic approach, exploiting sequences of theentire TCR locus.The development of a new tool named antiTracKeR,to analyse the anti-TCR repertoire.The arrays of therapies to be used in animal modelsand particularly in the humanised mice modelshould result in novel therapeutic approaches.Marc De BaetsUniversity of Maastricht (UM)Maastricht, The NetherlandsSara FuchsMiry SouroujonTsvee LapidotWeizmann Institute of Sciences (WIS)Rehovot, IsraelAmnon PeledOrly eizenbergBiokine Therapeutics Ltd. (BKT)Jerusalem, Israelwww.biokine.comEugene BoswansEpsilon Biotech (Ebiot)Antwerp, BelgiumPaul ParrenGenmab B.V. (GMB)Utrecht, The Netherlandswww.genmab.comNicolas PasqualImmunId Technologies (IDT)Grenoble, Francewww.immunid.comOrgad LaubOMRIX biopharmaceuticals Ltd.Nes-Ziona, Israelwww.omrix.com/index.aspMichael RobertsRegulon A.E.Athens, Greecewww.regulon.org| Thymic Hyperplasia in early onsetmyasthenia gravis patient.The stainingin red (anti-keratin) represents theepithelial network all over the thymus,and the staining in green (anti-CD21)labels B cells and follicular dendriticcells visualizing the germinal centers.The picture was obtained by an originaltechnique using a scanner for microarray.115

ACRONYMContract number: LSHB-CT-2006-037479 | EC contribution: € 2 480 000 | Duration: 36 monthsStarting date: 1 December 2006MYOAMPSUMMARYMany groups have used animal models toinvestigate the possibilities of usingautologous cell therapy for muscular dystrophies,but these data are dispersed,not always comparable and little attentionhas been focused on the transfer ofthis knowledge towards applications fortherapeutic trials.Data exist on injecting murine cells intomouse muscle, but information regardinghuman cells is sparse. The feasibility ofautologous myoblast transfer therapyhas already been demonstrated for cardiacrepair, even if in cardiac therapy,injected cells were mainly used to counteractthe development of fibrosis inpatients devoid of any defect in skeletalmuscle.The fact that pre-clinical trials developedin mouse models of muscular dystrophieshave been successful as comparedto clinical trials, which used mostly allogeniccells and resulted in very limitedclinical benefit for the patients, illustratesthe urgent need for pre-clinicalstudies using human cells.MYOAMP will aim to define conditionsand guidelines to produce transducedhuman stem cells as vectors for clinicaltrials. MYOAMP will synergize expertisesfrom European leaders in their respectivefield to set up conditions for autologoustransfer of human stem cells in GMP conditionsfor the treatment of DMD byexon-skipping. It will ensure that theseconditions and guidelines are transferredto SME and clinicians, defining efficientintegration through dedicated partnerswithin the 3-years duration of this project.Amplification of human myogenic stem cellsin clinical conditionsBackgroundMany clinical trials using muscle cells have beendeveloped in the past for Duchenne MuscularDystrophy with very limited success. The recentemergence of new therapeutic venues, basedupon post-transcriptional genetic correctionscalled ‘exon-skipping’, has raised new hope forthis disease. Using viral transfer approaches ithas given very promising results but cannot reachevery muscle of the body and trigger an immuneresponse to the vector. Autologous cell therapymay bypass this reaction and be used as a complementor alternative if the cell type used fulfilledboth being an efficient vector and bringinga functional benefit to the diseased muscle.Autologous muscle cells cannot be used sincethese are already defective in dystrophic muscle,while stem cells from other origins are ideal candidates,as long as their myogenic and proliferativepotentials are ensured. In this perspective mesoangioblasts,which have already been used ina mouse model of muscular dystrophy, and AC133cells have a therapeutic potential as demonstratedin the mouse, but very little is known about the conditionsrequired to amplify in GMP conditions thesestem cells isolated from humans, which is anessential step required before any clinical trial.AimMYOAMP will address the question of the amplificationof these cells used as autologous cell therapyvectors and their safety.The cells transduced with a lentiviral constructallowing exon-skipping will be selected and furtheramplified. It should be noted that transduced cellsmay be cloned so that their integration site is determined),as will be proposed in the part of MYOAMPthat focus on safety and ethics. In vitro and in vivoapproaches will bring understanding on the regulationof proliferation, while the telomere length(reflecting the mitotic clock status of the cell) willbe monitored, as well as a combination of receptorsknown to trigger proliferation, (FGF, IGF1, … ).The stability of the parameters initially examinedin non-GMP conditions, will be checked throughamplification in various conditions, to allow thedefinition of both guidelines for GMP productionand key-parameters to be followed during theGMP amplification.The number of cells to be injected at each implantation,which is purely empirical in many clinicaltrials, will be tested and optimized in a model ofimplantation of human cells in immuno-deficientmice, in order to define the maximum number ofcells to be finally amplified in GMP conditions.Expected resultsThe main expected result is to obtain the finalproduct, i.e. protocols to obtain amplified humanstem cells, in a state that will allow an optimizedefficiency in injections in vivo.In addition to basic knowledge on the amplificationmechanisms, MYOAMP will bring guidelinesand standard operative procedures to obtainthese cells in a reproducible and safe manner thatcan be directly transferred to SMEs and cliniciansfor clinical applications.These guidelines will therefore address technical,ethical and safety issues in a GMP environment.Potential applicationsPre-clinical Protocols, Standard Operating Proce -dures to characterize, amplify and assess myogenichuman stem cells for autologous celltherapy treatments in muscle disease.Ethical and safety procedures to cover the protocols.Specific culture medium with a defined set ofgrowth factors.116

Key words: human stem cells, neuro-muscular diseases, cell proliferation, cell therapy, exon-skippingROLE OF SMEs3H Biomedical cell provider and responsible for defining standard operating procedures(SOP) for cell handling.CELLGENIX development of adapted serum-free culture medium and definition of SOP.GENOSAFE development of safety procedures and assays for the process.Scientific coordinatorVincent MoulyINSERMUMR S 787 MyologieInstitut de Myologie105 bd de l’Hôpital75634 Paris Cedex 13Francemouly@ext.jussieu.frwww.inserm.frwww.institut-myologie.orgPartnersLuis GarciaINSERMParis, FranceYvan TorrenteUniversity of MilanMilano, ItalyGiulio CossuFondazione Centro San Raffaeledel Monte TaborMilano, ItalyJenny MorganImperial CollegeLondon, United KingdomOtto MertenGénéthon,Evry, Francewww.genethon.frMallen Huang3H BiomedicalUppsala, Swedenwww.3hbiomedical.comRoland BosseCellgenix GmbhFreiburg, Germanywww.cellgenix.comVincent GiulianiGenosafe S.A.Evry, Francewww.genosafe.comAnton OttaviInserm-TransfertParis, Francewww.inserm-transfert.fr117

ACRONYMContract number: LSHB-CT-2006-037245 | EC contribution: € 1 433 600 |Duration: 36 monthsStarting date: 1 January 2007NanoSensewww.nanosense.euSUMMARYThere is a need for high sensitivity nonseparationimmunoassay technology forgeneral clinical chemistry instrumentplatforms. This need is particularly evidentfor large protein disease markers oflow concentration, such as NT-proBNP,PSA, and a long list of other plasma proteins,protein hormones and specificantibodies. Such new technology will significantlychange the diagnostic industryand healthcare providers much greaterefficacy.Moving sensitive immunoassays fromslow and expensive to fast and affordablenanoparticle-based methodsBackgroundTraditionally, immunoassays have been separationbased, meaning that the analyte of interestgoes through several steps of antibody binding,washing and separation before final detection.This type of assay requires a high use of consumables,which is expensive and time consumingdue to all the steps. On the other hand, in anon-separation assay no separation steps areinvolved and the use of consumables is limited,making the assay less expensive and with a muchshorter assay time. A non-separation assay willtypically be run on a clinical chemistry platformintended for high-throughput of analytes, makinghomogeneous non-separation immunoassaysa high potential market growth opportunity.AimExpected resultsTo achieve the goal of this project, methods andtechniques will be used to optimise each componentin the assay. When technology, as describedabove, was developed for small molecule markers15 years ago, a large change in the diagnosticindustry was seen and two small SMEs grew intobig industrial corporations. The project foreseesthat similar effects may occur when such technologyis also developed for large molecule markers.Potential applicationsNew high sensitivity high speed assay productson automated clinical chemistry platforms for usein laboratories throughout the healthcare system,for higher throughput and for improved costeffectiveness.The aim of the project is to move immunoassaysfrom slow and expensive methods to fast, highthroughputsuper-sensitive nanoparticle basedmethods. In addition, the project aims to generateintellectual property for such technology.118

Key words: nanoparticles, clinical assays, turbidimetry, high sensitivityROLE OF SMEsThere are five participants in this project, with three being SMEs. The co-ordinator role isundertaken by one of the SMEs, Dalen Diagnostics AS in Norway. In addition to the coordination,the company possesses the necessary expertise for improved signal generation inhomogeneous nanoparticle assays. The other two SMEs are: 77 Elektronika Kft in Budapest,Hungary, which specialises in the field of medical electronics and manufactures blood glucosemeters, urine analysers and rapid test readers; and Getica AB, a small, Swedish biotechcompany specialising in bioorganic coupling chemistries and bioprocessing of proteinconjugates and nanoparticles.In the consortium, there is also a large industrial company, Merck Chimie SAS, Europe’slargest producer of nanoparticles, and an academic participant, the GroningenUniversity Medical Centre, which provides a reference laboratory for measurements inlarge epidemiological studies.Scientific coordinatorGuri SkjeltorpDalen Diagnostics ASKolsroedveien 1201599 Moss, Norwayemail@dalendiagnostics.nowww.dalendiagnostics.no/dalendiagnostics/vis.phpPartnersErling SundrehagenIngrid HulthénGetica ABTösse, Swedenwww.getica.seRichard VidalCécile GeniesMerck Chimie SAS EstaporFontenay-Sous-Bois, Francewww.estapor.comUzonka FarkasPéter Jakus77 Elektronika Muszeripari KftBudapest, Hungarywww.e77.huDick de ZeeuwStephan J L BakkerDepartment of Clinical PharmacologyUniversity Medical Center GroningenGroningen, The Netherlandswww.umcg.nl119

ACRONYMContract number: LSHM-CT-2006-036534 | EC contribution: € 3 299 809 |Duration: 36 monthsStarting date: 15 October 2006NEOBRAINwww.neobrain.euSUMMARYNEOBRAIN brings together small andmedium-size enterprises (SMEs), largercompanies and academic groups devotedto the diagnosis, management and neuroprotectionin newborns with perinatalbrain damage. The focus of NEOBRAIN isthe prevention of brain damage mainlyobserved in pre-term newborns.The objectives of NEOBRAIN are:• to generate marker profiles of damage inmultiple animal models and in humanpre-term infants using genomic/genetic,proteomic and metabolomic approaches,as well as imaging and electrophysiologicmodalities;• to develop neuroprotective strategiesby identifying candidate molecules forintervention in animals;• to implement a platform for an observationalclinical epidemiologic study inhuman infants designed to contributeto objective 1 above, and to transferfrom the animal to the human levelinsights gained in objectives 1 and 2;• to prepare for drug testing by using theproject structure as a platform for initialsteps in clinical testing of potentialinterventions discovered in NEOBRAIN.The project further envisages developingthe clinical platform in such a fashion that itcan serve as the basis for subsequent largescalepan-European perinatal neuroprotectiveresearch initiatives (Euro-Neo-Net,EURAIBI).Neonatal estimation of brain damage riskand identification of neuroprotectantsBackgroundPrevention of perinatal brain damage is of majorimportance for public health and obviously forindividual wellbeing. Both white and grey brainmatter are affected in perinatal brain damageobserved in pre-term infants. Long-term consequencesof extreme prematurity are devastating,and perinatal brain damage clearly plays a role inthis scenario. The current pathogenetic paradigmof perinatal brain damage in pre-term infantshas multiple interrelated aspects and includesinfection/inflammation, hypoxia-ischemia, excitotoxicity,and free radicals. It is likely that thesemechanisms do not act alone, but in concert.The absolute number of neurological handicapsof perinatal origin is increasing in western countriesdue to the increasing survival of pre-terminfants. The major brain lesions associated withcerebral palsy (CP) and cognitive impairment arewhite matter damage (WMD), mostly occurring invery pre-term infants (born in less than 32 weeksof gestation), and cortico-subcortical lesionsmostly observed in term infants. For financial,technical and ethical reasons, the pharmaceuticalindustry has difficulties in making substantialinvestments in this area, and this has left perinatologistswith a limited therapeutic arsenal. At thepresent time, despite major improvements inneonatal care, there are no established therapeuticregimens for the prevention or treatment ofperinatal brain lesions that are successful.Nevertheless, epidemiological and experimentaldata have allowed the identification of potentialtargets for neuroprotection. New animal models,such as those employed in NEOBRAIN, clearlyshow the pathophysiology involved in neurodegenerationand will help identify neuroprotectivestrategies in the newborn.for interventional neuroprotection. The consortiumwill study, in various established animal models,the mechanisms that lead to perinatal brain damagein order to identify genomic, proteomic andmetabolomic biomarkers to generate biomarkerprofiles. They will also establish biomarker profilesin human newborns in an observational clinicalstudy involving extremely pre-term infants bornbefore completion of 28 weeks gestation (normalpregnancy duration: 40 weeks).Once identified biomarkers of damage and potentialavenues for neuroprotection, the project willstart developing an intervention, using multipleanimal models to pursue this goal. Only the mostpromising strategies will be considered worthy ofbeing translated from bench to bedside.Further step of the project will be to implementa clinical platform• to design a biomarker profile of perinatal braindamage in experimental animals and in humannewborns (see above). Thus, participants willestablish a functional network of institutions caringfor newborns that can serve as the basis forsuch a clinical study, designed to identify humanbiomarker profiles based on genetic and biochemicalmarkers, electroencephalographic (EEG)patterns and magnetic resonance imaging (MRI);• the consortium will use and expand this platformfor clinical drug testing both within the 36 monthsof NEOBRAIN and thereafter.Finally, NEOBRAIN will pave the way for clinicaldrug development. In essence, the clinical platformwill be designed in a way that allows forquick expansion (i.e. recruitment of further centres),so that bench-to-bedside translationalsteps (i.e. a clinical trial) can be taken quickly afterNEOBRAIN is finished.AimTo help reduce the enormous individual, familialand societal burden that perinatal brain damagerepresents, the first objective of this project is toidentify early damage markers and novel pathwaysExpected results/potential applicationsNEOBRAIN provides an obvious potential impactin helping to reduce mortality and stamp out developmentaldisabilities associated with perinatalbrain damage.120

Key words: newborns, hypoxia/ischemia, inflammation, perinatal brain damage neuroprotectantsROLE OF SMEsFive companies (three of them being SMEs) play crucial roles in the NEOBRAIN project. TwoSMEs are devoted to develop biomarkers in the field of metabolomics (BIOCRATES life sciences,Austria) and proteomics (BIOANALYT, Germany). A larger company, NEUROPHARMA (Spain) andTHERAPTOSIS S.A., an SME (France) are designing and developing innovative neuroprotectivedrugs. BrainZ, a New Zealand based company (but not an SME) producing electroencephalography(EEG) hard- and software, is interested in the development of EEG-markers of perinatal braindamage. BrainZ has expertise and services not available in Europe and offers important assistanceat no cost to the NEOBRAIN project. All efforts of the NEOBRAIN research are directedtowards the development of neuroprotective pharmacological strategies that will be directlyexploited by the SMEs participating in the project. The involvement of the companies providesa unique opportunity for using the research results in product development without delay.The most important source of societal sufferingfrom perinatal brain damage is at the individualand family level. Four out of five pre-term infantsare limited in their everyday activities. Moreover,brain-damage-associated cognitive and learningdifficulties represent a potentially preventablesource of suffering. It is NEOBRAIN’s goal to contributeto an improvement of this situation forfuture generations.Also the economic burden of prematurityimmense, taking into consideration cost of hospitalinpatient admissions plus non-hospitalinpatient health care costs, such as costsincurred through family practitioners, educationaland social services, considering that approximately60 000 infants sustaining some sort ofbrain injury.In addition to the societal and economic impact,the close cooperation and integration of enterprisesand academic centres offers the uniquechance to exploit new business areas and positionthe participating companies as market leadersnot only in Europe, but also in the USA,Australia and Asia.New multi-parametric biomarker measurementtools will be developed based on metabolomicand proteomic techniques. These tools, in turn,will help improve clinical diagnostics with regardto perinatal brain injury, and this will contributeto a greater potential for neonatologists to consultwith parents and within their therapeuticteams about the individual child’s prognosis. Thegrowing medical subdiscipline of ‘neonatology’is a potential market for tools to be developedin NEOBRAIN.Another potential market among sick and pretermnewborns is called ‘theranostics’, the individualisedsurveillance of therapy efficacy andresults. NEOBRAIN will contribute to this fieldby offering improved strategies for biomarkermeasurements, including imaging and electroencephalographicmarkers of infant wellbeing.Scientific coordinatorOlaf DammannHannover Medical SchoolCarl-Neuberg-Str. 130625 HannoverGermanydammann.olaf@mh-hannover.dePartnersMedizinische Hochschule HannoverHannover, GermanyBIOCRATES life sciences GmbHInnsbruck, Austriawww.biocrates.atBrainZ Instruments Ltd.New Zealandwww.brainzinstruments.com/index.aspBioanalyt GmbHPotsdam, Germanywww.bioanalyt.comTHERAPTOSIS S.A.Romainville Cedex, Francewww.theraptosis.com/english/home/index.htmNEUROPHARMA S.A.Tres Cantos, Madrid, Spainwww.neuropharma.esUniversity Medical Center UtrechtUtrecht, The Netherlandswww.umcutrecht.nl/zorgGöteborgs universitetGoteborg, Swedenwww.gu.seInstitut National de la santéet de la Recherche MédicaleParis, Francewww.inserm.frUniversité de GenèveHôpitaux Universitaires de GenèveGeneve, Switzerlandwww.unige.ch/medecine/index.htmlCharité Universitätsmedizin BerlinBerlin, Germanywww.charite.deUniversità degli Studi di SienaSiena, Italywww.unisi.itLunds UniversitetLunds, Swedenwww.lu.se121

ACRONYMContract number: LSHB-CT-2007-037590 |EC contribution: € 2 981 000 | Duration: 36 monthsStarting date: 1 February 2007Net2DrugSUMMARYNew high-throughput methods allow thegeneration of massive amounts of molecularbiological data. These, mainly phenomenological,data are often difficult toascribe to the activation of particular signaltransduction pathways and/or transcriptionalregulators. A way to facilitatedata interpretation is to construct generegulatory networks that include signaltransduction mediators, transcriptionalregulators and target genes. This isa complex task, not only because of thehuge number of molecules involved, butalso because of variations across tissues,developmental stages and physiologicalconditions. However, these networks holdthe key to the understanding of the regulatoryprocesses within a cell and, thus, tomost life processes in general. The aim ofthis project is, therefore, to developa toolbox that combines the differenthigh-throughput experimental methodstogether under the roof of bio- andchemo-informatics, to allow the exploitationof the full potential of the includedmethods, as well as the generated data.The toolbox will comprise a combinationof the most innovative bioinformatictechniques, based on databases andmethods of artificial intelligence, modernmethods of chromatin structureanalysis, micro-array technologies,transcription factor-binding site identification,as well as chemoinformaticsmethods for computer-aided predictionof biological activity spectra.From gene regulatory networks to drug predictionBackgroundComplex diseases such as cancer are caused bythe disregulation of expression of many differentgenes, resulting in the malfunction of complex cellularprocess. Every cellular state is characterisedand precisely organised by differential expressionsof specific sets of genes. Gene expression ismainly regulated at transcriptional level throughsequence-specific binding of transcription factors(TFs) to their target sites in regulatory regions ofgenes, where the combination of these sites andbound factors provide the required specificity. Forthe whole genome, we might expect millions offunctional sites regulating expression of genesunder different conditions, of which we have theknowledge of only a few per million. Therefore,computational methods for the prediction of TFbinding sites in genomes are needed.New experimental high-throughput approacheshave been introduced to study the gene regulatory(and other molecular) mechanisms of complex diseases.Among them are the ChIP (ChromatinImmuno Precipitation)-on-chip method for the identificationof target genes for various transcriptionfactors on a high-throughput scale, and RNAiapproaches (gene silencing by small doublestrandedinterfering RNAs) for the functional elucidationof selected genes. Novel computationmethods are needed for the automatic interpretationof high throughput data in order to formulatea hypothesis of molecular mechanisms of diseases.AimThe main aim of this project is to develop anintegrated technology, comprising cutting edgebioinformatics, chemoinformatics and experimentalmethods, to study the mechanisms thatcause complex diseases. Understanding themechanism of diseases is the key to rationalisingdrug development.Expected resultsThe aim of this project is to develop a toolbox thatcombines and puts different high-throughputexperimental methods together under the roof ofbio- and chemo-informatics, to allow the exploitationof the full potential of the included methods,as well as the generated data.This toolbox shall provide a cost- and time-effective,knowledge-based approach that allows identificationof signal transduction mediators and/ortranscriptional regulators responsible for certainchanges or responses of the cell, in particularthose which lead to diseases, thereby facilitatingthe discovery of new targets and consequently therational design of target-specific drugs.Potential applicationsIdentification of drug targets in breast cancer andother diseases.122

Key words: transcription factors, ChIP-on-chip method, microarray, analysis of promoters, drug targetsROLE OF SMEsA number of SMEs (BIOBASE, Progenika and ISB), particularly from the bioinformatics sector,take part in the project, thereby strengthening the link between basic research anda possible later application of the developed technology, either in the form of a service forthe pharmaceutical and biotechnological industry, or as a marketable product.BIOBASE is a coordinator of the project. Among the tasks carried out are:• manual annotation of project relevant data into existing databases, namely TRANSFAC®,TRANSPATH®, and TRANSCompel®;• providing the data collected to the community;• DNA sequence analysis: search for putative binding sites for TFs;• development of software for the reconstruction of a gene regulatory network (transcriptionnetwork) from the microarray experiments;• causal analysis of experimental data provided by other partners of the consortium andcomputational identification of drug targets; and• maintaining the workflow for the chemoinformatics group, providing drug targets forfurther prediction of perspective chemical compounds.Progenika carries out the microarray analysis and gene validation by RNA interference.ISB is responsible for the visualisation of gene regulatory networks, automatic in silicoreconstruction of pathways, and methods of semi-quantitative modelling of gene regulatorynetworks. It is involved in the development of a microarray database format and userinterface, composite modules, methods of artificial intelligence and data mining, and theprediction of the most promising drug targets and markers for breast cancer.Scientific coordinatorAlexander KelBIOBASE GmbHHalchtersche Str. 3338304 WolfenbüttelGermanyalexander.kel@biobase-international.comwww.biobase-international.comPartnersProgenika Biopharma S.A.Derio, Spainwww.progenika.comNational Public Health InstituteHelsinki, Finnlandwww.ktl.fiFraunhofer Gesellschaft zur Förderungder angewandten Forschung e.V.Munich, Germanywww.fraunhofer.deUniversitätsmedizin GöttingenGeorg-August-Universität GöttingenStiftung Öffentlichen RechtsGottingen, Germanywww.med.uni-goettingen.deInstitute of Systems Biology, Ltd.Novosibirsk, Russian FederationInstitute of Biomedical Chemistryof Russian Academy of Medical SciencesMoscow, Russian FederationKarolinska InstitutetStockholm, Swedenwww.ki.seNational Research Council – CNRRome, Italywww.cnr.it© Shutterstock123

ACRONYMNPARIwww.npari.orgContract number: LSHM-CT-2006-037692 | EC contribution: € 2 800 000 | Duration: 36 monthsStarting date: 1 December 2006SUMMARYThe apoE and apoB human proteins haverecently been linked to the innateimmune system. Peptide sequencesderived from these proteins have beenshown to have varied anti-infective propertieswhich can be modified by smallchanges to the core peptide sequence.Thus, the apoE and apoB peptidesexhibit antibacterial, antifungal andantiviral properties and present an excellentopportunity to develop novel therapeuticsand medical device coatings.Specifically the exploitation of thesenovel peptides allows for the potentialdevelopment of a new array of agents targetingagainst the growing problems ofantibiotic resistant microorganisms.Tailoring of Novel Peptide coatings and therapeuticsderived from a newly identified component of thehuman innate immunity Against Resistant InfectionsBackgroundInfectious diseases represent the most commoncause of morbidity in the world (WHO). Over thelast 40 years, major advances have been made inthe development of numerous classes of antimicrobialagents to treat serious life threateninginfections. This is particularly true for antibacterialagents. However, microorganisms are slowly turningthe tide and becoming increasingly resistant tothe agents developed by man. Long term andindiscriminate use of antibacterials has led toresistance developing for all the major classes oftherapeutic agents. Increasingly clinicians arefighting a rearguard action with a dwindlingarmoury of drugs to combat serious life threateninginfections. Nosocomial or hospital acquiredinfections (HAIs) represent an increasingly seriousproblem across Europe and the rest of the world.Data from the SENTRY Antimicrobial Surveillanceprogram of 25 European university hospitals highlightedthe five most common bacterial bloodisolates. The most prevalent organisms (E. coli,S. aureus, P. aeruginosa and K. pneumoniae) arealso the most prevalent CVC associated infections(Clin Inf Dis 30; 3). Candida species were alsocommon organisms isolated from blood and carrieda crude mortality rate of up to 40 %. Theseorganisms are the same organisms where resistanceis a major issue. The incidence of resistantbacterial and fungal nosocomial infections ishigh. The European Study Group on NosocomialInfections (ESGNI) reports on blood stream infectionsindicated 72.8 % of infections were nosocomialand mortality due to bacteremia was 7.1 %.The most frequently isolated microorganismsfrom BSI were S. aureus (15.1 %), E. coli (14.5 %),S. epidemidis and coagulase negative staphs(CNS) (17.8 %), P. aeruginosa / K. pneumoniae(both 5.3 %) and Candida spp and enterococci(both 4.6 %).(ESGNI-001, ESGNI-002).AimThe aims of the NPARI consortium are to fullyexploit the exciting properties of this novel peptideclass. Specifically the consortium aims totarget peptide sequences into two areas; coatingagents for medical devices and therapeuticsagents.A major application for the apoE peptides is ascoatings for medical devices such as catheters.ApoE derivative peptides are already in developmentas coatings for contact lenses. The projectaims to extend this application to use active peptidesas coating agents for catheters. Catheterrelated infection causes significant morbidity andmortality across the EU and resistant bacteria andfungi are often responsible.Another focus for the application of apoE peptidesis as therapeutic agents. The project will focus ontargeting specific resistant bacteria and fungi inorder to rapidly establish in vivo efficacy in a varietyof animal models. It will specifically target respiratoryinfections caused by Pseudomonas andApsergillus. This will have direct clinical relevanceto the 30 000 European CF patients where resistantPseudomonas aeruginosa infections are a majorcause of mortality. Colonisation with Aspergillus isalso a major problem is this patient group.Expected results• The design of a small peptide library which willbe tailored to the proposed exploitable applicationof the project.• Determination of the activity spectrum of activepeptides and the ranking of peptide variants.• Optimisation and toxicity profiling of activepeptides.• Efficacy profiles against a panel of resistantorganisms growing as biofilms.124

Key words: peptide, resistance, infection antibacterial, antifungal, therapeutic agent, coating agentROLE OF SMEsA vital component of the project is the participation of several SMEs who each haveexpertise in the field of drug development. This, combined with the academic expertise ofthe remaining partners, allows for an experienced and focused consortium.Nikem Research is an Italian based company who specialise in drug development. Nikemhas developed a wide range of ADMET and toxicological assays which can be applied tothe project. In addition, Nikem has a range of bioanalytical capabilities which will beemployed to monitor the pK/pD profiles of the peptides.Similarly, F2G has expertise in the discovery and development of anti-infective agents,specialising in anti-fungals. With a range of HTS screening capabilities, chemistry andpharmacology experience, F2G is able to rapidly assess and develop peptides for use intherapeutic candidates.The focus of Ai2 is on the use of peptides to prevent colonisation of medical devices, whichvery well complements the expertise within the consortia.• Pharmacological and efficacy evaluation ofpeptides in a range of models.• Efficacy data for candidate coatings in dynamicbiofilm models.Scientific coordinatorMike BirchF2G Ltd.Lankro Way, EcclesManchester, United Kingdommikebirch@f2g.comPartnersChristophe d’EnfertInstitut PasteurBiologie et Pathogénicité FongiquesParis, Francewww.pasteur.fr/ip/index.jspJean-Marc GhigoInstitut PasteurGroupe de Génétique des BiofilmsCNRS URA 2172Paris, Francewww.pasteur.fr/recherche/unites/GgbChiara Bigogno, Giulio DondioNiKem Research s.r.l.chiara.bigogno@nikemresearch.comwww.nikemresearch.comNiels HøibyDepartment of Clinical MicrobiologyUniversity Hospital of CopenhagenCopenhagen, DenmarkCurtis DobsonAi2 Ltd.Manchester IncubatorManchester, United KingdomPotential applicationsThe exploitation of this new class of antimicrobialpeptides offers the potential to develop newtherapeutic against a range of the most resistantand problematic organisms facing EuropeanInfectious Disease Clinicians.The rate infection by resistant bacteria is increasingbut new chemical agents are some way fromthe clinic. This project aims to develop candidatepeptide therapeutics which target the most problematicorganisms and develop them to the pointwhere they show sufficient potential for furtherdevelopment.In addition, the project focuses on the preventionof infection by the same resistant organismsthrough the coating of medical devices with activepeptides.By preventing the colonisation of catheters byresistant microorganisms it is expected that seriouslife threatening infections can be avoided.125

ACRONYMOMVacContract number: LSHB-CT-2006-037653 | EC contribution: € 2 320 000 | Duration: 36 monthsStarting date: 1 October 2006SUMMARYOtitis media (OM) is one of the most frequentdiseases in childhood and themost common indication for the prescriptionof antibiotics. Due to the poor evidencefor the effectiveness of thistreatment and widespread drug-resistances,there is a need for a prophylacticvaccine to reduce the misery of childrenby preventing the occurrence of OMaltogether. This study focuses on thecomprehensive identification of antigencandidates from two of the maincausative agents of OM, namely nontypeableHaemophilus influenzae (NTHi)and Moraxella catarrhalis. The antigenomeof both pathogens will be identified byscreening of bacterial surface displaylibraries with human sera from exposedindividuals and complementary proteomicapproaches. Selected antigenswill be evaluated by testing in animalmodels, characterisation of their role inpathogenesis with special emphasis onbiofilm formation and study of the naturalimmune response. This approach willenable the project to transfer the mostpromising vaccine candidates to clinicaltrials for the prevention of OM.The consortium comprises proven andrenowned experts of OM research, proteomics/massspectrometry and vaccinedevelopment. Therefore, this multidisciplinaryapproach will go beyond anyeffort that could be undertaken by a singleparticipant by the complementarityof the technologies.Novel prevention and treatment possibilitiesfor Otitis Media through the comprehensiveidentification of antigenic proteinsBackgroundApproximately 80 % of all children undergo anOM episode by 3 years of age. The maincausative agents are the bacterial pathogensStreptococcus pneumoniae, Haemophilus influenzaeand Moraxella catarrhalis which colonise themiddle ear, often after a primary viral infection.After introduction and widespread use of pneumococcalvaccines, there is evidence that theimpact of the latter two species increased. Acuteotitis media (AOM) is characterised by the presenceof middle ear effusion accompanied by therapid onset of signs of inflammation such as otalgia,otorrhea or fever. Recurrent OM affects up to40 % of children and may persist for weeks tomonths causing symptoms ranging from hearingloss and tinnitus to anorexia or conjunctivitis. AsAOM is very painful, it results very often in antibiotictreatment although solid evidence is lackingthat this therapy alters the course of OM diseasein children. Also in case of recurrent OM the failurerate of antibiotic therapy is quite high, oftendue to antibiotic resistances of the pathogens.Considering also the high direct and indirect costsof OM, there is an urgent need for an alternativeand effective therapy.AimThe OMVac project addresses as main objectivesthe identification of vaccine candidatesfrom Moraxella catarrhalis and non-typeableHaemophilus influenzae (NTHi) to develop a prophylacticvaccine against OM and the comprehensivecharacterisation of natural immuneresponses against proteineacous antigens ofthe major three bacterial pathogens causingOM. Moreover, the role of selected antigens duringpathogenesis and biofilm formation will beinvestigated.Expected results• Comprehensive identification of antigens fromM. catarrhalis and NTHi by screening of bacterialsurface display libraries.• Characterisation of the membrane proteomeand surface located proteins from bothpathogens by 2D-PAGE and 2D-LC-MS 2 andserological proteome analysis.• Selection of the most promising vaccine candidatesby validation in vitro and in animal models.• Characterisation of protective antigens withrespect to their role in pathogenesis of M. catarrhalisand NTHi (including biofilm formation).• Definition of natural immune responses againstthe identified antigens from M. catarrhalis, NTHiand S. pneumoniae using the available sera andIg preparations.Potential applicationsThe achievement of the goals will drive the developmentof a prophylactic vaccine against OM andthereby will have a large benefit for the health ofchildren in Europe and beyond. Because NTHiand M. catarrhalis not only cause OM in childrenbut also other infections of the respiratory tractlike sinusitis, pneumonia or bronchitis, sucha vaccine could proof useful for prevention ofthese diseases as well.As the project will contribute to science studyingthese bacteria and their pathogenesis, itmight also offer new approaches for alternativetherapies of OM.126

Key words: Otitis Media, vaccine development, Streptococcus pneumoniae, Haemophilus influenzae,Moraxella catarrhalis, biofilm formationROLE OF SMEsIntercell AG is an international vaccine company founded in 1998 and located in Vienna,Austria and Livingston, Scotland. Intercell’s current activities include the discovery anddevelopment of innovative immunological products and technologies for the prevention andtreatment of infectious diseases. Within the OMVac project, Intercell will lead the antigendiscovery and validation process using proprietary technologies. Moreover, Intercell isresponsible for all project management activities.AGOWA GmbH is an internationally acting genomics company founded in 1993 and locatedin Berlin, Germany. It is recognised as a competent outsourcing partner for customers in privateand public research, with the company offering a broad spectrum of services rangingfrom library construction, custom DNA sequencing service, genotyping and bioinformaticsup to the complete analysis of genomes. In the course of the OMVac project, AGOWA willsupport the antigen discovery process by high-throughput sequencing.Scientific coordinatorAndreas MeinkeIntercell AGCampus Vienna Biocenter 61030 Wien, Austriaameinke@intercell.comwww.intercell.comPartnersAndreas J. KunglInstitute of Pharmaceutical SciencesUniversity of GrazGraz, Austriawww.uni-graz.atWolfgang ZimmermannAGOWA GmbHBerlin, Germanywww.agowa.deÉva Bán2 nd Department of PediatricsSemmelweis UniversityBudapest, Hungarywww.sote.huJohn HaysErasmus MCRotterdam, The Netherlandswww.erasmusmc.nlPeter WM HermansLaboratory of Pediatric Infectious DiseasesRadboud UniversityNijmegen Medical CentreNijmegen, The Netherlandswww.umcn.nlBirgitta Henriques-NormarkKarolinska InstitutetSolna, Swedenki.se127

ACRONYMContract number: LSHG-CT-2006-037793 | EC contribution: € 2 268 531 | Duration: 36 monthsStarting date: 1 December 2006OptiCrystwww.opticryst.orgSUMMARYThe OptiCryst project aims to providea support platform for Europe’s StructuralGenomics initiatives. The project aimstohelp such initiatives take a leap forwardscientifically and commercially, in orderto obtain high-quality crystals of proteinswhich are currently proving difficult tocrystallise.Optimisation of protein crystallisationfor european structural genomicsBackgroundExpected resultsThe wealth of information obtained by StructuralGenomics has allowed protein structure-baseddrug design to complement screening and combinatorialchemistry to provide more efficient drugdevelopment. Ultimately, this approach will reducethe time of production cycles and therefore costper drug.Structural Genomics has coincided with the era ofhigh-throughput, resulting in major advances inthe automation of protein preparation and X-raycrystallographic analysis, and in automating andminiaturising crystallisation trials (thousands perday). Despite this, the success rate in going fromcloned gene to high-resolution protein structureis still relatively low in all current StructuralGenomics projects, with a major bottleneck situationfrom purified protein to diffracting crystals.This problem clearly needs to be addressed. Thiscan be done through the production of a designthat will offer new and improved optimisationmethods, in order to turn crystal leads into usefuldiffracting crystals.Moving away from current approaches, and applyingmethods based on understanding the fundamentalprinciples of crystallisation, the OptiCrystproject will focus on designing techniques toactively control the crystallisation environment asthe project progresses through its stages.Potential applicationsStructural Genomics is a key discipline in postgenomicbiology, and today the pressure to producediffraction-quality crystals that can yieldnew protein structures is greater than ever. Asa result, the science of crystallisation is becominga rapidly developing field and it is gatheringnew momentum. The work being carried out bythe OptiCryst project will go a significantly longway towards addressing the outstanding needswithin that research area.AimThe key objective of the OptiCryst project is toaddress the critical post-protein production bottleneckarea in the field of Structural Genomics.To date, this area has been consistently ignoredby initiatives worldwide. The project proposes toenhance the state-of-the-art in protein crystaloptimisation by increasing the success rate of theproduction of diffraction-quality crystals from thecurrent rate of 21 % to at least 40 %.128

Key words: structural genomics, SME, protein crystallisation, phase diagrams, nucleation, robotics,high throughput, structural genomicsROLE OF SMEsThe OptiCryst consortium is composed of seven SMEs and four academic groups. The role ofthe SMEs in OptiCryst is to develop new equipment and tools to aid crystallisation. This willbe achieved by designing new and improved apparatus, based on the joint research results ofthe academic partners and the SMEs. These results will be made available to the communityby commercialising the apparatus and turning new techniques into crystallisation kits.Scientific coordinatorRoslyn BillAston UniversityDept. of Life and Health SciencesAston TriangleBirmingham B4 7ETUnited Kingdomr.m.bill@aston.ac.ukProject managerEric BourguignonAston UniversityDept. of Life and Health SciencesBirmingham, United Kingdome.bourguignon@aston.ac.ukPartnersNaomi ChayenImperial CollegeBiological Structure and FunctionBiomedical SciencesLondon, United KingdomPatrick Shaw StewartDouglas Instruments Ltd.Hungerford, United KingdomFlip HoedemaekerKey Drug Prototyping B.V.Amsterdam, The NetherlandsAnthony SavillMolecular Dimensions Ltd.Newmarket, United KingdomLea VaianaTriana Science & Technology S.L.Armilla, Granada, Spain| OptiCryst Kick-Off meeting at the DESY facility in Hamburg (March 2007).Rolf HilgenfeldInstitute of BiochemistryUniversity of LübeckLübeck, GermanyMarcus SwannFairfield Scientific LimitedCrewe, United KingdomJuan Manuel Garcia-RuizConsejo Superior De InvestigacionesCientificas (Csic)Laboratorio de Estudios CristalograficosPT Ciencias de la SaludArmilla, Granada, SpainChristian BetzelPLS Design GmbHHamburg, GermanyLena GustafsonGothia Yeast Solutions ABGothenburg, Sweden129

ACRONYMContract number: LSHM-CT-2007-037669 | EC contribution: € 2 170 000 | Duration: 36 monthsStarting date: 1 November 2006PHECOMPSUMMARYCompulsive disorders, including drugabuse and compulsive overeating, representprevalent neuropsychiatric diseasesthat have a large health andsocio-economic impact in the Europeanpopulation. These disorders are producedby an alteration of the capabilityto control seeking for reward, and seemlinked by common neurobiological substrates.However, there is an importantgap in the availability of reliable behaviouralmodels in animals that permit toinvestigate compulsion towards rewardin the perspective of human pathologies.The present proposal will use newsophisticated behavioural and neuroimagingtechniques for the characterisationof four new and complementaryanimal models of compulsive disorders,allowing to analyse precisely the maincomponents of those behavioural alterations.The study will be performed inmice and rats, including the transfer of ratmodels to mice when necessary. Thebehavioural and molecular characterisationof the models, along with parallelneuroimaging (PET), will provide a completeanatomical and functional illustrationof the reward pathways imbalance inthe above-mentioned pathological situations.Novel behavioural paradigms willbe proposed, tested and validated withinthe project, taking advantage of cuttingedgeimaging technologies. Molecularstudies will characterise changes inducedin several key elements of the reward circuitsduring these behavioural disorders.After the full characterisation of the models,they will be used on genetically modifiedmice for glucocorticoid receptors toascertain correlations between behaviouraland genetic components of compulsionin drug addiction and eatingdisorders. Hence, reliable and predictiveanimal models will be fully characterisedand employed to better understandthe mechanisms involved in those alterations,and to design new therapeuticstrategies in neuropsychiatric disordersrelated to compulsive behaviour.Phenotypical characterisation of animalmodels for neuropsychiatric disorders relatedto compulsive behaviourBackgroundBoth drug addiction and food intake disorders constituteincreasingly serious health care and socialproblems in the EU and are also responsible for theloss of millions of working hours every year.However, there is still a lack of suitable specific animalmodels to further elucidate the neurobiologicalsubstrate of such disorders. In this context,PHECOMP offers an impact in new animal modelsfor probing these and other related psychiatric disordersand compulsive behaviours.The present proposal is a multidisciplinary projectbringing together new and sophisticated behaviouralmethodologies as well as cutting-edgemolecular and imaging techniques which will beapplied to the phenotypical characterisation of targetedand refined animal models. The characterisationof new animal models and their transfer tomice when needed will allow the use of theserodent behavioural models for the study of thecompulsive components in addiction and relatedpsychiatric disorders.AimThere are three main aims of the specific-targetedresearch project:• deliver four phenotypically well-characterisedanimal models, namely the modified conflict, thedeprivation and the reinstatement models ofcompulsive drug intake, and the compulsivefood-seeking/-taking model, addressing differentcomponents of compulsion using rats andmice;• elucidate the role of selected gene activities andprotein receptors in the neurobiological mechanismsinvolved in compulsive disorders;• provide complete new structural and functionalillustration of the reward pathways imbalancefound in compulsion, using cutting-edge imagingtechniques (PET).The ultimate objective of this STREP Project isto provide new knowledge that can be used bythe participants, by other research groups or byEuropean pharmaceutical companies, in order todevelop new drugs for the treatment of both drugcraving and relapse, core features of the compulsivecomponents of addictive disorders, or for providingnew drugs for treating compulsive eatingleading to obesity and metabolic imbalance.Expected resultsThe neurobiological bases of compulsive behavioursshare common mechanisms, as drug-seekingor compulsive food intake promote activation andneuro-adaptations within the common neuronalnetworks. The general strategy of the project is,first, to carry out a complete phenotypical characterisationof four animal models, addressing differentcomponents of compulsive disorders thatare already being studied in partner laboratories,namely:• the modified conflict model (Dr. Piazza’s group atBordeaux);• the deprivation model (Dr. Spanagel’s group atMannheim);• the reinstatement model (Dr. Maldonado’s groupat Barcelona); and• the compulsive food-seeking/-taking model (Dr.Heyne’s group at Reutlingen).Those models will be transferred from rat to mousewhen needed (involving the former groups as wellas that of Dr. Dierssen at Barcelona). The proposalwill investigate selected genes and proteins(Dr. Przewlocka’s group at Krakow) which couldplay a role in compulsive-derived brain plasticityand its pathophysiological response. Moreover,the availability of specific feeding patterns evaluationtools (Dr. Célérier’s group at Cornellà) andthe set-up of potent neuroimaging technologiesadapted to small experimental animals (Dr. Millán’sgroup at Barcelona) will allow correlating anatomicfunctionalevents with behavioural and genetic paradigms.Finally, a mechanistically targeted-orientedarray of genetically modified mice (Dr. Tronche’sgroup in Paris) will be used to specifically addressthe elucidation at molecular level of the neurobiologicalbasis of compulsive disorders, i.e. the role ofglucocorticoid receptors.130

Key words: compulsive disorders, animal models, behavioural paradigms, Positron Emission Tomography (PET),drug abuse, eating disorders, glucocorticoid receptorsROLE OF SMEsThree SMEs, leaders in their fields, are crucial partners in PHECOMP and share 42 % of thebudget. The German company medimod will develop a set of novel tools for preclinical testingof compounds with putative anti-obesity efficacy. The Spanish manufacturer Panlabwill contribute with an array of technical and software solutions in the precise and accurateanalysis of the pattern of eating and drinking behaviours in rodents. Finally, the SpanishInstitute of Advanced Technologies (IAT) will apply current expertise and know-how toinnovation through adaptation of functional PET neuroimaging of small experimentalanimals to set up new techniques of imaging in mice. Their participation will enable theconsortium to carry out a complete phenotypical characterisation of selected animalmodels of compulsive disorders and their transfer from rat to mice when needed, as wellas a fruitful transfer of knowledge to the market.Scientific coordinatorRafael MaldonadoLaboratory of Neuropharmacology-NeuroPharUniversitat Pompeu FabraBarcelona Biomedical Research Parkc/Dr Aiguader 808003 Barcelona, Spainrafael.maldonado@upf.eduPartnersMara DierssenCentre for Genomic RegulationBarcelona Biomedical Research ParkBarcelona, SpainBarbara PrzewlockaInstitute of PharmacologyPolish Academy of scienceKrakow, PolandPotential applicationsThe optimisation of targeted animal models willrender them suitable for finding new treatmentapproaches for these compulsive disorders andready-to-use in pre-clinical research to testputative anti-obesity and anti-addictive compounds.It is recognised that both opioid,dopamine and cannabinoid systems play keyroles in regulating not only addiction but alsoother aspects of limbic and motor function. Thepotential for the use of these animals to investigateother CNS diseases as well as to developand test new pharmacotherapies is accordinglyvery high.Moreover, PHECOMP offers three SMEs, leadersin their fields, to take great advantage of participatingin a project at the European level, thusenabling the possible outputs of the project tofinally benefit the same (and other) SMEs, thusincreasing their know-how and commercial competitivenessin and outside Europe. In particular,at the end of the project, medimod (DE) will havea fully-operative food-seeking/food-taking modelin rat ready for the preclinical search for new pharmaco-therapeuticsolutions in food intake disorders.Also, IAT (ES) will develop and validate newPET built-in methodologies for neuroimaginganalysis of mice, correlated with behavioural andmolecular data. Finally, Panlab (ES) will set-upand validate specific devices that will improve thequality and efficiency of animal feeding patternsevaluation tools.Rainer SpanagelCentral Institute for Mental HealthMannheim, GermanyPier Vincenzo PiazzaINSERM u588Paris, FranceAndrea Heynemedimod pharmacology services GmbHReutlingen, Germanywww.medimod.com/welcome.htmlOlga MillánInstitut d’Alta TecnologiaBarcelona, Spainwww.iat-prbb.com/ingles/index.htmlFrançois TroncheCNRS (UMR 7148)Paris, FranceEvelyne CélérierPanlab SLUBarcelona, Spainwww.panlab.com| Alcohol sensitization and reward areinfluenced by circadian genes andrhythm (Abarca et al., Proc Natl AcadSci USA 99, 9026-30, 2002).131

ACRONYMContract number: LSHM-CT-2007-037765 |EC contribution: € 2 700 000 | Duration: 36 monthsStarting date: 1 January 2007PHOTOLYSISSUMMARYFlash photolysis is widely applied in cellphysiology to initiate neurotransmitterand other ligand-receptor interactions inconditions that are subject to poor diffusionalaccess and receptor desensitisation,and for ligands that are particularlylabile. It has the potential to initiate reactionson physiological time and spatialscales (sub-msec and sub-micron) in complextissues such as brain slices and invivo, and is often combined with electrophysiologyand optical imaging.However, this potential is unrealised in neuroscienceand medicine in several areas:• photolabile ‘cages’ optimised to makeuse of the localisation achievable withexcitation by the two-photon effect;• wavefront modulation of photolysislight to make z axis location and spot sizereadily changeable;• application in high-throughput screeningfor drug discovery of ligands acting atrapidly desensitising neurotransmitterreceptors in the brain.The PHOTOLYSIS consortium comprisesneuro physiologists, photochemists, opticalphysicists, specialists in high-throughputpatch clamp screening and ion channel targeteddrug discovery, to address theseareas. New photochemistry of cages combinedwith new pulsed lasers and newadaptive optics will optimise the efficiency,depth and location of photolysisin whole brain in vivo and in vitro.These developments will be combinedwith deep imaging to:• identify mediators and cell types in neurovascularcoupling of blood perfusionto neuronal activity;• applied to synaptic transmission to studypostsynaptic channels in situ, identifytheir role in synaptic plasticities; and• investigate the interactions betweenmetabotropic receptors and fast transmitterchannels;• finally, adapt near-UV flash photolysis topatch clamp HTS technology, in order tocharacterise drugs acting at fast activatingand desensitising neurotransmitterreceptors, to study the functional pharmacologyof genetically-linked channelopathies,and in developing somaticcell replacement therapies.Development of flash photolysis for deepuncaging in vivo and high-throughputcharacterisation of neurotransmitter gatedion channels in drug discoveryBackgroundExperimentally it is difficult to separate the contributionsof presynaptic and postsynaptic mechanismsto the efficiency and strength of asynapticconnection. The method of flash photolysis canprovide a way of determining the properties ofsynapses between neurones in situ that are currentlystudied only in recombinant receptors invitro, and would allow the testing of putativemediators of local vasoregulation in the brain.These applications of photolysis in neuroscienceare impeded by the poor photochemical propertiesand stability of caged neurotransmitters, bythe unavailability of many mediators in photo -labile caged form, and by the unsuitability ofpresent optical methods.Currently, high throughput screening methods tofind ligands acting at brain synapses use conventionalperfusion methods to apply the activatingneurotransmitter or analogue. These methods aretoo slow to activate receptors on a physiologicaltimescale because of diffusional access to the cellsurface, and for this reason, potential medicinesthat affect the degree of activation of synapsesand act in a use-dependent way will not be optimallydetected. The application of this method inhigh-throughput screening to test for new medicineshas the potential to detect use-dependentligands acting at the rapidly desensitising aminoacid receptors that mediate neuronal signalling.AimTo develop new photochemical probes and opticalmethods in localising and extending the rangeof photolysis for use in neuroscience; to adaptphotolysis to current parallel patch clamp methodsin the development of new medicines.Expected resultsImproved photochemical properties of probes,particularly making better use of the twophotoneffect for localisation and extending therange of synaptic and local messenger systemsto which the method can be applied. Improvedmethods in drug discovery of ligands active atbrain synapses. Specific therapeutic targetingof genetically linked channelopathies and applicationsin developing somatic cell replacementtherapies.Potential applicationsTo investigate neurotransmitter receptors in synaptictransmission in situ. To investigate mediatorsin neurovascular regulation. To improve methodsof deep imaging in vivo. To develop better drugsacting at synaptic receptors in the brain.132

Key words: photolysis, caged neurotransmitters, synaptic transmission, synaptic plasticity, neurovascular regulation,wave front engineering, optical imaging, high throughput screening, channelopathiesROLE OF SMEsThe three high-tech SMEs in the Photolysis project, Flyion, GeneCraft and Tocris-Cookson,will play three important roles. One is to further develop the library of caged neurotransmitterligands available to neuroscience researchers as probes in experiments to investigatesynaptic transmission and its modification in disease. The second is to develop theapplication of photolysis in drug discovery to improve the detection of ligands that act atfast-responding neurotransmitter receptors. This will be based on existing parallel patchclamp technology modified to introduce a light path for- irradiation with a pulse of near-UVlight to initiate photorelease of the neurotransmitter. Thirdly, through their connectionswithin the community of drug discovery and ion channel therapies, the SMEs will beeffective in translating the proven power of photolysis in investigating synaptic functionto the task of identifying potential drugs.The company Inserm Transfert takes care of the administrative project management.Scientific coordinatorDavid OgdenCNRS UMR 8118Physiologie CérébraleUniversité René Descartes Paris 545 Rue des Saints PeresF-75006 ParisFrancedavid.odgen@univ-paris5.frProject managerIsabelle GeahelInserm-TransfertParis, Franceisabelle.geahel@inserm-transfer.frwww.inserm-transfert.frPartnersSerge CharpakInstitut National de la Santéet de la Recherche MédicalINSERM FR 101Paris, FranceGail McConnellJohn GirkinUniversity of StrathclydeGlasgow, United KingdomMichael FejtFlyion GmbHTubingen, Germanywww.flyion.comDuncan CrawfordTocris-Cookson Ltd.Bristol, United Kingdomwww.tocris.com/UKLadislav VyklyckyDept. of Cellular NeurophysiologyInstitute of PhysiologyPraha, Czech RepublicYair FeldGeneGraftIsrael133

ACRONYMContract number: LSHP-CT-2006-037587 |EC contribution: € 2 079 016 | Duration: 36 monthsStarting date: 1 December 2006PlasmodiumdUTPaseSUMMARYThere are around 500 million clinicalcases of malaria each year and about1-2 million people die from this debilitatingdisease. There is an urgent need forthe development of new drugs becauseof drug resistance issues. New drugsshould have novel mechanisms of actionto prevent cross-resistance with existingdrugs. Some novels, drug-like and selectiveinhibitors of the enzyme deoxyuridinetriphosphate nucleotidohydrolase(dUTPase) from Plasmodium falciparum,the causative agent of malaria have beendiscovered. The role of this enzyme is tohydrolyse dUTP to dUMP, maintaininga low dUTP:dTTP ratio. The aim of thisproject is to optimise these early leadmolecules to generate late-stage leadsor preclinical drug candidates.The project will include:• medicinal chemistry activities for thepreparation and optimisation of leadcompounds;• ADME-Tox assays to ensure that thecompounds have correct ‘drug-like’properties;• biological evaluation to determine theefficacy of the compounds;• mode of action studies;• crystallography of inhibitors with theenzyme active site to assist in the drugdesign process.Deoxyuridine triphosphate nucleotidohydrolaseas a drug target against MalariaBackgroundAs part of a Framework 5 programme (QLRT-2001-00305), the project team discovered a novel classof inhibitors, which selectively inhibit dUTPaseform Plasmodium falciparum, the causative agentof malaria.AimThe aim is to optimise these early lead moleculesin order to generate advanced leads or preclinicaldrug candidates.Expected resultsThe expected results are compounds that areadvanced leads or preclinical drug candidates forthe treatment of malaria.Potential applicationsThe potential applications of outputs of this projectare compounds, which could go through topreclinical development for the treatment ofmalaria and if successful proceed to clinical trials.134

Key words: Malaria, drug discoveryROLE OF SMEsThis project is an exciting collaboration between an SME, the Swedish Pharmaceuticalcompany Medivir AB and 4 academic institutions. The group has characterized theenzyme deoxyuridine triphosphate nucleotidohydrolase (dUTPase) from the protozoanparasite Plasmodium falciparum, which causes malaria, in an approach to develop novelantimalarials. The project is a drug discovery project focusing on the optimization anddevelopment of inhibitors of this promising new malaria drug target. Medivir is able tobring its considerable experience in drug discovery to the project. Medivir is driving theproject towards a preclinical Candidate Drug status and carries a major part of the projectwork, including the synthesis of compounds and provision of a large compound libraryfor testing as potential inhibitors of dUTPase. For this strong Swedish drug developmentSME, the development of an antimalarial drug targeting dUTPase, may in addition constitutea proof of principle for dUTPase as a drug target for treatment of also other diseases.Scientific coordinatorIan GilbertSchool of Life SciencesUniversity of DundeeMSI/WTB/CIR ComplexDow StreetDundee DD1 5EHUnited Kingdomi.h.gilbert@dundee.ac.ukwww.dundee.ac.ukPartnersNils Gunnar JohanssonMedivir ABHuddinge, Swedenwww.medivir.seDolores González PacanowskaInstituto de Parasitologíay Biomedicina “López-Neyra”Consejo Superiorde Investigaciones CientíficasArmilla, Granada, Spainwww.ipb.csic.esKeith WilsonUniversity of YorkDepartment of ChemistryStructure Biology LaboratoryHeslington, United Kingdomwww.york.ac.ukReto BrunSwiss Tropical InstituteParasite ChemotherapyBasel, Switzerlandwww.sti.ch© Shutterstock135

ACRONYMContract number: LSHB-CT-2007-037933 | EC contribution: € 2 497 815 | Duration: 36 monthsStarting date: 2 January 2007POC4lifewww.poc4life.euSUMMARYThis project aims to improve the healthcareof patients by elaborating a uniquePOC diagnosis platform which will helpspecialists to deliver an earlier diagnosisand to decide on appropriate treatment.The goal is to provide the clinicians withmultiparametric measurement of themain 4/5 essential markers and to supportdecision with a software tool. Thiswill be a cost-effective breakthrough inthe diagnosis market.Multiparametric quantum dot bioassayfor point of care diagnosisBackgroundEach year 377 000 new European citizens developlung cancer and 340 000 die from it. Studies showthat early diagnosis and accurate cancer typingcould save a number of lives. Laboratories nowadayshave a wide panel of reproducible diagnostictests at their disposal: these are mostly routinetests realised in centralised laboratories. Theneeds for early diagnosis, multiparametric analysisof results and quick monitoring of diseaseprogression or therapeutic sensitivity were progressivelyleft aside, whereas they could be fulfilledwith using decentralised diagnostic tools,close to the patient.Among the possible applications of this new concept,the partners have chosen to work on the primarydiagnosis of the histological types of lungcancer to help to give an improved initial diagnosisand to eliminate the 15-20 % problematic orlate diagnosed cases. The study will pay specialcare to women (lung cancer death rates forwomen have been still increasing in Europe sincethe 1990s and marker patterns may be different).It will then have a huge impact on health by contributingto the fight against cancer and the developmentof gender dimension in research. For thispurpose, the multidisciplinary project will involveacademic researchers (from Germany, Spain andFrance) and SMEs (from Sweden and the UK) gatheringaround the initiators of the project (the SMECEZANNE, the University of Strasbourg in Franceand the University of Potsdam in Germany) whichhave the skills to build a multiparametric device,to develop immunoassays and to design an interpretationsoftware.AimObjective 1: Elaborate an innovative medicaldevice: a unique point of care diagnosis platformwhich will help specialists to make earlier diagnosisand provide more appropriate treatments.Objective 2: Provide the best possible integrationof parameters by means of a consortium composedof public and private partners such asresearch intensive SMEs and academic entitiesEurope-wide.Objective 3: Elaborate the new device for a specificapplication: the primary diagnosis of the differenttypes of lung cancer. The project will thenhave a huge impact on health by contributing tothe fight against cancer and the development ofgender dimension in research.The objective of the project is to generalise thisapproach to combinations of immuno-assaymeasurements to deliver a clear diagnosis of thedisease or monitoring information. The generalisationmeans first that the diagnosis should beaccessible to various types of medical practices(medical doctor to hospitals) and thus a low cost,easy to use ‘Point of Care’ (POC) device shouldbe developed. However, this should not bedone to the detriment of quality and precision.A homogeneous technology known for high levelprecision can therefore be a judicious choice.Generalisation also means that various pathologiescould be addressed: typically from 2 to 4 or 5immuno-assays. The project therefore aims toallow the simultaneous measurement of 4 to 5immuno-assays on the POC device with one drawof patient sample (1 droplet). Finally, generalisationmeans universality of the measurement techniqueand of the data reduction process. In thisway, fluorescent measurement based on FRET(Fluorescence Resonance Energy Transfer) seemsan excellent choice, since it may be extendedin the future to other diagnostics such as DNAanalysis, coagulation, microbiology etc.136

Key words: lung cancer, point of care, quantum dots, uv light source, flash lamp, fluorescence, immuno-diagnosis,multiparameter, blood separation, expert system, molecule coupling, luminescent tagsROLE OF SMEsThe SMEs will bring to the consortium the complementary and comprehensive expertiserequired by the other public researchers.CEZANNE S.A. brings competence in two complementary scientific and technical fields:immuno-assay development and scientific instrumentation, which over the years CEZAmanaged efficiently to cross-fertilise.FUJIREBIO DIAGNOSTICS brings competence related to antibody development andcharac terisation (hybridoma technology, phage display, gene expression analysis, c-DNAimmunisation, DNA-shuffling, affinity maturation) and competence in assay development.EDINBURGH INSTRUMENTS brings experience in flash lamps, laser diodes, fluorescencespectrometry and a prototype nanosecond plate reader.Scientific coordinatorEmmanuel BoisCezanne SAS280 allée Graham BellParc Scientifique Georges Besse30035 Nîmes cedex 1Francecontact@cezanne.frwww.cezanne.frPartnersOlle NilssonFujirebio DiagnosticsGöteborg, SwedenDesmond SmithEdinburgh Instruments2 LivingstonScotland, United KingdomExpected resultsThe project should attain the following challengingobjectives:• develop a functional prototype of POC multiparametricmeasurement for immuno assays,based on Homogeneous Time Resolved Fluores -cence (HTRF), for which main characteristics are:equivalent to an A4 sheet of paper, cost of lessthan EUR 2 000, works with a sample dropletdeposited on a disposable reagent vessel containingdried reagents;• define the panel of assays and how to combinethem into a decision making software (to bedeveloped).Potential applicationsMultiparametric diagnostics in the followingfields:• cancer;• prenatal diagnostics;• sepsis;• cardiac.Philippe PieriCentre National de la RechercheScientifiqueParis, FranceHans-Gerd LöhmannsröbenUniversity Of PotsdamInstitut für Chemie und InterdisziplinäresZentrum für PhotonikPotsdam – Golm, GermanyYves CaristanCommissariat à l’Énergie AtomiqueGrenoble, FranceKlaus-Dieter WeltmannEckhard KindelInstitute Of Low TemperaturePlasma PhysicsGreifswald, GermanyRafael MolinaHospital Clinic BarcelonaLaboratory of BiochemistryHospital Clinic CBarcelona, SpainPetra StieberInstitute For Clinical ChemistryUniversity Hospital Munich-GrosshadernMunich, Germany© Shutterstock137

ACRONYMContract number: LSHP-CT-2006-037494 | EC contribution: € 2 345 358 |Duration: 36 monthsStarting date: 1 December 2006PRIBOMALSUMMARYMalaria is one of the major public healthchallenges in the world, causing morethan one million deaths each year. Thedisease primarily affects children of thedeveloping world. The available measures,such as personal protection ordrugs, have proven to be insufficient tocontrol the disease. A safe, affordableand efficacious paediatric malaria vaccine,which fits in the existing WHOExpanded Programme on Immunisation,would alleviate tremendous suffering inhuman kind.Taking up this challenge, the PRIBOMALconsortium proposes to generate and testin preclinical models the safety and efficacyof an innovative malaria vaccine. Thevaccine consists of a prime, to be administeredat birth, of a novel recombinant BCGvector carrying preferentially multipleantigens derived from the Plasmodiumfalciparum parasite, the cause of malaria.The priming vaccine is followed at week 14after birth by a booster vaccination usingindustrially developed, recombinant adenoviralvector carrying the identicalPlasmodium falciparum antigens as therBCG-based malaria vaccine.Generation of these novel vaccine candidates,as well as testing in establishedand novel pre-clinical models to determinepotency and safety, requires a combinedEuropean effort to bring togetherthe required expertise on basic parasitebiology, malaria epidemiology, diseaseonset and progression, recombinant vectortechnology, fundamental immunology,advanced animal models, andsophisticated proteomics. The internationalPRIBOMAL consor tium bundles allrequired experience and as such is wellpositioned to successfully conduct thisresearch programme.Preclinical studies towards an affordable,safe and efficacious two-component paediatricMalaria vaccineBackgroundIt is estimated that more than 300 million individualssuffer from acute disease caused by themalaria parasite and that more than 1 million peoplesuccumb to this disease each year. Malaria,which is highly endemic in sub-Saharan Africa,claims its victims predominantly among childrenwith the peak incidence of clinical malaria and90 % of malaria deaths in children younger than5 years.The challenge faced by the PRIBOMAL consortiumis to design a safe, affordable paediatric malariavaccine that provides long lasting protectionagainst malaria and that fits within the existingWHO Expanded Programme on Immunisation (EPI)so as not to further complicate operational vaccinationlogistics. The first vaccination that childrenwould receive is at birth with Bacille Calmette-Guérin (BCG) a live and attenuated strain ofMycobacterium bovis, which is currently the onlyavailable vaccine against tuberculosis. BCG hasbeen globally used as the TB vaccine for decadesand has proven to be safe in hundreds of millionsof children. In recent years BCG receives additionalattention as a potential vaccine vehicle.The PRIBOMAL consortium considers that abooster immunisation will be required to achievelong-lasting protection. Therefore, a choice wasmade to boost the rBCG.malaria vaccine, given atbirth either alone or in addition to classical BCG,with a recombinant adenoviral vector, carryingthe identical P. falciparum derived antigens, at14 weeks after birth, thus compliant with WHO EPIschedule. Like rBCG, replication deficient adenoviralvector has an excellent safety record withtens of thousands of patients receiving recombinantadenoviral vectors in diverse gene therapyand vaccination trials without adverse effects.To ultimately eradicate malaria disease hundredsof millions of vaccine dosages will need to bemanufactured at low cost per dose, given thatcountries in sub-Saharan Africa do not have theeconomic means to purchase expensive vaccines.The manufacture of rBCG follows the exact sameprotocols and procedures as established for BCGand guarantees that sufficient doses of rBCGmalaria vaccine can be manufactured at a priceper dose similar to BCG. Consortium memberCrucell has extensive expertise in adenoviralvaccine manufacturing, employing a mammaliancell line, coded PER.C6 ® , which can be culturedin suspension in large volumes. Therefore, thePRIMOBAL consortium members consider the proposedtwo-component paediatric malaria vaccineto be affordable, thus applicable in developingcountries such as sub-Saharan Africa.AimTo demonstrate feasibility (safety and efficacy) inpreclinical studies of a novel, affordable, twocomponent,paediatric malaria vaccine.Expected resultsThe ultimate deliverable of this programme is anefficacious paediatric malaria vaccine candidatethat will eventually be advanced to GMP developmentand clinical trials. Besides reaching this aim,the consortium expects that during the executionof this programme extensive knowledge will begathered regarding immunological features ofdifferent vaccination schedules, in combinationwith information on their protective ability. Thisinformation will help elucidate correlates of protectionand facilitate rational design of futuremalaria vaccines.Potential applicationsIt can be envisioned that vaccines against otherdisease such as for instance HIV, TB or even cancervaccine development can directly benefitfrom the PRIBOMAL research. Like malaria thesediseases are considered to require vaccinesthat elicit strong humoral and cellular immuneresponses against a broad range of epitopes.138

Key words: Malaria, rBCG, rAd35, paediatric vaccineROLE OF SMEsThis project forms part of a wider effort by the coordinating Dutch biotech SME Crucell todevelop a malaria vaccine based on several pre-erythrocytic antigens presented bya BCG/adenovirus-based prime-boost approach. This FP6-funded project contributes tothe preclinical testing of this approach in three different animal models, which involvesa number of European partner groups and thus requires support at European level.Crucell’s role in the project is very strong, with a large work-share in the generation of thecandidate product but also in all other work packages, underpinning the importance ofthe project for this SME-based European vaccine development project.Scientific coordinatorJaap GoudsmitCrucell Holland B.V.Archimedesweg 4PO Box 20482301 CA Leiden, The Netherlandsj.goudsmit@crucell.comwww.crucell.comPartnersStefan H.E. KaufmannMax Planck Institutefor Infection BiologyBerlin, Germanywww.mpiib-berlin.mpg.deLeif LindforsStockholm UniversityDepartment of ImmunologyStockholm, Swedenwww.wgi.su.seTom Van der PollAcademic Medical CentreUniversity of AmsterdamLaboratory of ExperimentalInternal MedicineAmsterdam, The Netherlandswww.amc.uva.nlRonald BontropBiomedical Primate Research CentreRijswijk, The Netherlandswww.bprc.nl© Shutterstock139

ACRONYMContract number: LSHB-CT-2007-037740 | EC contribution: € 2 200 000 |Duration: 36 monthsPRISMStarting date: 1 March 2007SUMMARYIn this specific targeted research project,cutting-edge nuclear magnetic resonance(NMR) techniques are used to developa sensitive, rapid and integrated approachto understanding the mechanisms of lipidbinding proteins. The project will generaliseand accelerate the efforts to characterisea range of peripheral membraneproteins, thus providing new insight intoan important class of proteins which playa key role in regulating complex cellularpathways. Model membranes will betested to mimic various types of cellularmembranes for selected protein moduleswhich will be prepared by specificadvanced tailored protein expressionmethods. The generation of lipid librarieswill allow definition of membrane specificity,and spin labels and micelle-formingcompounds will facilitate the measurementof the angles and depths ofbilayer insertion. These advances in NMRmethodology will be complemented bynew computer modelling approaches formicelle:protein complexes. Predictiveprinciples of membrane insertion will beused to model membrane orientations ofstructures of proteins. To demonstratethe impact for endocytosis, exocytosisand signal transduction, the protocolsand products will be developed andtested using the signalling domains andmodules involved in the trafficking ofmembranes and modification of lipids.Phospholipid and glycolipid recognition,interactions and structures by magnetic resonanceBackgroundLipids and the proteins that bind them are of significantsocietal value and medical importancedue to their central roles in health and disease,and their relevance to the discovery of novel therapeuticagents. Phospholipids such as phosphoinositidesand sphingolipids have crucial rolesboth in cancer development and progression.They act as bioactive lipid mediators, affectingfundamental cellular functions which include proliferation,differentiation, survival, migration,adhesion, invasion, and morphogenesis. Thesefunctions influence many biological processesincluding neurogenesis, angiogenesis, woundhealing, immunity, and carcinogenesis. While initialdiscoveries on lipid binding domains havespurred interest among structural biologists, littleis known about the precise control or specificity ofmembrane insertion and recognition. This projectwill therefore have effects on public health by aidingin the design of new types of agents that bindto membrane interaction sites and provides newavenues to modulate target protein activities.AimPrism project main objectives are:• test and validate model micelle systems tomimic properties of cellular membranes forresearch of membrane-associated proteins;• develop molecular screening methods in orderto define lipid/micelle specificity profiles ofprotein modules;• apply dynamic nuclear polarization methodsand paramagnetic spin label studies for themeasurement of lipids and protein interactions;• design, express and screen novel tags andlipid binding domains involved in membranetrafficking and signalling;• test and evaluate new computer modellingapproaches for membrane:protein complexes.Expected resultsThe expected goals of this project are the developmentand dissemination of biophysical toolsand structural models for protein membraneinteractions that can be used by other researchersin an industrial or academic environment. Thespecific results include:• tools for studying protein phospholipid interactions;• NMR techniques using tags and DNP;• efficient preparation of membrane proteinsand intracellular probes;• protocols for the preparation of membranemodels and lipid systems; and• new insights into protein-lipid interactions anddynamics.Potential applicationsThe proposed research will be focussed ona selection of model proteins and membranetypes to achieve realistic goals. However, theresults of this project will be of wider importancedue to the provision of basic answers which canlater be applied to other members of the sameclass of proteins, and general physico-chemicalprinciples can be extrapolated to other lipid interactingproteins. Broad applicability is guaranteedby the fact that approximately a third of the proteomeand half of the known drug targets aremembrane-associated proteins. The tools andresults will be used by researchers interested inmembrane-associated proteins, lipidomics, functionaland structural genomics, biophysical techniquesincluding NMR spectroscopy and DNPapplications, and groups interested in membranebiology and signalling mechanisms.140

Key words: membrane protein, signal transduction, phospholipid, glycolipid, NMR spectroscopy, dynamic nuclear polarization,structural biologyROLE OF SMEsThe PRISM project includes two SME partners. Oxford Instruments Molecular Biotools Ltd.(OIMBL) offers advanced scientific instrumentation and expert knowledge for biomolecularanalysis. HyperSense is OIMBL’s groundbreaking dynamic nuclear polarisation (DNP)polarizer which is capable of amplifying the NMR signal to noise ratio by a factor of up to10 000. This instrument is the first commercial DNP system, and has been installed atHWB•NMR. This project provides PRISM with access to DNP-NMR technology for the studyof proteins and lipids.ProtaMAX Ltd. offers bespoke mutagenesis, custom randomisation of protein sequences,and efficient saturation mutagenesis to produce DNA libraries and designer proteins includingbiopharmaceuticals. ProtaMAX Platform Technology allows encoding of selected or fullyrandomised amino acids, for example, within binding site residues of a protein structure.The technology was invented and patented at the University of Aston, UK, and is availableto PRISM researchers to obtain and screen for novel protein probes and tags.Scientific coordinatorMichael OverduinUniversity of BirminghamEdgbaston, Birmingham, B15 2TTUnited Kingdomm.overduin@bham.ac.ukwww.nmr.bham.ac.ukPartnersHarald SchwalbeJohann Wolfgang Goethe-UniversityBMRZ-Center for BiomolecularMagnetic ResonanceFrankfurt, GermanyKai SimonsMax Planck Institute of MolecularCell Biology and GeneticsDresden, GermanyJean GruenbergUniversité de GenèveFaculté des SciencesDépartement de BiochimieGeneva, SwitzerlandGerrit van MeerUtrecht UniversityUtrecht, The NetherlandsAndrew SowerbyOxford Instruments MolecularBiotools Ltd.Oxfordshire, United Kingdomwww.oxford-instruments.co.uk/wps/wcm/connect/Oxford+Instruments/Internet/HomeJohn SlackProtaMAX Ltd.Birmingham, United Kingdomwww.protamax.com141

ACRONYMContract number: LSHB-CT-2006-036813 | EC contribution: € 2 540 651 | Duration: 36 monthsStarting date: 1 November 2006PROLIGENproligen.euSUMMARYPROLIGEN aims to enhance the endogenousregenerative capacity of injuredkidneys based on information derivedfrom genomics/proteomics and functionalgenomics. The approach of PROLIGEN is:• to define and identify set of genes/proteinsassociated with functional recoveryfrom renal injury;• to build up high throughput test systemsto follow the basic biologicalprocess involved in regeneration and touse these read out systems for functionalgenomics; and• to develop biologicals and cell basedtherapy to foster proliferation.Currently, studies are focused on evaluatingsingle factors as growth factors orstem cell therapy. The project proposes toenhance regeneration by knowing howthe genes/proteins that determine differentsteps in kidney regeneration arerelated, and how these settings can beinfluenced to improve regeneration. Then,the project will provide new therapeutictools able to promote recovery from acuterenal failure (ARF) based on functionalgenomic studies and cell therapy.Hypoxic renal proliferationBackgroundPROLIGEN differs from previous approaches inthat it splits the regeneration process into thedifferent main biological process (apoptosis, formationof pro- versus anti-inflammatory mediators/macrophagephenotype and cell proliferation),and aims to study regeneration as the result of theirinterdependence. The project takes into accountthat macrophages are at the centre of a complexregulatory network receiving and distributingsignals from and to all biological process, thusaffecting recovery. At variance with previous studiesparticularly focus is not only on the identificationof markers relevant for regeneration ratherthan the use of functional genomic technologywhich provide a new network of gene function andnew platforms to deliver a new cellular basedtherapy strategy.AimExpected results• Provide new therapeutic tools able to promoterecovery from acute renal failure (ARF).• Gain insight into principles of the regeneration.• Provide the conceptual basis for the developmentof new therapeutic strategies.Potential applicationsThe resulting gene function and new cell therapyinformation may provide the PROLIGEN consortiumthe necessary tools to deliver new biologicalsand cell-based therapies for kidney regeneration.Potential applications of the generated know -ledge to improve the regeneration in other tissuesavoiding the use of stem cells may also result.PROLIGEN aims to enhance the endogenousregenerative capacity of injured kidneys based oninformation derived from genomics/proteomicsand functional genomics.142

Key words: acute renal filure, regenerative medicine, kidney regeneration, functional genomics, genomics,proteomics, macrophage therapyROLE OF SMEsThe PROLIGEN consortium brings together selected academics, clinitians and industryexperts. Three SMEs play key roles in the research activities of the project, namelyGalapagos NV provides its expertise on functional genomics, Genedata AG takes care ofbioinformatics and ProtEra s.r.l. contributes to protein synthesis.Scientific coordinatorGeorgina HotterInstituto de InvestigacionesBiomédicas de BarcelonaConsejo Superior de InvestigacionesCientíficas (IIBB-CSIC)Rosellon 16108036 Barcelona, Spainghcbam@iibb.csic.eswww.csic.esPartnersBernhard BrüneUniversity of Frankfurt – Medical SchoolFrankfurt, Germanywww.uni-frankfurt.deJoan TorrasFundació Privada Institut d’InvestigacióBiomèdica de BellvitgeLab.4122 Experimental NephrologyL’Hospitalet de LlobregatBarcelona, Spainwww.csub.scs.esBob. v.d. WaterLeiden/Amsterdam Centerfor Drug ResearchLeiden UniversityLeiden, The Netherlandswww.leiden.eduJochen KoenigGenedata AGBasel, Switzerlandwww.genedata.com| PROLIGEN aims to enhancethe endogenous regenerativecapacity of injured kidneysbased on information derivedfrom genomics/proteomicsand functional genomics.Richard JanssenGalapagos NVLeiden, The Netherlandswww.glpg.comRebecca del ConteProtERA s.r.l.Sesto FiorentinoFirenze, Italywww.protera.it143

ACRONYMContract number: LSHB-CT-2006-037293 | EC contribution: € 1 492 500 | Duration: 24 monthsStarting date: 1 September 2006QuAGSICwww.uni-ulm.de/quagsic/index.phpSUMMARYThe partners will develop methods andinstruments to analyse the copy numberof nucleic acid sequences down to the singlecell/single molecule level, with thegoal of developing an early diagnosis systemfor a children’s disease, namely hemophagocyticlymphohistiocytosis (HLH).The underlying technique is amplificationbased counting (ABC), which enablesresearchers to quantify the copy numberof genetic sequences with a resolutionof about 100 base pairs in single cells.The method provides a resolution whichis of a magnitude higher than that ofFluorescence In Situ Hybridisation, andworks quantitatively with much lowersample amounts than quantitative PCR. Toprove ABC’s effectiveness for clinical applications,the partners will develop a singlecell manipulation unit that picks cells froma solution and transfers them onto anintegrated PCR and hybridisation slide(AmpliGrid). The AmpliGrid contains driedonPCR reagents, as well as hybridisationprobes to detect the presence and specificityof the PCR products. The single cellson the AmpliGrid will then be processedautomatically in an integrated PCR andhybridisation machine (AmpliHyb). Clinicalsamples will be investigated, in whichcopy number deviations are pathologic asin genetic diseases. As a model system,QuAGSiC chose HLH which is hard todiagnose and fatal without specific therapeuticmeasures, as well as trisomy 21,which is relevant in prenatal and postnataldiagnostics.Quantitative analysis of genes in single cellsBackgroundMany basic questions in Biology and Medicinedemand methods for the analysis of the basic unitof life, the single cell. The partners will thusdevelop methods and instruments to analyse thegenetic content of single cells, with regard toquantitative variation of sequences (copy numbervariations), as well as qualitative variation ofsequences (single nucleotide polymorphisms).AimShortly after the end of the project, QuAGSiC willput on the market machines and consumablesthat allow gene measurements down to the singlecell level with high precision, in a parallel format(an Ampligrid can accommodate 48 cells), witha high amount of automation.Expected resultsBy the end of the project the partners will be ina position to quickly market systems which allowgene analysis at the single cell level at low cost,with high speed, reliability and throughput.Potential applicationsThe technologies developed demand a minimumamount of material to be analysed. Withoutdoubt, the single cell is the basic entity of a livingorganism (or it is even the whole organism).Therefore, applying the methods mentionedabove to single cells is not only a technologicalchallenge but it is also the major important taskin system biology over the coming years, particularlyto be able to address medical diagnosticsin the regime of single cells. Single cell analysisbecomes more and more attractive because of limitedcell population of interest, cell heterogeneityof samples, or when cells are isolated automaticallyas early dissemination of tumour cells.It is hoped that the project’s efforts will developbreakthrough analytic tools and systems for prevention,diagnosis, or monitoring of a broad rangeof diseases.144

Key words: single cell analysis, hybridization, amplification based counting, AmpliGridROLE OF SMEsThe three SMEs in the project have central roles:• MMI (Molecular Machines & Industries) is developing an automated cell picker from itssemi-automatic two dimensional cell selection tool, capillary based cell handling system,to a fully automated three dimensional cell finding and sorting system (cellector 3D).• Adavlytix is using its photolithographically structured microscope slide AmpliGrid thatis suitable for performing 48 different 1μl PCR reactions on the same substrate. Thespecial AmpliGrid surface chemistry will be used to define a physical platform for theintegrated PCR and hybridisation at the single cell level.• Genewave is developing an integrated system which will allow both the PCR and opticaldetection of hybridisation in an unsupervised single machine.Scientific coordinatorClaude WeisbuchGenewave SASXTEC – Bâtiment 404École Polytechnique91128 PalaiseauFranceclaude.weisbuch@polytechnique.frwww.genewave.comPartnersWolfgang MannAdvalytix AGMünchen, Germanywww.advalytix.deStefan NiehrenMolecular Machines& Industries AG (MMI)Glattbrugg, Switzerlandwww.molecular-machines.comAndres MetspaluEstonian BiocentreTartu, Estoniawww.ebc.eeMarion SchneiderClinical Centre,University of UlmUlm, Germanywww.uni-ulm.de| Imaging of an Ampligrid.145

ACRONYMContract number: LSHM-CT-2006-037846 | EC contribution: € 3 400 000 |Duration: 36 monthsStarting date: 1 January 2007RATstreamwww.ratstream.euSUMMARYThe RATstream Consortium will concentrateon the comprehensive phenotypicalcharacterisation of rat models of neurodegenerativediseases such as Huntington’sdisease (HD), Parkinson’s disease (PD) andspinocerebellar ataxia type 17 (SCA17).Ultimately, the project will deliver a procedurefor low-cost automated drug screeningalong with a set of data describing thephenotype for each of the models.To achieve this goal, automated home cagesystems for behavioural and physiologicalphenotyping will be developed by twoSMEs and validated independently by twoacademic partners, and individual data willbe incorporated into an integrated databasedeveloped by a third SME. In a jointeffort, the groups will develop a comprehensiveset of behavioural and physiologicalphenotyping procedures, including PETand DTI technologies, in order to detectsystematically neuropsychiatric correlatesof neuronal dysfunction and disease progressionin rat models of HD, PD, andSCA17. The resulting set of biomarkers willlead to a valid set of minimised experimentsand markers best suited to provideread-out parameters in pre-clinical studiesapplying novel substances delaying orpreventing neurodegeneration.European project on the characterisationof transgenic rat models for neurodegenerativeand psychiatric diseases: Automated home cageanalyses, live imaging and treatmentBackground/AimRATstream is an ambitious European projectthat aims to characterise and use three transgenicrat models of neurological diseases which – inhumans – present with a wide range of neurologicaland psychiatric phenotypes:• transgenic rat model of HD ( 1 );• transgenic rat model of PD overexpressingalpha-Synuclein with the A30P mutation; and• transgenic rat model of SCA17 with 64 expandedCAG repeats in the TATA binding protein. Suchtransgenic rat models are unique worldwide.The project aims to pursue a completely novelgene-to-function approach resulting in a comprehensivephenotyping process which will comprisethe following components:• classical phenotyping;• monitoring of behavioural and physiologicalperformance in fully automated physiologicaland behavioural home cage test systems;• non-invasive imaging technologies which havebeen adapted to small animals;• neuropathology;• microarray analysis.The project will apply this approach to all rat modelsin order to achieve comprehensive high-qualitycharacterisation of models.Two members of the consortium (TSE, New -Behavior) aim to develop automated home cagetest systems for rat models which do not exist yet,but which are imperative in view of the upcominglarge number of transgenic rat models in both industryand academia. Collaboration with the academicpartners FAU and Uni Tübingen will provide an optimalenvironment for development and refinementof home cages which are validated via correlationwith data from classical read-outs and by crosscomparison between two experienced academicpartners. Cage systems will be suitable for continuousmonitoring of spontaneous, social, cognitive,emotional and physiological measures(drinking, feeding, metabolic performance/calorime -try, telemetry for temperature and biopotentials) inhome-cage-like environments for rats.This phenotyping set up (1-5) will be used todevelop a minimised and essential set of biomarkers,in order to monitor disease progressionreliably in the transgenic rat models of PD, HD,and SCA17. Phenotype data are also correlated toneuropathological features such as protein aggregates,neuronal cell loss, and neurotransmitteralteration at different disease stages. The phenotypingapproach will be used to characterise foreach disease model a minimised set of markersbest suited as read-outs in pre-clinical studies,applying novel compounds delaying or preventingneurodegeneration.The objective of this project will be to provide theproof-of-principle that it is possible in the rat:• to develop, validate, and use standardised automatedhome cage systems, and to adapt in vivoimaging techniques for phenotyping neurologicaland cognitive function (1 st year);• to harvest large data sets on gene functions andcorresponding phenotypes thereof (2 nd year);• to determine and validate a minimised set ofpredictive parameters (2 nd year) and experimentsas well as of appropriate time slots foreach rat model (low-cost approach); and• to develop and apply specific quality standardsapplicable for phenotyping tools and models(over the entire project duration);• furthermore, these rat models will be usedto scrutinise novel experimental, pre-clinicaltreatments (year 1-3), chiefly with regard toeffectiveness, side-effects, applicability, andtransferability.Expected results• Validated novel automated behavioural andphysiological test systems.• Behavioural markers derived from correlationanalysis of data from automated and classicalscreening for transgenic rats.• Data on MRI (DTI), PET and Microarray expressionprofiling as regards disease progression intransgenic rats.146

Key words: brain research, neurodegeneration, transgenic animal models, comprehensive phenotyping,automated behavioral phenotyping, in vivo imaging, pre-clinical treatment studiesROLE OF SMEsFour SMEs, sharing 30% of the project’s research budget, play key roles in the project. TSESystems, based in Bad Homburg, Germany and New Behavior, based in Zurich, Switzerland,develop cage systems for automated screening for behavioural, cognitive and physiologicalmalfunctions of transgenic rat models. The aim is to identify minimal parameter sets as regardsnumber of treated animals, study time and number of parameters to be applied in preclinicaltreatment studies. Those systems will be validated against classical methods of screening byacademic partners of the consortium. Trophos S.A., a French biopharmaceutical company, specialisingin the discovery and development of drugs for neurodegenerative diseases optimisestwo promising drug candidates for preclinical studies and develops respective analyticalmethods. CrossLinks, a spin-off company of the Department of Bioinformatics of theErasmus University Medical Center in Rotterdam, develops, adjusts, implements and hostsa data collection, storage and analysis system to support high-throughput (HTP) data collectedfrom automated cages, genomics data and imaging data. One of the crucial aims is thecalculation of the minimised sets of parameters and markers best suited for treatment studies.• Full scale phenotyping data for tg rats.• Standardised progression features of tg rats.• Minimised parameter sets for pre-clinical trialsin transgenic rat models.• Power calculation for pre-clinical trials.• Pharmocokinetic and toxicity data for compoundsto be applied in pre-clinical trials.• Study reports on preclinical trials.• Data base for phenotyping and treatment studiesof transgenic rats.Potential applicationsThe commercial impact of the project can be estimatedexplicitly for the two SMEs engaged in developmentof automated home cage test systems.NewBehavior expects a growing share (10-25%) inthe market for rat behavioural equipment, estimatedto be about €5 million per annum in Europeand € 15 million worldwide. TSE expects, in 2008,a share in Europe worth € 1.5 million and, for therest of the world, worth €0.15 million. In 2009, thisis expected to increase up to € 3.75 million inEurope and € 1.8 million in the rest of the worldrespectively. While the market itself is not large incomparison with other fields of biotechnology, onecan expect sustainability over a long period, sinceautomated home-cage testing systems will graduallyreplace existing rat testing equipment in everyuniversity and larger pharmaceutical company.Big pharmaceutical companies such as BoehringerIngelheim and Novartis have already expressedinterest in the generated transgenic rat models ofPD and HD. With widespread distribution of themodels and their proven validity for therapeuticalstudies, this interest and thus the interest in thebehavioural test systems will be further increased.For instance, based on the publication of the rat HDmodel( 2 ), more than 40 academic and pharmaceuticalpartners were interested in investigating treatmenttools (stem cells, drugs, viruses) with thehelp of this model. With the publication of the PDand SCA17 models, an even greater interest is foreseeable(for PD because of the limitations of themouse models and because of the impact in drugdevelopment for pharmaceutical companies).For Trophos, the commercial gain consists ofa potential reduction in the risk to further clinicaldevelopment of its drug candidate for the indicationtargeted in this STREP, in case the models arevalidated and found predictive of the human disease.This can lead to significant advantage toother commercial competitors, once outcomescan be approved in clinical trials in humans, andcan point to significant potential earnings.CrossLinks’ product, namely an integrated databaseand software tool for complex phenotypingof transgenic animals, will bridge a gap in the market.To our knowledge, such a tool does not exist.References(1) von Hörsten et al. 2003, Hum Mol Genet 12:617-624.(2) Idem.Scientific coordinatorOlaf RiessProject managerHolm GraessnerEberhard-Karls-Universität TübingenDepartment of Medical GeneticsCalwerstr. 772076 Tübingen, Germanyholm.graessner@med.uni-tuebingen.dewww.uni-tuebingen.de/klinische_genetikPartnersStephan von HoerstenFriedrich-Alexander-Universität ErlangenGermanywww.fpz.uni-erlangen.de/Exp_Biomedizin.htmHans-Peter LippNewBehavior AGSwitzerlandwww.newbehavior.comSilvia BrendaTSE Systems GmbHGermanywww.newbehavior.comBertrand TavitianCommissariat à l’Énergie AtomiqueFrancewww-dsv.cea.fr/en/instituts/institut-d-imagerie-biomedicale-i2bm/unites-de-recherche/service-hospitalierfrederic-joliot-shfj-a-syrota/laboratoired-imagerie-moleculaire-experimentale-limeRebecca PrussTrophos S.A.Francewww.trophos.comRonald NaningaCrossLinks B.V.The Netherlandswww.crosslinks-it.comAnnemie van der LindenUniversity of AntwerpBelgiumwebh01.ua.ac.be/biomag147

ACRONYMContract number: LSHP-CT-2006-037276 |EC contribution: € 1 770 361 | Duration: 36 monthsStarting date: 1 January 2007RespVirusesmedical-surveillance.com/index.htmlSUMMARYThe RespViruses project will study theinnate and acquired immune response ofthe elderly against the new and knownrespiratory viruses. Clinical and basicresearch aspects will be addressedequally, and new diagnostic assays toevaluate the immune status of the elderlywill be developed.Immune response to viral respiratoryinfections and vaccination in the elderlyBackgroundDuring the last few years some new respiratoryviruses (HMPV/hCoV-NL63/SARS/Bocavirus/fluH5N1) have emerged. In addition to other viruses,such as RSV, EBV, and Paramyxoviruses, they areable to induce severe respiratory diseases inhigh-risk patients, in particular young childrenand elderly.AimThe first objective of the project will be to studythe innate and acquired immune response of theelderly against the new and known respiratoryviruses, both clinical and basic research will beaddressed, in addition, a new diagnostic assays toevaluate the immune status of the elderly will bedeveloped. Within the project, an animal model forthe investigation of the elderly’s immune responsewill be established. In this model, antiviral agentswill be tested for their ability to support thepatient’s immune response. Up to 40 000 elderlysera collected during the last 9 years will be testedfor antibodies to emerging respiratory viruses(HCoV-NL63/HMPV/RSV/EBV/fluH5N1), providinga wide view of the epidemiology of theseviruses. For a precise view on the elderly’s immuneresponse to the viruses, a defined and uniformpanel of relevant clinical data related to respiratoryinfections will be collected. Internationallystandardised prospective data mining and a newmulti-lingual software tool will be developedwithin the project and used by the partners.Expected resultsThe project expects to gain detailed knowledgeon the innate and acquired immune responseto emerging respiratory viruses in the elderly.A thorough basic investigation of emerging respiratoryviruses will provide further handles todevelop antiviral strategies based on siRNA andexternal guide sequences (EGSs). Furthermore,known antivirals will be evaluated with the finalgoal to support the elderly’s immune responsewhilst reducing mortality in the elderly caused byrespiratory infections.Potential applicationsNew diagnostic assays; new antiviral therapies;optimised treatment and vaccination strategies;new software tool for surveillance and clinicaldata mining.148

Key words: new respiratory viruses, immune response of the elderly, mouse models, diagnosis, siRNA, EGSROLE OF SMEsThree European SMEs are partners in RespViruses, and are based in Belgium, Germany andSpain. These SMEs will receive approximately 50 % of the project budget. Having as partnerINGENASA skilled in enzyme immunoassays, monoclonal antibodies production, nucleicacid cloning and recombinant protein expression will help to develop new prototypes fordiagnostic assay development in respiratory diseases. INGENASA is a SME Biotechnologycompany dedicated to the research, development, production and commercialisation ofproducts for diagnostic sector with 25 years’ history in this field, mainly for viruses thataffect livestock animals or pets. INGENASA is also active in areas of prevention of animaldiseases (vaccines) and has participated in several funded European projects (BRIDGE,BIOTECH, FAIR, FP5 and FP6 programmes).The Belgian SME, RNA-TEC, with its profound knowledge and expertise in oligonucleotidechemistry plays a crucial role in the project by designing and synthesizing suitably stabilizedsiRNAs and external guide sequences that target highly conserved RNA sequencesof the respiratory viruses that are the subject of the study. The partners will test thesecompounds in vitro and also in suitable animal models. A long term goal of the project isto identify potent lead compounds that can be further exploited as potential antiviraltherapeutics using appropriate delivery systems that we can access.As software developer and consulter in IT departments, SME Mattes Hamann will cover twomean parts during the project. One will be the internal communication and the presentationof the project information. In the other part he is responsible for collecting and evaluatingmedical data. Therefore MH will develop multilingual software for acquiring relevantmedical data around respiratory disease. SME MH already made some needful experiencesin surveillance tools. MH will create and develop the project website, a Contact ManagementSystem and a software tool for acquiring project information. He will also consult any teammember if necessary.Scientific coordinatorOliver SchildgenInstitute for Medical MicrobiologyImmunology, and ParasitologyDepartment of VirologyUniversity of BonnSigmund-Freud-Strasse 2553105 Bonn, Germanyo.schildgen@medical-surveillance.euwww1.uni-bonn.de/startseite/jsp/index.jspPartnersMaria Grazia CusiUniversity of SienaSiena, Italywww.unisi.itLia van der HoekAcademic Medical CenterAmsterdam, The Netherlandswww.amc.uva.nlCatherine ManohaUniversity Hospital DijonDijon, Francewww.chu-dijon.frMatthias HamannHamannGermanywww.hamann-software.deBrian SproatRNA-TECLeuven, Belgiumwww.rna-tec.comBeatriz LazaroINGENASASpainwww.ingenasa.esMichael KleinesUniversity Hospital AachenAachen, Germanywww.ukaachen.de/content/folder/1202162149

ACRONYMSAGEContract number: LSHB-CT-2007-037241 | EC contribution: € 1 843 427 | Duration: 36 monthsStarting date: 1 April 2007SUMMARYAn attractive alternative to the currentstate-of-the-art in protein production, isthe use of plant systems for the productionof pharmaceutical glycoproteins(including antibodies), given their costefficiency and overall safety. The SAGEproject targets an improved plant productionplatform for pharmaceutical glycoproteins,to produce large quantities ofantibodies for use in cancer diagnosticand therapeutic systems.SME-led antibody glyco-engineeringBackgroundThe use of plant systems for the production ofpharmaceutical glycoproteins (including antibodies)offers an attractive alternative to the currentstate-of-the-art in protein production, given theircost efficiency and overall safety. Producing largequantities of antibodies for use in cancer diagnosticand therapeutic systems using plant systemscould therefore prove a viable and financiallysound approach.However, the differences in glycan structuresadded by plants, in comparison to those found inhumans, pose significant obstacles and in factresearchers recognise that the plant speciesused, as well as the tissue and cell type and theage, have a huge impact on the final glycoform ofan antibody.AimThe SAGE project targets an improved plant productionplatform for pharmaceutical glycoproteins.The partners, a high-calibre team of expertsin plant-based production technology andimmunology, will use four plant-based expressionsystems (including transgenic plants, virusinfectedplants and transformed plant cell lines)and mammalian cells as a control to generatea therapeutic antibody that recognises the wellcharacterisedcarcinoembryonic antigen (CEA),as well as their experience and know-how tolaunch protein therapeutics on the market.The partners, part of an international consortiumof four research organisations, one small andmedium-sized enterprise (SME) and two companies,will produce an antibody as a panel of differentglycoforms, which will be tested for thefollowing:• stability;• efficacy (e.g. in Fc-receptor binding assays,tumour cell binding assays and tumour grafting);• pharmacokinetic properties, such as serum halflife and antibody-dependent cellular cytoxicity(ADCC).The project partners will use the results todevelop safer and more active glycoform varietiesfor therapeutic applications.By using the plant expression systems and BY-2cells to generate the same recombinant antibody,the consortium targets the production of H10,a human full-length immunoglobulin G (IgG) thatrecognises the CEA.SAGE will also conduct a comprehensive, comparativestudy to establish how the structural, functionaland clinical properties of the antibody areinfluenced by the glycan structures. The projectpartners will compare the properties of the H10antibodies with those of a control H10 moleculegenerated in Chinese Hamster Ovary (CHO) cells.150

Key words: glycol-engineering, plant-made pharmaceuticals, recombinant antibody, transgenic plantsROLE OF SMEsgreenovation Biotech GmbH has developed innovative technologies for the production ofproteins in mosses. The production technology is based on protein secretion into thesurrounding medium of mosses which are cultivated under liquid conditions in photobioreactors.Moreover, greenovation has developed expertise in the genetic modification ofmosses and in plant glyco-engineering. The SME will produce the H10 antibody in mossand the effect of glycan modifications on therapeutic applications will be analysed in vitroand in vivo.Expected resultsThe use of advanced plant-based expression technologieswill help SAGE generate innovative therapeuticand diagnostic antibodies. The consortiumwill establish which best plant-based expressionplatform should be used to produce therapeuticantibodies, as well as identify the glycan structuresthat give antibodies superior properties ina clinical setting.The team will also determine the effects the variousplant-derived glycans have on the physicaland functional properties of antibodies. Thisaction will support SAGE’s intention to produceimproved antibody-based therapeutics with superiorperformance, as well as to provide treatmentfor many more people who need it. Ultimately,SAGE will be instrumental in improving healthcarefor everyone and in bringing down the costs fortreatment.With strong business support, SAGE will convertany new knowledge or product developed duringthe duration of the three-year project directlyinto strategic advantage. The project partnerBayer BioScience will utilise IP managementsupport to conduct IP searches and secure extraIP protection, if needed.SAGE will also transfer the acquired knowledgeto other scientific groups working in the samefield. Results and information will be disseminatedvia electronic mail, peer-reviewed articles,abstracts and posters. The SAGE consortiumwebsite will also make key findings available tothe public.Scientific coordinatorStefan SchillbergFraunhofer-Institut für Molekularbiologieund Angewandte Oekologie IMEDepartment of Plant BiotechnologyForckenbeckstrasse 652074 Aachen, Germanystefan.schillberg@ime.fraunhofer.dewww.ime.fraunhofer.de/EN/index.jspPartnersYuri GlebaICON GeneticsHalle, Germanyicongenetics.com/html/home.htmGilbert Gorrgreenovation Biotech GmbHFreiburg, Germanywww.greenovation.com/english/index.phpGerben van EldikBayer BioScienceGhent, Belgiumwww.bayer.be/cms/benelux/byc_cpstd_befr.nsf/Dirk BoschDion FlorackGerard RouwendalPlant Research International B.V.Wageningen, The Netherlandswww.pri.wur.nl/UKEva StogerUniversity of Natural Resourcesand Applied Life SciencesVienna, Austriawww.boku.ac.at/home.htmlHardev S PandhaUniversity of SurreySurrey, United Kingdomwww.surrey.ac.uk| Regeneration of transgenicplants producing pharmaceuticalsin petri dishes.151

ACRONYMContract number: LSHP-CT-2006-037796 | EC contribution: € 827 313 | Duration: 36 monthsStarting date: 1 December 2006SERO-TBSUMMARYThere is a great need for simple androbust diagnostic methods for the diagnosisof tuberculosis (TB). From thebasis of a through-screening processten M. tuberculosis antigens have beenidentified, exhibiting potential as serodiagnosticTB antigens. Two to three ofthese antigens will be selected with theaim of achieving the highest sensitivityand specificity in a setting with a highnumber of latent TB infections and HIVco-infection. The selection will be basedon evaluating patients with TB, latentlyinfected individuals and symptomaticnon-TB patients.The selected antigens will be incorporatedinto an immunochromatographictest (ICT) which will be optimised for thedetection of M. tuberculosis-specificantibodies. Prototypes of the test kitwill be produced and in-house proof ofperformance data generated. Finally,the performance of this test kit will beevaluated in a real life scenario in twoindependent hospital settings in Turkeyand Ethiopia.Development of a Specific Serological Kitfor the Diagnosis of TBBackgroundGlobally, TB is a severe problem, and the rapidand accurate diagnosis of active TB is the cornerstoneof TB control. There is a direct need for:• better TB diagnostics methods in developingcountries;• the development of a simple and rapid test basedon antibody monitoring, which will be of greatimportance in controlling the global epidemic.There are currently a number of serology-basedcommercial TB tests available, but none with therequired sensitivity and specificity.The publications of the genomic regions of differencebetween M. tuberculosis and M. bovis BCGallows identification of genes that are presentonly in M. tuberculsosis. From these gene regions100 proteins have been screened, specific for theM. tuberculosis complex. From these, ten antigenshave been selected, which are frequentlyrecognised by both HIV negative and HIV positiveTB patients.AimExpected resultsBy the end of this project, it is expected that theidentification of two or three M. tuberculosis antigens,which can form part of a serodiagnosticassay as a tool for detecting active TB in a highand a medium TB incident setting, will have beenachieved. Furthermore, performance data on theICT prototype are also expected. As a part of this,data which highlight the influence of TB incidenceon the performance of an antibody based kit fordiagnosis of active TB are expected.Potential applicationsThe development of the proposed ICT assaywould lead to an inexpensive and more accessiblediagnostic TB tool whilst enabling local and familyphysicians in the field to perform the TB diagnosisfrom the bed-side. This will permit an earlier diagnosisof the disease and therefore an early initiationof the treatment of a contagious diseasewhich will lead to a decrease of the transmission.Only by preventing the spread of the disease inthe local community can long-term control of TBbe achieved.To identify the best combination of two to threeantigens to be incorporated into an immunochromatographictest, which will be evaluated forperformance in two real life settings.152

Key words: tuberculosis, serodiagnosis, antibodies, diagnostics, immunochromatographic testROLE OF SMEsThe SME role is undertaken by Vircell, a company specialised in infectious diseases andmore specifically focused on respiratory infections, but which has previously had no TBspecific activities. This project is regarded as an opportunity to enter the field of TB diagnosis.In addition, this project will establish a new collaboration between SSI and Vircell. Thefinancial support of this project will allow a SME company like Vircell to undertake a projectwith the aim of providing developing countries with a diagnostic kit, regardless of thecommercial compensation obtained. Vircell is part of the Work Package (WP) managementteam in the project and leads WP 2 “Development of a TB immunochromatographic prototype”and WP3 “Demonstration of performance of prototype”.Scientific coordinatorMark DohertyStatens Serum InstitutDepartment of InfectiousDisease ImmunologyArtillerivej 5, 2300 Copenhagen SDenmarktmd@ssi.dkwww.ssi.dkPartnersArantxa CortésVIRCELL P.I.Granada, Spainwww.vircell.comIsmail CeyhanRefik Saydam NationalInstitute of HygieneAnkara, Turkeywww.rshm.saglik.gov.trAbraham AseffaArmauer Hansen Research InstituteAddis Ababa, Ethiopia| Principle of an immunochromatographic test.© Vircell153

ACRONYMContract number: LSHG-CT-2006-037415 | EC contribution: € 2 499 999 |Duration: 48 monthsStarting date: 1 December 2006SMARTERwww.smarter-chromatin.euSUMMARYThe identity of a given cell within a metazoanorganism is primarily defined by theexpression pattern of its genes. The activationand repression of genes is tightlyregulated by the concerted action of transcriptionfactors that recognise and bindspecific DNA sequences within regulatoryregions.Work done over the last 20 years revealedthis basic mechanism of gene activationand repression, while recent experimentsexposed an additional layer of regulationinvolving modifications of DNA and boundhistones. These modifications are involvedin cellular inheritance of transcriptionalstates through cell division and development,and as they are not coupled to DNAsequence, are referred to as epigenetic.Many factors that impact on epigeneticphenomena are clearly distinct frombasic transcription factors and areinvolved in regulating chromatin structure.Modulation of chromatin structureis frequently achieved by intrinsic enzymaticactivities that either mark particularregions within the genome foractivity or repression, or use the hydrolysisof ATP to remodel nucleosomalarrays. This variation of gene expressionpatterns in response to external andinternal signals has a major influence onstem cell differentiation, the maintenanceof tissue integrity, and the adaptationof organisms to environmentaldynamics.Recently, small molecules that target histonedeacetylases (HDAC) have been usedin the treatment of cancer, opening upnew avenues in therapeutic research.The SMARTER project aims at the developmentand improvement of such compounds,which is the primary mission ofChroma, the SME participating in theconsortium.Development of small modulators of geneactivation and repression by targeting epigeneticregulatorsBackgroundThe epigenetic level of gene regulation is beinganalysed intensively worldwide. However, theknowledge gained from these studies has notbeen transferred to drugs or drug candidates forthe treatment of major diseases. Equally, developmentof small molecules targeting epigeneticregulators have so far not been the major focus ofdrug discovery efforts.To pursue this promising approach it is obviouslyimportant to further improve understanding howthe eukaryotic genome in general, and the humangenome in particular, operates. Therefore knowledgeabout its DNA sequence, its epigenetic controlsystems and its dynamic structure in relationto gene expression must be integrated.AimThe SMARTER project aims at the developmentand improvement of compounds targeting epigeneticregulators. These compounds will be testedin various assays making it possible to collectdata sets of several parameters as histone modifications,chromatin states, gene expressionpatterns and physiological characteristics in anintegrative manner for the first time.Therefore major objectives are:• identification of small molecule inhibitors thattarget various histone-modifying enzymes;• validation of these inhibitors through in vivoanalytics of histone modifications states;• establishment of histone modification states asstandard readouts for drugs that target epigeneticmodifiers;• improvement of known epigenetic modulatorsthrough medicinal chemistry;• identification of target genes that are regulatedby the SMARTER molecules;• application of the SMARTER molecules in standardanimal model systems to verify their activityin living organisms.Expected resultsOur proposal will thereby promote the developmentand improvement of a new branch of cancerdrugs and as well support validation of newpotential drug target enzymes. Additionally, toolswill be generated, which allow new insights infundamental mechanisms of gene regulation byepigenetic modification.Potential applicationsIn the context of human health, an understandingof gene regulation is central to our understandingof many medical complaints and conditions.Fundamental aspects of chromatin function areincreasingly recognized as important factor in thedevelopment of many severe and often untreatablediseases. Therefore many proteins that areinvolved in the regulation of chromatin structureare potential drug targets and small moleculesdirected against these factors will play an increasinglyimportant role in treating patients that areaffected by one of these maladies.154

Key words: epigenetics, small molecules, histone deacetylases, chromatinROLE OF SMEsThe SMARTER project is specifically designed to strengthen the knowledge base ofChroma Therapeutics, a privately-held biotechnology company focused on the discoveryand development of novel small molecule drugs targeting epigenetic modifiers. The collaborationwith leading chromatin laboratories will be of great benefit by facilitating theanalysis of SMARTER inhibitor molecules that have been and will be discovered byChroma in high-throughput screens. A rapid testing in various biological systems willallow Chroma a more directed optimization of the small molecules by their medicinalchemistry specialists. The new knowledge gained from this project will be efficientlytranslated into new therapies and clinical practice through Chroma’s well-establishedR&D pipeline.Scientific coordinatorAxel ImhofHistone Modifications Group/Protein Analysis Core FacilityAdolf-Butenandt InstituteLudwig Maximilians University of MunichSchillerstr. 4480336 Munich, Germanyimhof@lmu.demolekularbiologie.web.med.uni-muenchen.de/groups/imhofProject managerJulia HochstatterAdolf-Butenandt-InstitutLMUMunich, GermanyJulia.Hochstatter@med.uni-muenchen.dePartnersScott CuthillChroma TherapeuticsOxford, United Kingdomwww.chromatherapeutics.comDirk SchuebelerFriedrich-Miescher-InstitutBasel, Switzerlandwww.fmi.ch/html/research/research_groups/epigenetics/Dirk_Schuebeler/Dirk_Schuebeler.htmlManel EstellerCNIOMadrid, Spainwww.cnio.es/ing/grupos/plantillas/presentacion.asp?grupo=50004270Tony KouzaridesGurdon InstituteCambridge, United Kingdomwww.gurdon.cam.ac.uk/~kouzarideslab/tony.html155

ACRONYMContract number: LSHB-CT-2007-037703 | EC contribution: € 2 500 000 | Duration: 36 monthsStarting date: 1 June 2007STEMDIAGNOSTICSwww.stemdiagnostics.comSUMMARYThe StemDiagnostics project aims at thedevelopment of next-generation of medicaltests and tools for significantlyimproving the survival rate of patientsundergoing haematopoietic stem celltransplant also known as HSCT – a medicaltreatment for life threatening conditionssuch as leukaemia and lymphoma.The development of new diagnostic tests, newtools and non-invasive methods for the prevention,early diagnosis and monitoring for haematopoieticstem cell transplantation (HSCT)BackgroundOver 7 000 allogeneic haematopoietic stem celltransplants (HSCT) are carried out each year inEurope alone, as a treatment for leukaemia andlymphoma. Techniques and cure rates are improvingbut the overall survival rate remains between40-60 %.MOSAIQUES), ELISA kits (SME APOTECH) andprotein biochip prototypes (SME ORLA), for thedevelopment of fast high throughput technologies;• development of novel reagents for monitoringgraft versus leukaemia, GvHD and targeted therapy(SME MULTIMUNE; SME NASCACELL);• comparative studies in an autoimmune diseasemodel of inflammation, rheumatoid arthritis.AimThis project will develop new proteomic, biologicaland genomic tests and tools for early diagnosisand monitoring of patient response to noveltherapeutics for the most severe complication ofHSCT; graft versus host disease (GvHD) and willbring to the clinic a new generation of diagnosticsthat will significantly improve HSCT therapy andpatient outcome.The Consortium unites 5 European SMEs withexpertise and markets in genomic and proteomictesting, diagnostic assay development andbiochips, with clinical partners selected for theirworld leading research in HSCT and access to clinicalsamples and patient groups.The project will focus on the role of relevant genesand biomarkers associated with acute and chronicGvHD, using retrospective samples from establishedbiobanks and prospective clinical trials to:• identify novel bio and genomic markers fordiagnostics;• develop novel diagnostic tools using genomics,proteomics, in vitro bioassays and biochips;• test the new diagnostics in animal models & onclinical samples;• exploit the new tools for commercial use.Expected resultsThe above will be realised by:• development of diagnostic tests using singlenucleotide polymorphism (SNP) analyses (SMEIMGM), based on results from previous ECfunded research (EUROBANK, TRANSEUROPE);• using proteomics via mass spectrometry evaluation/developmentof diagnostic patterns (SMEThe SMEs primary specific Aims include:• development of new tools for novel diagnostics,novel drug targets and therapeutics for use bothin the transplant and autoimmune setting;• access to important clinical and biological samplesand data for use in accurate assessment ofresults and confirmatory studies for the developmentof novel diagnostics;• testing and evaluation of new diagnostics onindependent cohorts and correlation of dataacross HSCT centres;• testing of new prototypes against currentassays via collaboration between SMEs;• use of new target molecules in monitoring ofresponse to therapy and during the post transplantperiod to assess acute and chronic GvHD.Potential applications• Identification of new diagnostics in the form ofnovel proteins associated with graft versus hostdisease (GvHD) compared to viral disease.• Development of early diagnostic tools for GvHDand rheumatoid arthritis using gene profiling.• The fast throughput development of novel monoclonalantibodies and ELISA kits for research,diagnostics, and potentially therapeutic use.• Development of novel peptides for use in monitoringGvHD and graft versus leukaemia effectsin transplant patients.• Development of prototype biochips (Fig. 1).• Identification of new single nucleotide polymorphisms(SNPs) for analysis in prognostic/diagnosticindices.156

Key words: haematopoeitic stem cell transplantation, graft versus host disease, graft versus leukaemia, proteomics,genomics, pharmacogenomics, clinical trials, early diagnosticsROLE OF SMEsThe STEMDIAGNOSTICS Consortium comprises SME’s that are already key players in theEuropean diagnostics market and already have the infrastructure and established market credibilityto turn research outputs from the STEMDIAGNOSTICS Project into marketable diagnosticproducts. The SMEs will target not only the European market, but also international healthmarkets including opportunities in the USA, Japan and Asia. The Consortium consists of 5 SMEswith expertise in state of the art technologies (IMGM, MOSAIQUES, mi, APOTECH, ORLA).APOTECH is a life science reagents company discovering, developing and producing new productsin the field of apoptosis and inflammation for laboratory based diagnostic tests.ORLA has already developed a platform technology, which may form the basis of a clinic basedor bedside assay. Orla Protein Technologies is a leader in the emerging European nanotechnologysector. The company has developed a ‘surface biology platform’ which is finding applicationin many areas including nanoscale diagnostics.Multimmune GmbH is a biopharmaceutical company dedicated to the discovery and developmentof novel products, including antibodies and peptides, for the treatment of cancer throughits innovative manipulation of the immune system.IMGM Laboratories GmbH is one of the leading SMEs for functional genomics and biomedicalresearch in Germany and has extensive experience in molecular diagnostics. IMGM is amongthe top 5 laboratories in Europe that are experienced in the ABI microarray technology.Microarrays, real-time PCR low-density arrays and SNP-detection technologies will be usedthroughout the project.MOSAIQUES’ established protein discovery systems will contribute to discovery of new biomarkers.Mosaiques Diagnostics will define and identifiy peptides and proteins in body fluids,which will enable diagnosis, of graft versus host disease as well as and response to therapybased on patterns of polypeptides in patients urine samples. To this end, MosaiquesDiagnostics has developed proprietary technology and software which enable the diagnosis ofdiseases based on polypeptides.CENAMPS is a not-for-profit technology commercialisation company, established in 2003.Cenamps is dedicated to the development and exploitation of emerging small-scale technologiesfor applications in healthcare, ambient intelligence and consumer products. The companywill play a major role in management and exploitation of the project using state of the artmanagement software and aid in bringing new developments to market and protecting IP.| Fig. 1Phase 1: Patient conditioning leadsto tissue damage in host tissuesproducing pro- and anti- inflammatorycytokines influenced by the patientnon-HLA genotype.Phase 2: In coming donor T cells andtheir activation is influenced by donornon- HLA genotype with further releaseof cytokines and upregulation ofsurface HLA Class II and adhesionmolecules on target tissues.Phase 3: Patient and donor non- HLAgenotype may influence theexacerbation or reduction of severityof GvHD. Molecules involved in earlyevents in phases 1 and 2 of cellactivation via activation of theinflammasome.(Reprinted from Dickinson A.M., andCharron, D. 2005. Non-HLAimmunogenetics in hematopoietic stemcell transplantation. Curr. Opin.Immunol., 17, 517. withpermission from Elsevier.)The cytokine storm and involvement of the inflammasome/non HLA geneticsPhase 1: Patient conditioning- activation of inflammasome and early eventsHost antigen presenting cells (APC)Irradiation/chemotherapy157Host tissues:skinLiverGI tractPhase 2: Donor T cell activation- further activation of inflammasomeDonor T cellPhase 3: Inflammatory effectorsTCR-MHCPro-inflammatory cytokinesTNF-alpha, IL-1, IL6-Heat shock protein activationAnti-inflammatory cytokines IL-1Ra, IL-10Host APC, fibroblasts,epithelial/endothelial cellsTNF-α IL-2 IFNγIL-1 TNF-α, chemokines; IL-8TNitric oxideTNF-α(IL-1Ra IL-10)Target cellAPOPTOSISNKand tissuedamageDifferential cytokine IL-1, IFNγ / chemokine releaseIL-10 IL-1Ra TGFβImmune ModulationTh1 IL-2, IFNγTh2 IL-4, IL-6,IL-10aGvHDcGvHDScientific coordinatorAnne DickinsonUniversity of Newcastle upon Tyne,School of Clinical and Laboratory Sciences,Haematological Sciences, The Medical SchoolFramlington Place, Newcastle upon TyneNE2 4HH, United Kingdoma.m.dickinson@ncl.ac.ukPartnersErnst HollerKlinikum der Universität RegensburgDept. Hamatology und Internistiche OnkologieRegensburg, GermanyHarald MischakMosaiques Diagnostics GmbHHannover, Germanymosaiques-diagnostics.deGabriele Multhoffmultimmune GmbHMunich, Germanywww.multimmune.deRalph OehlmannIMGM LaboratoriesMartinstried, Germanywww.gene-expression-center.dewww.imgm.comLars FrenchDepartment of DermatologyZurich University HospitalZürich, SwitzerlandOlivier DonzéCSO and Operating ManagerApotech Corporation (Headquarters)Epalinges, Switzerlandwww.apotech.comHans-Jochem KolbKlinical Cooperation Group Hematopoietic CellTransplantation, Institute of MolecularImmunology, Forschungszentrum fuerUmwelt und GesundheitMuenchen, GermanyDale AtheyOrla Protein Technologies Ltd., NanotechnologyCentre, University of Newcastle upon TyneNewcastle upon Tyne, United Kingdomwww.orlaproteins.comGérard SociéAssociation de Recherche sur la Greffede CSP, Aplasies et HPNParis, FranceHildegard GreinixBone Marrow Transplantation UnitUniversity Hospital of ViennaVienna, AustriaIlona Hromadníková3rd Medical Faculty, Charles UniversityPrague, Czech RepublicShak GohirCENAMPSThe Fabriam Centre, Middle Engine LaneNewcastle upon Tyne, United Kingdomwww.cenamps.com

ACRONYMContract number: LSHG-CT-2006-037586 | EC contribution: € 2 850 851 | Duration: 36 monthsStarting date: 1 January 2007STREPTOMICSwww.streptomics.orgSUMMARYThe Gram-positive soil bacterium Streptomycesis an invaluable host for thesecretory production of biopharmaceuticalsand other heterologous proteins.STREPTOMICS aims to further evaluatethis host as a cell factory for the industrialproduction of proteins of diverse originincluding from mammalians, bacteria andarcheae of interest for human health andenvironment.Systems biology strategies and metabolomeengineering for the enhanced production ofrecombinant proteins in StreptomycesBackgroundThe biotechnology industry is constantly searchingfor better hosts for the production of biopharmaceuticalsand enzymes of diverse origin. TheGram-positive soil bacterium Streptomyces hasalready proved an invaluable host for this purpose,since it can secrete several heterologousproteins in satisfactory amounts. However, inorder to optimise strain selection, knowledge isrequired concerning the following points:• how protein secretion processes are integratedwithin the metabolome, and how they interact;• how heterologous protein secretion stressesthe metabolome and induces negative cellularcascades.Systems biology, the science of analysing andmodelling genetic, macromolecular and metabolicnetworks, provides the means to addressthese questions. By combining biochemical informationwith genetic and molecular data, theStreptomics consortium hopes to gain novelinsights into the functions of genes related to proteinsecretion, as well as how that protein secretionmechanism responds to external and internalstimuli. With a better understanding of this mechanismat the cellular level, it should be possible tooptimise protein secretion.AimStreptomics aims to enhance the production ofheterologous proteins, using Streptomyces as ahost. More specifically, it has the following goals:• to evaluate Streptomyces lividans as a cell factoryfor the production of heterologous proteinsof interest;• to investigate the transcriptome and proteomeof the host strain under different growth conditions,with different expression/secretion vectors,and using different fermentation strategies, inorder to identify the genes important for optimalcell performance, with respect to hetero logousprotein secretion;• to analyse metabolic flux control and flux balancewith a view to engineering metabolic pathwaysfound in a Streptomyces background, andhence to exploit cellular pathways which provideimproved energy transduction, balancedgrowth and supramolecular assembly;• to engineer better production/secretion strainsof Streptomyces based on the above, and basedon information about secretion bottlenecks thatwill be identified through the production ofmuteins, either via direct mutation of specificamino acids, or by directed evolution;• to optimise the protein production process.Expected resultsBased on a better understanding of metabolomesecretomeinterplay, strategies for improvedprotein secretion will be designed. These willcombine better energy generation and directedenergy consumption for either cell mass productionor heterologous protein secretion. Ulti -mately, a ‘toolbox’ of Streptomyces strains willbe engineered and refined, which optimally oversecreteproteins of interest during fermentation.Consequently, Streptomics will generate knowledgewhich will assist SMEs in the biotechnologyand other industries to develop new andmore efficient systems for the industrial productionof heterologous proteins, using S. lividansas a cell factory. These systems will be useful inboth red (medical) and white (industrial) areasof biotechnology.Potential applicationsThis project aims to increase the number of efficientcell factory platforms for the production ofheterologous proteins important in health, biocatalysisand the environment, using Streptomycesas a host. It will therefore contribute to a competitive,knowledge-based economy and sustainabledevelopment in Europe, by serving the needs ofa research-intensive industrial sector in whichmany SMEs have traditionally been involved.158

Key words: systems biology, streptomyces, protein secretion, enzymes, biopharmaceuticals, directed evolution,metabolomics, transcriptomics, proteomicsROLE OF SMEsThe four SMEs involved in the project, Prokaria (Matis) (Reykjavik, Iceland), Direvo, (Köln,Germany), Eurogentec (Liège, Belgium) and BioXPr (Namur, Belgium) each have their specifictask, from assessing the Streptomyces protein production platform for the production of proteinsof their interest (Prokaria and Direvo) to helping to strain improvement of proteins whichplay a role in protein secretion via directed evolution (Direvo). Prokaria will take responsibilityfor cloning, expressing and secretion of various enzymes from extremophiles, primarily frombacterial and archeal thermophiles into Streptomyces. These thermostable enzymes have previouslybeen proven to be difficult expressed or produced in other hosts like E. coli or Thermusthermophilus. Direvo, a leading company in protein engineering by screening-based directedevolution and its application to biomolecules, specifically to biocatalysts for chemical, technical,industrial, scientific and pharmaceutical purposes, will test Streptomyces lividans andevaluate expression/secretion levels and product characteristics for the production of engineeredproteins/enzymes with market potential in Pharma and Industrial Biotechnology, andevaluate whether SecA mutants could improve secretion characterization. As such, Direvo complementsthe expertise of the other partners with its broad and advanced technologicalportfolio in Directed Evolution and high-throughput protein screening. Eurogentec will takeresponsibility for the transcriptomic analysis of S. lividans. This SME developed previously incollaboration with different members of this project a complete DNA micro array based on longoligo’s representing the entire set of ORFs specific to Streptomyces coelicolor. The use of theS. coelicolor DNA array for S. lividans transcriptomic analysis will be validated and the arraymodified if necessary. Eurogentec will act as service provider for transcriptomic analysis for allpartners of this project. Data will be generated in collaboration with different partners for analysisof up and down regulated genes in different experimental conditions. BioXpr will organiseand set-up a data repository system that will allow all the member of the consortium to storethe results of their work packages on a centralized system. The central database used to storethe data will also be the source of information for analysis and visualisation system that willcombine proteomics, transcriptomics and metabolomics information to define the best conditionsfor protein secretion. BioXpr will therefore collect information to combine the sourcesof data into one picture.The successful integration of the various aspects of this project STREPTOMICS will providein-depth knowledge about interactions that may occur at the genetic or proteomic level duringthe heterologous protein secretion process in S. lividans of heterologous proteins.Partners will work together to apply a step-by-step approach to analyze the physiologicalstate and performance of the cell, and based on these results, to engineer strains that mayovercome or suppress negative effects.Scientific coordinatorJozef AnnéRega InstituteCatholic University of LeuvenLaboratory of BacteriologyMinderbroedersstraat 103000 Leuven, Belgiumjozef.anne@rega.kuleuven.bewww.kuleuven.be/regaPartnersMichael HeckerErnst-Moritz-Arndt-UniversityInstitute for MicrobiologyGreifswald, Germanywww.uni-greifswald.de/indexuk.htmlWayne M. CocoDirevo Biotech AGCologne, Germanywww.direvo.comAnastassios EconomouFoundation of Researchand Technology FORTHInstitute of Molecular Biologyand Biotechnology,Iraklio, Crete, Greecewww.forth.grMarc DaukandtEurogentec S.A.DNA MicroArray Dept.Seraing, Belgiumwww.eurogentec.com/eu-home.htmlJakob KristjánssonProkaria Ltd.Reykjavik, Icelandwww.prokaria.isBenjamin DamienBioXpr S.A.Namur, Belgiumwww.bioxpr.beRoy GoodacreUniversity of ManchesterSchool of ChemistryManchester, United Kingdomwww.chemistry.manchester.ac.ukAnna Eliasson LantzTechnical University of DenmarkCentre for Microbial BiotechnologyLyngby, Denmarkwww.cmb.dtu.dk/English.aspxDaniel BadcockGlaxoSmithKlineHarlow, United Kingdomwww.gsk.com| Automated protein engineering: A precision robot arm retrievesa custom manufactured 1536-well plate in one corner of a room fullof robotics-compatible equipment including nano-liter volume liquidhandlers, single cell sorters, humidified incubators, heating andcooling blocks, centrifuges, confocal laser-based plate readers andother equipment integrated for fully automated high throughputprotein engineering at Direvo Biotech AG in Cologne, Germany.159

ACRONYMContract number: LSHG-CT-2006-037231 | EC contribution: € 1 840 719 |Duration: 36 monthsStarting date: 1 September 2007SYSCOwww.biobase-international.com/pages/index.php?id=438SUMMARYThe overall objective of the SYSCO projectis to decipher the intracellular biologicalpathways and basic cellular processesthat act in physiological conditions aswell as in the context of intracellular parasitism,in order to highlight the alterationin gene expression that stems fromthe conflict between the host andpathogen genomes. More specifically,the project will use human and mousemacrophages as cellular targets, and theLeishmania parasite as a prototype forintracellular pathogens. Leishmania isone of the most intensively studied biologicalmodels in terms of parasite, hostimmune response and genetics.Systematic Functional analysis of IntracellularParasitism as a model of genomes conflictBackgroundA study conducted by an international expertpanel for the University of Toronto, ranked thecomputational examination of host-pathogeninteractions among the top 10 biotechnologiesmost likely to improve global health in the next10 years ( 1 ). However, information about fundamentalaspects of the cellular machinery involvedin the interactions between macrophages andintracellular pathogens has not yet been sufficientlycategorised, particularly with regard tomacrophage function, and there is a need fora systematic and integrative approach to theidentification of interconnected functional modulesand salient modifications triggered byintracellular parasitism.AimSYSCO will decipher and modularise the cascadeof intracellular events generated by parasite-cellinteractions, and also how they result in either parasiteelimination or infection in humans. A comparativeanalysis with mouse strains expressingdiffering susceptibilities will help identify keydeterminants of natural resistance or susceptibilityto parasites acting at the macrophage level.In a combined strategy of experimental and theoreticalwork, the SYSCO consortium will systematicallycapture data at different levels of cellularinformation, using state-of-the-art, multi-parametricmolecular technologies (both in humanand in mouse). These data will be used to identifyregulatory motifs through systematic promoteranalysis, and to populate computer models withthe relevant motifs and associated signallingpathways. The computer models will be designedas independent modules covering gene regulation,gene expression, protein interactions andsignalling. This modular approach will be used tomimic different types of innate macrophageresponses, and to map theoretical predictions toexperimental data.Expected resultsAfter 36 months, SYSCO will have achieved thefollowing aims:• development of a hybrid, in silico model for theinnate response of macrophages to an intracellularpathogen, based on the composition ofinterconnected modules that mimic differentcellular events;• development of a comprehensive systemsontology;• experimental investigation and categorisationof four different modules, namely gene regulation,gene and protein expression and signaltransduction;• complementary high throughput analysis ofthe macrophage transcriptome by Affymetrixoligonucleotide arrays and serial analysis ofgene expression, both in parasite-infected andin non-infected cells;• prediction and validation of the regulatory networksin macrophages;• experimental determination of cell regulation byquantitative transcription factor assays and byRNA interference.Potential applicationsLeishmaniasis is one of the world’s major parasiticdiseases, but there is no vaccine for it asyet, and the drugs currently prescribed to treat itare fairly toxic. Millions of people living in developingcountries, mainly in southern and east -ern Mediterranean regions and in central andSouth America, are exposed to leishmaniasis. TheLeishmania parasite is also a major co-pathogenin the context of HIV infection in southern Europe.The results of this project will be significant,not only in the context of leishmaniasis, butalso for the understanding and treatment ofinfection by other intracellular pathogens, suchas Mycobacterium tuberculosis, the bacteriumwhich causes tuberculosis.References(1) Daar et al, 2002.160

Key words: intracellular parasitism, host-pathogen interaction, functional genomicsROLE OF SMEsBIOBASE is the leading content provider of biological databases, knowledge tools andsoftware for the life science industry. They offer well-structured data, assembled by highlyqualified subject-matter experts, organized in an accessible and easily searchable mannerthat enables researchers to identify connections between disparate pieces of informationand to apply that knowledge to their specific topic of interest.The tasks of BIOBASE are high quality manual literature annotation of project relevantdata into the proprietary databases TRANSFAC(R), TRANSPATH(R) TRANSCompel(R) andProteome. They collect data on mechanisms of gene regulation, transcription factors andtheir binding sites and on signal transduction pathways in the human cells in response toLeshmania. The collected data along with the full content of the databases will be providedto the consortia. BIOBASE will also do DNA sequence analysis: search for putative bindingsites for TFs in promoters of genes regulated during cellular response to the parasite attack.Biobase will be involved in development of software for the reconstruction of a gene regulatorynetwork (transcription network) and in designing artificial promoters which can beused to study mechanisms of gene regulation in various immune responses.Furthermore, BIOBASE will manage the project. Management activities include communicationwith the commission, organisation of regular financial audits, dissemination andexploitation of project results, and regular project meetings.Skuld-Teck (SKT) set up one bioinformatics platform, and two gene profiling technicalplatforms one based on the SAGE and one based on real-time quantitative PCR (qPCR).The SAGE platform has two advantages: the exhaustiveness of the results and the networkof its users (who share their gene profiles data). Through its two gene profiling platformsSKT has developed a first thematic dedicated to Leukaemia (end of 2002). This has permittedto identify a set of genes allowing for the design of a Leukaemia diagnosis/prognosistool. This tool is being validated within clinical trials to draw up the gene profiles of patientssuffering from Leukaemia and to monitor them during the treatment.SKT will provide a relational database integrating all public and private SAGE data. SKT willdevelop another relational database integrating the data generated along the project i.e.:the gene profiles data that is being generated using SAGE and those that will be generatedusing Affymetrix. This platform will include two interfaces: a working interface that allowsintroducing annotations and integrating new data (under PostgreSQL/Linux) and anexploitation interface, regularly updated that will be easy to query for non-specialists.Considering the increasing volume of data in public databases, the working interface will beimplemented under Oracle. SKT will also validate the expression of target genes obtainedin WP2 through its Real-Time PCR (qPCR) platform.Scientific coordinatorAlexander KelBIOBASE GmbHDepartment of Research and DevelopmentHalchtersche strasse 3338304 Wolfenbüttel, GermanyAlexander.kel@biobase-international.comwww.biobase-international.com/pagesPartnersDavid PiquemalSkuld-Tech SARLMontpellier, Francewww.skuldtech.comRalf HerwigMax Planck Institutefor Molecular GeneticsBerlin, Germanywww.molgen.mpg.deBéatrice RegnaultInstitut PasteurParis, Francewww.pasteur.fr/english.htmlPatricia RenardFacultés Universitaires Notre-Dame de la PaixUnité de recherche en biologie cellulaireNamur, Belgiumwww.fundp.ac.beKoussay DellagiInstitut Pasteur de Tunis,Laboratoire d’immunopathologie,vaccinologie et génétique moleculaire (LIVGM)Tunis, Tunisiawww.pasteur-international.orgWinston HideUniversity of the Western CapeSouth African NationalBioinformatics InstituteBellville, South Africawww.sanbi.ac.zaPierre-Andre CazenaveUniversité Pierre et Marie Curie-Paris VILaboratoire d’immunophysiopathologieinfectieuse – URA 1961Paris, Franceenglish.upmc.fr/UK/info/00161

ACRONYMSysProtwww.sysprot.euContract number: LSHG-CT-2006-037457 | EC contribution: € 2 097 268 | Duration: 36 monthsStarting date: 1 January 2007SUMMARYSysProt aims at the development of a newparadigm for the integration of proteomicsdata into systems biology. Thegoal is to gain relevant knowledge onbiological processes that are importantfor human health and to use thisknowledge for the purpose of diseasemodelling. The strategy to achieve thisobjective is an innovative, explorativesystems biology approach both on themolecular and physiological level witha strong focus on protein function andmodification.The consortium aims at demonstratingthe newly developed technologies ina proof-of-principle study in an obesityinducedtype-2 diabetes mouse model.System-wide analysis and modelling ofprotein modificationBackgroundBioinformatics methods for diagnostic screeningare a bottleneck in current biomedical research.While exploratory methods – such as statisticalhypotheses testing, clustering of gene expressionprofiles and classification methods – have beensuccessful in the detection of molecular markersfor interesting diseases, these techniques fail tovalidate these markers in their gene regulatorycontext and to integrate other data sources relevantfor diagnostic purposes. For these tasks,novel modelling techniques, network analyses,and data integration methods are indispensable.The analysis of processes involved in the courseof complex polygenic diseases, such as obesityand type-2 diabetes, is in fact a multi-step procedurethat has to cope with data from diverseexperimental functional genomics platforms(gene and protein expression), physiologicaldata, environmental factors, and others.AimThe project SysProt aims to develop a new paradigmfor the integration of proteomics data intosystems biology. The goal is to gain relevantknowledge on the biological processes that areimportant for human health and to use this knowledgefor the purpose of disease modelling.In order to achieve this objective, an innovative,explorative biological systems approach (on boththe molecular and the physiological level) will beadopted, with a strong focus on protein functionand modification. SysProt will produce proteomicsdata, indispensable for the identificationof novel circulating protein factors, and posttranslationalprotein modifications that are importantfor the onset, dynamics, and progression ofcomplex diseases.Data generation will be complemented by thedevelopment of computational analysis methodsfor these novel data types and the creation of adequatemodelling technology. The project will benefitfrom the utilisation of established mousedisease models, existing benchmarking modulesfor computational analysis, and the functionalgenomics platforms developed by and accessibleto the partners. In particular, the consortium aimsto demonstrate newly developed technologies ina proof-of-principle study within an obesityinducedtype-2 diabetes mouse model.The project consortium is headed by an SME andincludes four academic partners from threeEuropean countries. This composition of commercialand academic interests guarantees high-levelscientific research, as well as a strong focus onthe commercial relevance and exploitation of theproject’s results. As a consequence, the proposedproject will strengthen Europe’s scientific andcommercial competitiveness in the field of systemsbiology, one of the key technologies infuture medical and pharmacogenetics research.Expected resultsAn important feature of the project’s approachwill be the integration of phenotypic and physiologicalparameters with proteomics data andexpression profiles from time course series representingthe onset and progression of insulinresistance of type-2 diabetes. Ultimately, the platformwill enable medical researchers to combineheterogeneous biomolecular data with physiologicaland clinically relevant parameters to predictindividual predispositions to obesity-inducedtype-2-diabetes.The objectives of this project are:• model the knowledge about biological objects(genes, proteins and protein complexes) inthe context of nutrition and type-2 diabetes inequivalent computer objects;• integrate heterogeneous data types from proteomicsand functional genomics approaches;• develop and use a prototype framework for theautomatic detection and localisation of proteinmodifications on high-accuracy mass spectrometrydata;• generate specific proteomics and functionalgenomics data providing the necessary informationfor disease model generation with anappropriate animal model;162

Key words: systems biology, fundamental biological processes, proteomics, bioinformaticsROLE OF SMEsMicroDiscovery is coordinator of SysProt having as a bioinformatics company a strong focuson systems biology. The company sees a high potential for modelling and simulation technologiesin the life science arena. However, currently available methods are far from commercialapplications and need massive additional scientific and developmental efforts. TheSysProt consortium offers the possibility of an efficient technology transfer from key playersin the nutrigenomics, proteomics and systems biology field into a commercial application.MicroDiscovery intends to develop the resulting knowledgebase into a product ready for theLife Science market. There will be a rising demand for solutions in the area of systems biology.Systems biology will have a tremendous impact on the development of new drugs, diagnosticsof complex diseases and personal medicine. Pharmaceutical companies, and also toa large extent biotech companies, design and market products which affect, inhibit or excite,biological systems, often via highly specific intervention points. Nevertheless these productstypically change systemic aspects of cells, tissues, entire organs, or organisms. There is nodoubt that new knowledge extending the ability to control biological systems via combinedcomputational and experimental approaches will be key in health care and in particular in thedrug development process in the next 5-10 years. This will for example be highly relevant inthe area of complex diseases, such as obesity induced type-2 diabetes, where many genes areresponsible for a particular, pathogenic phenotype.The commitment of MicroDiscovery to the project guarantees the midterm conversion of theconsortium results into an applicable product. The long-term goal is the establishment of systemsbiology technologies in the life science arena. There are currently various companies outsidethe EU (e.g. Entelos (US), Gene Network Sciences (CAN), BioSeek (US), Genstruct (US),GeneGO (US)) with large financial backing positioning themselves competing into this emergingfuture market. There is still a large potential in the European academic community in systemsbiology field with has to be mobilised in order to cope with the efforts outside the EU.• gain new knowledge on the pathways andmarker genes relevant for obesity-inducedtype-2 diabetes disease progression that willlead to the discovery of novel diagnostic biomarkersfor disease susceptibility;• stimulate perturbations of the disease-relevantpathways;• develop tools and methods for the correlation ofphenotype and genotype;• accelerate the identification and positionalcloning of disease candidate genes by combininggene expression, proteomics, genotype, andclinical data;• set up a knowledge base that integrates all availabledata and methodology as an exploitableproduct for disease modelling.Potential applicationsThe main result of the project will be an exploitableprototype that allows medical researchers to drawpredictions on disease-relevant pathways. Thesepredictions will be valuable for diagnosis and drugdevelopment purposes. The platform will enablethe validation of potential drug targets in-silicoand thus give support in explorative data mining ofthe expanding body of gene and protein data togain the knowledge necessary to discover betterand safer drugs. In-silico disease modelling willnot only cut the costs of future drug developmentby reducing the number of false drug targets butwill also save development time. Additionally thein-silico systems will reduce the necessary numberof animal trails in drug development explicitly.Thus, the proposed platform has a high commercialisationpotential in future diagnostics applicationsas well as in drug development.Systems biology approaches will increasinglyhave an impact on Life Science and Health programmesin general and on drug development inparticular. They provide a huge potential forimproving the quality of life through the creationof highly skilled jobs, improved competitiveness,and economic growth in Europe, as well as betterhealthcare and new tools to address different andimportant challenges of the EC. Through the applicationand broadening of systems biologyapproaches, the SysProt project is likely to impacton the scientific understanding of biologicalprocesses, with particular relevance to improvinghuman health and wellbeing.Project coordinatorArif MalikMicroDiscovery GmbHNutriSystemicsMarienburger Str. 110405 Berlin, Germanyarif.malik@microdiscovery.dewww.microdiscovery.dePartnersHadi Al-HasaniDeutsches Institut fuerErnaehrungsforschung (DIFE)Department of Pharmacology-GermanInstitute of Human NutritionPotsdam-RehbrueckeNuthetal (OT Bergholz-Rehbruecke), Germanywww.dife.de/en/index.phpRalph SchlapbachEidgenössische TechnischeHochschuleule, ZürichFunctional Genomics Center ZurichZurich, Switzerlandwww.fgcz.ethz.chRainer CramerThe University of ReadingThe BiocentreReading, United Kingdomwww.biocentre.reading.ac.ukRalf HerwigMax Planck Institute for Molecular GeneticsDepartment Vertebrate GenomicsBerlin, Germanywww.molgen.mpg.de| C57BL/6J mouse (black), Swiss Jim Lambert (SJL)mouse (white) and New Zealand Obese (NZO) mouseare used as animal model for diabetes and obesity inthe SysProt project. The NZO mouse is an establisheddisease model in diabetes research and characterisedby heredity in obesity and by Typ2-diabetes withInsulin resistance. The SJL mouse never developsobesity and therefore serves as counterpart to theNZO mouse. C57BL/6J mice serve as control strain.163

ACRONYMContract number: LSHM-CT-2007-037472 |EC contribution: € 3 000 000 | Duration: 42 monthsStarting date: 1 January 2007TAMAHUDwww.tamahud.eu/home.jspSUMMARYHuntington’s Disease (HD) is a devastatingneurodegenerative disease withmany unmet patient needs. There are noknown ways of slowing or preventing theneurodegeneration associated with thedisease, and clinical trials in humans arehampered by the slow disease progressionand the absence of suitable biomarkersof short-term progression. Thegenetics of HD is characterised, andinvolves the expansion of a polyglutaminetract at the amino-terminus of theHuntingtin gene (HTT). However, thetranslation of this knowledge into therapeuticand diagnostic approaches is hamperedby the scarce knowledge of HTTbiology, the paucity of information onhow cellular signalling pathways interactwith the HD mutation, and the lack of systematicand modern approaches aimed atidentifying useful biopredictors of diseaseprogression in individuals diagnosedwith HD. The TAMAHUD projectaddresses key areas of HD patient needs,namely the discovery and developmentof therapeutically meaningful novel targetsand biomarkers. More precisely,TAMAHUD project aims to deliver solidlyvalidated, druggable targets accompaniedby developable small molecule modulatorsand candidate diagnostics formonitoring of disease progression. Toachieve these aims, a consortium of specialistpartners has been assembled, representingcomplementary and specificknow-how and expertise which will beintegrated and further developed in thecourse of the project.Identification of early disease markers,novel pharmacologically tractable targetsand small molecule phenotypic modulatorsin Huntington’s DiseaseBackgroundNo curative therapy is currently available forpatients with HD and the pathophysiology of HD isstill not well understood. Generally, the currenttreatment of HD combines non-pharmacologicaltherapy with management of the symptoms ofthe disease. Pharmacological treatment of thedisease must be tailored to the specific needs ofthe patient. Physicians may prescribe a number ofmedications to help control emotional and movementproblems associated with HD, althoughno drug is yet available to stop or reverse the progressionof the disease.The significant unmet medical need for HDincludes the following:• better understanding of pathophysiology toyield more relevant targets;• improved symptomatic treatments;• drugs that slow, halt or reverse disease progression;• diagnostics of disease onset/progression.AimThis project addresses the challenge of identifyingnovel tractable targets causally associated withthe pathology, to support the development of disease-modifyingtherapeutics for the cure of HDand of discovering novel early biomarkers leadingto the development of new diagnostic tools.High throughput-RNAi, focusing on genes encodingpharmacologically tractable proteins ratherthan on a whole-genome approach, will beemployed on a novel and robust HD cellular diseasemodel to identify genes whose inhibition ofexpression is protective against the HD mutation.Following a stringent target validation approach,selected validated targets will be progressed toassay development and primary screening activities,to identify druggable compounds active on thetarget and efficacious against the HD mutation incellular disease models. The complete process willbe accompanied by an extensive data and text miningworkflow providing background information forthe HD knowledge network. This network will guidethe experts in the generation of hypotheses aboutpossible relationships (proteins, genes, regulation,and pathology). Therefore, TAMAHUD aims atdelivering novel targets causally associated withaspects of the HD pathology in model systems,where biological target validation is accompaniedby demonstration of target relevance throughsmall-molecule pharmacological modulation. Inparallel, the biomaterial repository made availableto the consortium from a disease-specialist academicpartner will be investigated through stateof-the-artmetabonomics approaches to identifybiomarkers predictive of disease onset.Expected resultsThe expected results can be summarised into:• the identification of novel, tractable targetscausally associated with the pathology, alongwith small molecules capable of modifyingaspects of the pathology in cellular diseasemodels via modulation of target activity; and• biomarkers of disease onset/progression.Potential applicationsIf met with success, the scope of the project goesbeyond the 3.5 year granting period and theresearch outcomes are relevant to:• further development of therapeutic compoundsthrough preclinical and clinical studies;• reduction of costs in clinical development: thelack of reliable and predictive biomarkers of diseaseonset requires clinical trials of higher complexityin order to reach statistical significance;• creation and development of a network of competenciesaimed at progressing drug discovery insuch a specialist field as the neuroscience area.TAMAHUD aims to terminate its activities in theconstitution of a solid base for the later completionof pre-clinical development of potentialdrugs, comprising the demonstration of in vivoefficacy of TAMAHUD-derived chemical series alsothrough the use of TAMAHUD-derived biomarkers.At even later times, clinical studies on candidatedrugs originating from TAMAHUD activitieswill again benefit from the inclusion of TAMAHUDbiomarkers to determine clinical efficacy.164

Key words: Huntington’s disease, HT-RNAi, functional genomics, validated target, chemical hit, metabonomics,biomarker, text-mining, data-mining, data visualizationROLE OF SMEsTAMAHUD’s aims are designed to meet two unmet needs in Huntington’s Disease (HD): first,the identification of novel small molecule modulators of therapeutically relevant targets andsecondly, the identification of novel biomarkers. The coordinating SME, Siena Biotech, ispivotal to TAMAHUD as it will provide novel potential pharmacological targets of therapeuticrelevance in HD, contribute to their validation and exploit its pervasive drug discovery platformto discover small molecule modulators of such targets. A second SME, TCP InnovationsLtd., participates to identify novel biomarkers of HD onset and progression. Once achieved,these aims will form the basis for the development of novel pharmacological therapies andprovide the means to monitor their efficacy in pre-clinical and clinical studies.Scientific coordinatorAndrea CaricasoleSiena Biotech SpAvia Fiorentina 153100 Siena, Italyinfo.tamahud@sienabiotech.itwww.sienabiotech.it/index/index.jspPartnersDavid RubinszteinUniversity of CambridgeCambridge, United Kingdomwww.cimr.cam.ac.uk/index.htmlDavid GraingerTCP Innovations Ltd.Cambridge, United Kingdomwww.tcpinnovations.comChristian BlaschkeAlma Bioinformatics S.L.Madrid, Spainwww.bioalma.com/index.phpReinhard SchneiderEMBLHeidelberg, Germanywww.embl.de165

ACRONYMContract number: LSHG-CT-2006-037517 | EC contribution: € 2 351 818 | Duration: 36 monthsStarting date: 1 January 2007TargetHerpeswww.targetherpes.orgSUMMARYHerpesviruses are important humanpathogens. As of today, their infectionscan only be controlled by acyclovir orderivates. The TargetHerpes project willapply novel technologies provided bythree SMEs to design and develop novelclasses of antiviral treatments. Key tothe project is the SMEs connection withfundamental advances being made inEurope’s leading herpesvirus researchlaboratories. The technologies to beapplied to the search of novel, effectivetreatments against a broad spectrum ofherpesvirus diseases include the rationaldesign of peptide-based and siRNAbasedherpesviral inhibitors. The steps ofthe viral life cycle to be targeted are virusentry, evasion of host defences, persistencein infected individuals, reactivationfrom latency.Molecular intervention strategies targetinglatent and lytic herpesvirus infectionsBackgroundHerpes viruses cause many serious and life-threateningdiseases, especially in immunocompromisedpatients, such as transplant recipients andHIV-infected individuals. Even in healthy ones,herpesviruses can result in serious diseases. Forexample, the herpes simplex virus (HSV) remainsone of the most common sexually transmitted diseases,while human cytomegalovirus (HCMV) isa leading cause of birth defects, and human herpesvirus 8 (HHV-8) causes a number of cancers.At present, the options for antiviral therapy arelimited and, owing to toxicity, the current antiherpesvirusdrugs cannot be administered topregnant women. There is a continuing need todevelop new treatments, as drug-resistant virusesare constantly evolving.A principal characteristic of herpesvirus infections,is that after primary infection (usually inchildhood), the viruses establish a latent statethat remains for life. Up to 90 % of the populationmay be latently infected with one or more herpesviruses. The social and psychological consequencesof the herpesvirus infections are severe.AimTargetHerpes will translate basic knowledge ofviral replication strategies and evasion from hostattack into the concept of a multi-pronged attack,using combinatorial sets of antiviral compoundswith proven antiviral efficacy in cells and a smallanimal model. Specifically, TargetHerpes will performthe following actions:• develop peptide inhibitors that interfere withvirus entry;• generate synthetic peptides that enable antibodydependent cellular cytolysis against herpesviruses;• define, investigate and apply RNA silencingreagents that block the expression of viral genesthat enhance herpesvirus replication;• define, investigate and apply RNA silencingreagents that interfere with proviral host genes;• identify viral and cellular genes involved in herpesvirus-mediatedoncogenesis, and define RNAsilencing reagents and peptide inhibitors; and• develop approaches to inhibit the reactivationof HSV from latency. This programme of workwill provide innovative technologies for theidentification and development of future productstargeted at preventive and therapeuticinterventions for human herpesvirus diseases.Moreover, these strategies will be transferableto many other persistent infections.Expected resultsThe TargetHerpes project is divided into six experimentalwork packages (WPs). The aim of WP1 isthe development of peptide molecules that willinhibit the functions of herpesvirus glycoproteinsand their roles in entry of the virus particles intocells. Preliminary work has provided proof-ofprinciplethat mimetic peptides to HSV gH inhibitinfection. However, the first-generation peptideswere active only at very high concentrations, andas such they could only be applied to culturedcells. TargetHerpes expects to generate highlybioactive and specific peptides that do not exhibittoxicity to uninfected cells. Such peptides targetingHSV glycoproteins, will be suitable for futureanimal experimentation and translational researchby partners PRIMM and IBA. WP2 will generate166

Key words: herpes virus, chemiotherapeutics, herpes simplex virus, human cytomegalovirus, human herpesvirus 8,fusion, glycoproteins, siRNA, innate immunity, host response, IFNROLE OF SMEsFour SMEs are involved in the project. Their respective roles are as follows. BioDec,a young Italian spin-off company born out of University of Bologna, will perform bio -informatics searches, develop algorithms and software for the design of siRNAs orshRNAs and for prediction of protein structures involved in protein:protein interactions;IBA, a small German-based biotec industry will provide tools for si-RNA production aswell as for protein purification and studies of protein:protein interactions. PRIMM, anItalian small biotec company will provide tools for design and synthesis of antagonist andmimetic peptides as well as immunological reagents; ARTTIC, a transnational Europeancompany specializing in the management of large projects will take care of the managementof the project, dissemination of results to public, intellectual property issues.Scientific coordinatorGabriella Campadelli-FiumeUniversity of BolognaCentro Interdipartimentale Galvani (CIG)via S. Giacomo 1240126 Bologna, Italygabriella.campadelli@unibo.itwww.microbiology-virology.unibo.it/persone_en.htmlPartnersRoger EverettMedical Research CouncilMRC Virology UnitGlasgow, United Kingdomwww.mrc.co.uksynthetic peptides that enable IgG antibodies toexecute cell-mediated cytolysis against HSV andHCMV. Such peptides will be evaluated for theirindividual potency in vitro, then bioactive peptideswill be evaluated with regard to safety and harmlessnessto cells, as well as optimal stability in culturedcell systems. WP3, WP4, WP5 and WP6 willidentify suitable molecular targets for antiviralintervention by RNAi. These targets will includeimportant herpes virus gene products that haveknown or suspected roles in promoting viral replicationdirectly or indirectly. In case of WP5, siRNAstargeted at viral genes will be selected based ontheir capacity to interfere with HHV-8 mediatedcell transformation and immortalisation. WP6expects to identify the cellular interaction partnersof ICP0 (the viral protein that is necessary for HSVto reactivate from latency), and to define thoseelements that are required for its activity.Potential applicationsTargetHerpes will identify novel strategies, leadingto the development of new approaches toinhibit the replication of, or pathogenesis causedby, HSV, HCMV and HHV-8. Due to the conservationof genes and replication strategies within herpesviruses,the approaches discovered will beapplicable to other human herpesviruses as well.For example, treatments that target HSV-1 arehighly likely to be effective against HSV-2 and maybe adapted to counteract VZV. Similarly, treatmentsthat are effective against HHV-8 may alsobe applicable to EBV. Given the figures on thehealth burden and costs of herpesvirus infections,the potential impact of a successful outcome ofthe TargetHerpes project, is considerable.Hartmut HengelUniversity of DuesseldorfInstitute for VirologyDusseldorf, Germanywww.uni-duesseldorf.deJoachim BertramIBA GmbHGoettingen, Germanywww.iba-go.comFrank NeipelUniversity of ErlangenInstitut fuer Klinischeund Molekulare VirologieErlangen, Germanywww.viro-med.uni-erlangen.deMichael NevelsUniversity of RegensburgInstitute for MedicalMicrobiology and HygieneFaculty of MedicineMolecular Virology UnitRegensburg, Germanywww.uni-regensburg.deAngela PontilloPRIMM SrlMilan, Italywww.primm.itIvan RossiBioDec SrlBologna, Italywww.biodec.comWolfgang Laepple-BoettigerARTTIC S.A.Office MannheimSchifferstadt, Germanywww.arttic.com167

ACRONYMContract number: LSHB-CT-2007-037365 | EC contribution: € 3 389 184 |Duration: 48 monthsStarting date: 1 March 2007TargetScreen2SUMMARYElucidation of protein function is the nextpost-genomic challenge towards theunderstanding of biological processes inhealth and disease. Transcriptomics andproteomics approaches usually deliverlong lists of “candidate” genes that aresupposedly associated with the respectivediseases. However, neither functionalinformation nor a direct relationship withthe pathology is established.Novel post-genomic cell-based screens fordrug targeting in membrane protein disordersBackgroundExpected resultsStrategies and tools are thus criticallyneeded to distinguish genes and proteinswith mere pathologic associationfrom those primarily responsible for thebasic cellular defect(s) in such pathologies.Membrane proteins, includingreceptors, channels, antibodies, transporters,etc. play major roles in cells andorganisms as they are involved in importantcellular mechanisms, such as communication,immunity, signalling andresponse to environmental stimuli.By bringing together experienced academicand industrial (SMEs) partners ina close and balanced collaboration,utilising a multidisciplinary approach,TargetScreen2 proposes to develop cutting-edgepost-genomics functional cellbasedassays aimed at identifying novelgene targets to correct for traffic and/orfunction of three model membrane proteins(MC4R, ENaC and CFTR) involved inhuman disorders. TargetScreen2 will alsovalidate such targets in the most appropriatecellular systems and, throughstructural modelling of targets, novelsmall molecule compounds will be tailored-designed,optimised and tested tothe pre-clinical stage.The expected results will consist of novelcell-based assays to identify relevanttherapeutic targets in a wide number ofdiseases related to membrane proteins.As a proof-of-concept, TargetScreen2 willapply these innovative ‘from the bench tothe bedside’ approaches to ultimatelydeliver novel therapeutic small molecules,tested to preclinical stage andapplicable to common diseases such asobesity, hyperinsulinemia, hypertensionand cystic fibrosis.Membrane proteins include antibodies, receptors,channels, carriers, transporters, etc. and constitutesome of the largest families encoded in the humangenome, including the ATP-binding cassette (ABC)transporters superfamily, the G protein-coupledreceptors (GPCRs) as well as a large number ofchannels. Given their major roles in cells and organisms(e.g., communication, signalling, response toenvironmental stimuli, immunity, heart rhythm,multiple nervous system functions, etc.), membraneproteins are extremely relevant to a highnumber of human disorders, including commonones (like cardiovascular diseases, obesity, canceror diabetes) and rare genetic diseases. GPCRs andion channels currently represent the most attractivetarget classes for the drug discovery industry.AimThe objective of the TargetScreen2 proposal is todemonstrate the identification of novel therapeutictargets for disorders associated with membraneproteins, using as examples three model proteins,namely: one ABC transporter (the cystic fibrosistransmembrane conductance regulator, CFTR), oneoligomeric channel (the epithelial sodium channel,ENaC) and one GPCR (melanocortin receptor 4,MC4R). To achieve this, TargetScreen2 will developtools and standardise protocols for new postgenomicapproaches addressing the functionalstudy of membrane proteins. TargetScreen2 thusproposes to develop and establish several newhigh performance techniques which will be usedand fully exploited so as to demonstrate their applicability.Hence, the project’s ultimate aim is to facilitatethe generation of new knowledge in functionalgenomics.The major scientific and technological milestonesto be achieved within TargetScreen2 are:• development and establishment of robustimmunofluorescence-based microscopy highthroughputassays to study traffic and/or functionof membrane proteins;• development and establishment of a novel proteincomplementation platform (PCP) and a splitubiquitinassay to screen for proteins interactingwith a membrane protein of choice;• identification and validation of novel therapeutictargets following the application of the twoabove innovative approaches to the three disease-associatedmodel membrane proteins;• target-tailored design and pre-clinical validationof novel therapeutic small-molecules.Potential applicationsPotential applications include identification ofnovel target-tailored lead compounds to threemodel membrane proteins associated with humandiseases (obesity, hyperinsulinemia, hypertensionand cystic fibrosis) and possibly other proteintrafficking disorders. As additional potential applications,novel assays for the identification ofprotein-protein functional/physical interactionsinvolving membrane proteins will result fromthis project.168

Key words: functional genomics, membrane proteins, target-tailored drugs, protein trafficking disorders,protein-protein interactions, robotised confocal microscopyROLE OF SMEsThree SMEs (ECBio, SygnatureChem and Dualsystems) and one additional company participatein TargetScreen2. Their profiles and roles are, respectively:ECBio, is a biotech SME that established its own animal and human cell R&D laboratory in2002 and carries out its research and development activities towards the development ofvarious cell isolation and culture processes, including media development, cryopreservationand development of cytotoxicity and drug testing using innovative target cells. ECBio has alsomade a strategic alliance with a recently established Portuguese cell therapy GMP company,being responsible for human stem cell isolation, culture, cryopreservation and differentiation.Within TargetScreen2, ECBio will be mostly involved in the establishment/immortalisationof primary cultures for the production of novel cell lines in order to both validate the proteintargets resulting from the screens in more appropriate cellular systems and also test thetherapeutic effects of small molecules in such systems.SygnatureChem is a young computational-based drug discovery company with capacities incomputational compound design and synthetic medicinal chemistry, with particular experienceand focus on GPCRs and kinases. It has in-house experience in automated and semiautomatedlibrary preparation of small- and medium-scale compound libraries resulting fromsynthetic work. It also possesses state-of-the-art analytical and purification technology.The role of SygnatureChem within TargetScreen2 is to design and optimise novel small moleculesof potential therapeutic interest by specifically modulating the action of the targetsidentified in the screens and to be subsequently tested up to the pre-clinical phase.Dualsystems major focus is to provide tools and services in the field of interactive proteomicsto the life sciences community. Currently, Dualsystems uses two platform technologies toidentify and characterise novel protein-protein interactions. DUALhybrid is an improved yeasttwo-hybrid platform developed in-house, which allows screening for novel interactors of a proteinof interest. This technology is aimed mainly at soluble proteins, domains or protein fragments.The DUALmembrane system is a unique screening platform aimed at identifyinginteractions involving integral membrane proteins and membrane-associated proteins.Within TargetScreen2, Dualsystems will further develop this technology as novel geneticassays for protein-protein interactions, based on the split-ubiqutin system and other proteincomplementation assays.OSIS (until recently, OBS – Olympus BioSystem GmbH) develops integrated digital imagingsystems for life-science applications serving biological, pharmaceutical and medical researchinstitutions worldwide. With the launch of the real-time fluorescence imaging station cell inJune 2003 OSIS was setting a new standard for leading edge research imaging systems withhighest precision and optimum synchronisation. Meanwhile a whole family of cell ImagingStations are available. Based on the real-time technology of the cell Imaging Station a fullyautomated high speed image acquisition and image analysis system for screening applicationswas developed: the Screening Station scan (responsibility of K Joanidopoulos) that willbe launched in February 2006. OSIS is focused on innovative technology development and hasmore than 10 patents pending or granted. OSIS excels in system integration and has the followingdevelopment expertise: optics, mechanics, electronics, firmware development, softwaredevelopment, image analysis, data analysis. A well equipped workshop allows for fastprototyping and specific adaptations. OSIS can draw on the competence and experience ofa young team of physicists, biologists, chemists that still have close contacts to research laboratories,as well as highly qualified mechanical and electronics engineers and technicians.The role of OSIS in TargetScreen2 will be during the development of confocal microscopebasedsoftware to monitor the robotised screening assays, aimed at identifying protein targetsinvolved in the traffic and function of three model membrane proteins, which provesuitable for high-throughput screening (HTS) analyses.Scientific coordinatorMargarida D. AmaralDepartment of Chemistry and BiochemistryFaculty of Sciences, University of LisboaCampo Grande-C81749-016 Lisboa, Portugalwww.fc.ul.ptCoordinator Cystic Fibrosis Research UnitCentre of Human GeneticsNational Institute of HealthAv. Padre Cruz,1649-016 Lisboa, Portugalmdamaral@fc.ul.ptwww.dqb.fc.ul.pt/docentes/mdbotelho/PartnersRainer PepperkokEuropean Molecular BiologyLaboratoryHeidelberg, Germanywww.embl-heidelberg.deKarl KunzelmannUniversity of RegensburgRegensburg, Germanywww.uni-regensburg.de/Universitaet/welcome2.htmlJohn BC FindlayUniversity of LeedsLeeds, United Kingdomwww.leeds.ac.ukConstança CoelhoInvestigação e Desenvolvimentoem Biotecnologia, S.A.Oeiras, Portugalwww.ecbio.comSimon HirtsSygnature Chemical Services LimitedNottingham, United Kingdomwww.sygnaturechem.comDaniel AuerbachDualsystems Biotech AGZurich, Switzerlandwww.dualsystems.comKonstantin JoanidopoulosOlympus Soft Imaging Solutions GmbHPlanegg, Germanywww.soft-imaging.net169

ACRONYMContract number: LSHP-CT-2006-037217 | EC contribution: € 1 945 000 | Duration: 36 monthsStarting date: 1 December 2006TB-DRUGwww.tbdrug.euSUMMARYThe primary objective of this project is toidentify suitable drug targets and to discoverlead compounds suitable for developmentinto new drugs active againsttuberculosis. The plan of action is to:• express and purify each protein beingtargeted using available expressionsystems;• determine the structure of each proteinby X-ray crystallography;• develop biochemical assays suitable foradaptation to high-throughput screening(HTS);• screen for and identify inhibitors for eachprotein where a suitable assay has beendeveloped;• assess the effectiveness of the bestinhibitors identified against Mycobacteriumtuberculosis in vitro, and;• optimise lead compounds by medicinalchemistry.A SME-STREP for Tuberculosis Drug DevelopmentBackgroundTuberculosis (TB) causes more deaths worldwidethan almost any other infectious disease, withnearly two million deaths per year and has a devastatingimpact on developing countries. Moreeffective means of medical intervention arerequired, both to reduce the number of deathsfrom tuberculosis and to allow for more effectivetreatment of drug-resistant infections.AimThe TB-DRUG project aims to discover novel compoundsagainst Mycobacterium tuberculosiswhich can be developed into products that canalleviate the global burden of TB, by carefullyselecting proteins to be taken into the drug discoveryprocess as novel targets. In anticipation ofthe significant attrition rate of the drug discoveryprocess, it is suggested that the different targetsare included at the earliest stages of drug development,followed by a more focused approach onthe most promising candidates in the later stages.The project will be carefully managed by takingadvantage of industrial knowledge in planningand management. As a minimal outcome of thisconsortium, the aim is to identify 2-3 attractiveleads to be taken forward into a preclinical drugdevelopment phase.Expected resultsIt is expected that the proposed work will result in:• expression and purification of each proteinbeing targeted;• structure determination of each protein purifiedby X-ray crystallography;• development of biochemical assays suitable foradaptation to HTS for each target purified;• screening for and identification of inhibitors foreach protein for which a suitable assay has beendeveloped;• assessment of the effectiveness of the bestinhibitors identified against live M. tuberculosisin vitro;• optimisation of lead compounds by medicinalchemistry.Potential applicationsTB patients in parts of Eastern Europe and CentralAsia have a significant risk of acquiring multidrugresistantTB (MDR-TB). TB incidence rates alsocontinue to rise at an alarming rate in Africancountries with high HIV prevalence. This rise ofMDR-TB and increased susceptibility to TB causedby co-infection with HIV is driving the worldwideTB epidemic and is likely to worsen in the years tocome. The discovery of novel antitubercular drugsnot only promises to benefit people in the easternEuropean, Asian and African countries who suffermost from TB, but also to fight the spread of MDR-TB that could fuel a TB epidemic in all of Europe.By bringing together scientists from many differentdisciplines and by connecting academics withindustry research, TB-DRUG establishes an integrateddrug discovery and development process.The range of complementary expertise availablewithin the proposed Project, together with a stateof-the-artdiscovery technology, facilitates theentire process of preclinical drug discovery. TheTB-DRUG Consortium strives to have a significantimpact in the area of TB drug development andto contribute to the education of young scientistsby offering exceptional teaching and trainingopportunities for post-doctoral fellows andPhD students.170

Key words: microbiology, infections, pharmaceutical chemistry, drug targets, biochemistry, structural biology, tuberculosisROLE OF SMEsWithin this Consortium, there are two SMEs:Vichem is the coordinator and contributes with hit finding and lead optimization against thetarget molecules chosen. Following initial development of biochemical and cellular assaysfrom the different partners within this Project, Vichem will proceed to the development ofhigh-through put screenings assays.R&D Management GmbH organises and chair consortia meetings and gives generaladministrative support to the management of the project.Scientific coordinatorGyörgy KeriVichem Chemie Research Ltd.Herman Ottó utca 151022 Budapest, Hungarykeri@vichem.huwww.vichem.huPartnersMamadou DafféInstitut de Pharmacologieet Biologie StructuraleUniversité Paul SabatierCNRS UMR 5089Toulouse, Francewww.ipbs.frMenico RizziDipartimento di Scienze Chimiche,Alimentari, Farmaceutichee Farmacologiche (DiSCAFF)University of Piemonte Orientale‘Amedeo Avogadro’Novara, Italywww.discaff.unipmn.itPeter SanderInstitut für Medizinische MikrobiologieUniversity of ZurichZurich, Switzerlandwww.imm.unizh.chAndrea F. Degen IseliR&D Management GmbHZurich, Switzerlandwww.researchmanagement.ch© Shutterstock171

ACRONYMContract number: LSHP-CT-2006-037785 |EC contribution: € 2 000 000 | Duration: 36 monthsStarting date: 1 January 2007TB-trDNASUMMARYTuberculosis (TB) continues to be a globalthreat to public health of important socialand financial concern to the expandingEuropean Union and a cause of enormousmorbidity and mortality in much of thedeveloping world. Timely and accuratediagnosis is a critical obstacle to TB controland the currently available diagnosticmethods are marked by being insensitive,slow, and/or cumbersome to use. Nucleicacid amplification is the only rapid detectionmethod with proven sensitivity andspecificity, but is difficult to implement inits current format. A method that avoidedcomplex sputum processing and cell lysissteps that was applicable across multipleamplification formats (e.g. in addition toPCR) would be a tremendous advantage.There is growing evidence that short DNAfragments, arising from human or bacterialcells dying throughout the body, passthrough the renal barrier and appear inurine as transrenal DNA (Tr-DNA). Ina preliminary study conducted at theNational Institute of Infectious Diseasesin Rome, it has been shown that Tr-DNAfrom M. tuberculosis was detectable inthe urine by polymerase chain reaction(PCR) in 100 % of patients with pulmonarytuberculosis and that these DNA fragmentsdisappeared following anti-TBdrug therapy. TB tr-DNA aims to validatethe diagnostic potential of Tr-DNA detectionfor TB, to optimise and simplify thesample preparation methods, and toexplore the feasibility of using a diagnosticapproach based on this method ina developing world setting.Evaluation of transrenal-DNAdetection to diagnose tuberculosisBackgroundTuberculosis remains among the most prevalentcauses of death from an infectious disease in theworld. While global targets for rates of cure havebeen reached in many areas, case detectionremains a significant bottleneck to effective diseasescontrol. Microscopy, the only widely availablelaboratory diagnostic test for tuberculosis,is both difficult to implement and insensitive.Consequently, the availability of new diagnostictools that are more accurate and accessible maygreatly benefit individual patients and significantlycontribute to the control of the disease.AimTB tr-DNA aims to develop a new and highly innovativeplatform for the detection of povertyrelateddiseases (TB followed by HIV, malaria).This platform is based on the principle that dyingcells release cell-free DNA into the blood streamthat then passes through the renal barrier and cansubsequently detected in urine.Expected resultsTB-trDNA is designed to develop a rapid diagnosticprocedure for utilising transrenal DNA as a targetsample for the identification of Tuberculosispatients. The findings of TB-trDNA will also contributeto policy development through knowledgeand awareness of the importance of TB diagnosis,with close association with the respective ministriesof health and international organisationssuch as the World Health Organisation.Potential applicationsGiven the significant challenges of Mtb detectionand monitoring in developing countries, theapplication of the Tr-DNA test could providea very useful new diagnostic tool. By simplifyingthe sampling procedure and combining this withimproved molecular detection methods (whichcould eventually lead to simple dip-stick methods)the findings of TB tr-DNA could ensure that simple,cheap, efficacious TB diagnosis is made availableto the developing world to ensure targeted use ofthe available therapy.172

Key words: transrenal DNA, tuberculosis, diagnosisROLE OF SMEsThe SME of the project, FIND, is an independent, not-for-profit, foundation wholly dedicatedto the development, evaluation, and demonstration of diagnostics for infectious diseasesrelevant for the developing world. FIND has a minor role in most of the WPs of the project,but they will coordinate the interface between test development and product evaluationand conduct a project workshop in 2007 and project public health advisory meeting in2009. FIND will provide documentation and technical expertise related to the customerrequirements and design of the product version(s) to be tested and will ensure that clinicalprotocols will yield data that will have the greatest utility to determining the future of thetechnology for the public health sector.Scientific coordinatorJim HuggettCentre for InfectiousDiseases and International HealthWindeyer InstituteUniversity College London46 Cleveland St.London, W1T 4JF, United Kingdomj.huggett@ucl.ac.ukwww.ucl.ac.uk/medicalschool/infection-immunity/PartnersPeter MwabaDepartment of MedicineUNZA-UCLMS projectUniversity Teaching Hospital D BlockLusaka, ZambiaMichael HoelscherDepartment of Infectious Diseases& Tropical MedicineUniversity of MunichMunich, GermanyLeonard MabokoMbeya Medical Research ProgrammeMbeya, TanzaniaEnrico GirardiDipartimento di EpidemiologiaIstituto Nazionale per le MalattieInfettive L. Spallanzani – IRCCSRome, ItalyGiorgio RoscignoFIND, Foundation for InnovativeNew DiagnosticsCointrin, Switzerlandwww.finddiagnostics.org173

ACRONYMContract number: LSHG-CT-2006-037543 |EC contribution: € 2 086 720 | Duration: 36 monthsTEMPOStarting date: 1 October 2006SUMMARYTEMPO will combine functional genomics,proteomics, cell signalling, systems biologyand pharmacokinetics to optimisetherapeutic efficacy. In vivo, in vitro, in silicoapproaches are integrated through themultidisciplinary excellence in the consortium.TEMPO will offer a proof of principleof tailored chronotherapeutics in mousemodels for irinotecan, an active drugagainst colorectal cancers, and for seliciclib,currently in clinical testing. TEMPOwill gather the corresponding human prerequisitesand technology for subsequentapplication to patients.Temporal Genomics for TailoredChronotherapeuticsBackgroundNon-communicable, chronic diseases representthe bulk of morbidity, disability and prematuredeaths in Europe, and account for 75 % of disability-adjustedlife years. Among those diseases,cancer is the second most important cause ofmorbidity and mortality. Differences in the molecularcharacteristics of tumour cells, as well as differencesin patients’ genetic make-up, gender,age, lifestyle and circadian rhythms, account forlarge variability in the time-course of cancer andin patients’ responses to treatment.AimExpected resultsTEMPO combines functional genomics, proteomics,cell signalling, systems biology andpharmacokinetics to optimise the therapeuticindex in patients. This index in turn determines thechronotherapeutics schedules, according to whichtemporal delivery patterns of the same anticancerdrug vary. Each schedule is adjusted to a differentdynamic class of temporal genomics and phenomicsparameters, relating to interwoven circadianand cell division cycles as well as drugmetabolism. The multidisciplinary nature of theconsortium means that in vivo, in vitro and in silicoapproaches will be integrated to achieve this end.The general objective of TEMPO is to design mouseand in silico models that reflect this variability andallow the prediction of optimal chronotherapeuticdelivery patterns for anti-cancer drugs.Potential applicationsTEMPO epitomises the translation of basicresearch findings into useful clinical applications.Through the identification of nodes in the interplaybetween the circadian timing system, the cell divisioncycle and drug pharmacology parameters, itwill provide critically important information for thetargeted development of new anti-cancer drugs.174

Key words: cell cycle, circadian clock, chronotherapeutics, anti-cancer drugsROLE OF SMEsThree SMEs play a pivotal role for the impact of TEMPO on European health, economics andsociety. Novel and complementary in silico dynamic models of coordinated clock, cell cycleand pharmacology pathways will identify new therapeutic targets and delivery schedules ofactive molecules, thus improving drug development processes.Scientific coordinatorFrancis LéviInstitut National de La Santéet de la Recherche MédicaleINSERM U776 – Rythmesbiologiques et cancersHôpital Paul BrousseAvenue Paul-Vaillant Couturier 14Villejuif, Francelevi-m@vjf.inserm.frPartnersMetabolismProliferation| Schematic representation of cellular circadian rhythmsThe expression of many genes, proteins and enzymatic activities responsiblefor cellular metabolism and proliferation display marked 24-hour rhythms inhealthy mammalian tissues. These rhythms are generated by a molecular clockconstituted of 12 specific genes.Franck DelaunayCentre National de laRecherche Scientifique (CNRS)Université de Nice – CNRS UMR 6348 –Bâtiment de Sciences NaturellesPhysiologie cellulaire et moléculairedes systèmes intégrésNice, FranceLaurent MeijerCentre National de laRecherche Scientifique (CNRS)Laboratoire Mer et santé UMR7150Station Biologique –Amyloïds and Cell Division CycleRoscoff Cedex, FranceJean ClairambaultInstitut national de rechercheen informatique et automatiqueINRIA Rocquencourt Research Unit –Teams Bang and ContraintesLe Chesnay, FranceStefano IacobelliConsorzio InteruniversitarioNazionale per la Bio-oncologia (CINBO)Laboratori of molecular oncologycenter of excellence on aging Ce. S.I.Chieti, ItalyMarco PirovanoH.S. Hospital Services S.p.ATherapeutic deliveryAprilia (Latina), ItalyTodor VujasinovicHelios Biosciences SARLCréteil, FranceChristophe ChassagnolePhysiomics PLCThe Magdalen CentreThe Oxford Science ParkOxford, United KingdomIsabelle GeahelInserm TransfertEuropean Project ManagementDepartmentParis, France175

ACRONYMUSDEPwww.usdep.euContract number: LSHB-CT-2006-037560 | EC contribution: € 2 004 952 | Duration: 36 monthsStarting date: 1 November 2006SUMMARYThe threat of emerging or re-emerginginfectious diseases, as well as the risk ofbioterrorism, has enhanced the currentrequirements for novel, highly sensitiveand specific diagnostics technologies. TheUSDEP project will focus on improving thedetection of emerging pathogens, developingnovel techniques for pathogeniso lation and detection from clinical andenvironmental samples, including thosethat could be used in bioterrorism, andincreasing the sensitivity and specificity ofthe currently available detection methodsused for pathogenic bacteria and viruses.Capture and enrichment of emerging pathogensfor multiple and ultra-sensitive diagnosticBackgroundIn the 1970’s WHO proclaimed that eradication ofsmallpox should be attempted. This goal was successfullyachieved in 1979. Nonetheless, presentlythere is a general consensus that the list of newlyemerging or re-emerging pathogens is continuouslygrowing. Indeed, during the last decadespathogens such as Marburg, Ebola, Hepatitis-C,Hantavirus, HIV and more recently, SARS corona -virus have emerged. Furthermore, the apparentrisk of a new influenza pandemic again highlightsthe global threat of infectious diseases. In addition,the possibility of bioterrorist attacks usinghighly pathogenic viruses and bacteria can not beignored. In consequence, the current requirementsfor novel, highly sensitive and specific diagnosticstechnologies have increased.A major obstacle for the detection of pathogens inclinical or environmental samples are false negativeresults, e.g. for HCV ‘occult infections’. This ismainly due to the lack of a rapid and reliablepathogen concentration methodology, and theinability of most of the currently used technologiesto eliminate or neutralize interferingmolecules, ‘natural inhibitors’, present in mostcomplex samples.AimThe aim of this research programme is to exploitthe ‘non-self’ recognition and binding propertiesof human apolipoprotein H (ApoH) for thedevelopment of novel tools to isolate pathogensfrom complex biological mixtures. ApoH bindspathogens enabling their capture and concentrationfrom different biological samples. Magneticbeads coated with ApoH protein can be efficientlyused as a pre-treatment step to greatly improvethe detection threshold and thereby increasing thesensitivity for diagnosis of emerging pathogens,regardless of the molecular or immunologicaltechniques used in the final diagnostic step.Expected resultsThe project will focus on:• increasing the sensitivity and specificity of thecurrently available detection methods used forpathogenic bacteria and viruses;• on the development of novel techniques forpathogen detection from clinical and environmentalsamples including those that could beused in bioterrorism.Potential applicationsThe industrial partners will develop and standardisenovel technologies for rapid, multiple and ultrasensitivepathogen diagnosis such as mini-arraysystems with the objective of commercialisation.176

Key words: virus diagnostics, ultra sensitive detection, magnetic beads, Apolipoprotein H, emerging pathogensROLE OF SMEsThe USDEP project has a very complementary consortium, where the publicly funded partners,the Robert Koch Institut (RKI), the Institut de Recherches pour le Développement(IRD), the privately funded Pontifica Universidad Catolica de Chile, working in virology andpublic health will incorporate ApoH technology into their panel of regular techniques forpathogen detection. It will be the task of the industrial partners to develop and standardisethe new diagnostic technologies. Namely, ApoH-Technologies develop ApoH coated supportsfor diagnostic purposes, GenExpress is specialized in the development and optimisation ofmolecular biology assays, the Institut für Siliziumtechnologie (ISIT) is specialised in thedevelopment and production of microelectronic components and will supply the electronicbiochips, eBiochip Systems is focussed on manufacturing of technology for electronicbiochip applications, SKULD-TECH develops a mini array system for virus detection andIMMUNOCLIN provides strategic direction as well as management and laboratory servicesfor clinical development and pre-clinical contract research.Scientific coordinatorHeinz EllerbrokRobert Koch-InstitutCentre for Biological SafetyNordufer 20133353 Berlin, GermanyEllerbrokH@rki.dewww.rki.dePartnersDorothy BrayImmunoClin Ltd.London, United Kingdomwww.immunoclin.comElias StefasApoH-TechnologiesMontpellier, FranceFrancisco VeasViral Immuno-Physiopathology LabU178/IRD Viral Emerging DiseasesEA 3755 (Bacteriology-Virology)University of Montpellier 1Montpellier, FranceMarcelo Lopez LastraPontificia Universidad Católica de ChileSantiago, Chilewww.puc.clRoland LausterGenExpress Gesellschaftfür Proteindesign mbHBerlin, Germanywww.genexpress.deRainer HintscheFraunhofer Institutfür Silizium TechnologieItzehoe, Germanywww.isit.fhg.deRalf WörleBiochip Systems GmbHItzehoe, Germanywww.ebiochipsystems.comDidier RitterStamatis VarsamosSkuld-TechMontpellier, Francewww.skuldtech.com177

ACRONYMContract number: LSHG-CT-2006-037277 | EC contribution: € 1 488 560 | Duration: 36 monthsStarting date: 1 October 2006VALAPODYNwww.valapodyn.euSUMMARYThe VALAPODYN project seeks to furtherthe development of multidisciplinary functionalgenomics relating to complex biologicalprocesses and cellular networks.The project is concerned with both DNAand protein applications, to be followed byinnovative dynamic modelling of pathologicaldisease states, such as epilepsyand cancer, in order to validate the model.The overall aim is to develop an innovativesystems biology approach, in order tomodel the dynamics of Molecular Inter -action Networks (MINs) related to celldeath and survival in the organism.Validated Predictive Dynamic Model ofComplex Intracellular PaCell Death and SurvivalBackgroundSelecting the best therapeutic target(s) is one ofthe major challenges in developing new and efficientdrugs. In addition to its scientific relevance,it has a profound impact on the health/quality oflife of the European population, as well as thepharmaceutical industry, by decreasing the costof drug development.Nowadays, although our understanding of individualgene and protein function becomes important,it is not sufficient for unravelling the complexity ofbiological and pathological processes! Indeed,modern high throughput technologies in biologicalscience, such as genomics, transcriptomicsand proteomics, often generate lists of moleculesof interest. However, they do not always increaseour knowledge of the biological processes or thesubsequent identification of therapeutic targets.It therefore becomes critical to develop our understandingof biological system’s structure anddynamics.A biological system is more than an assembly ofgenes and proteins. Its properties cannot be fullyunravelled through static diagrammatic representationsof their interconnections. Although such diagramsrepresent an important step, we now needinformation on the dynamics of these interconnectionsand how we can control them. The challenge istherefore, to construct a descriptive model fromthese lists of molecules that could reflect theunderlying biological mechanisms as accurately aspossible and, ultimately, allow the identificationand selection of the best therapeutic targets totreat human disease.The aim of Systems Biology is to decipher the intricaciesof complex biological systems/organismsthrough the integration of biological, clinicalchemical, physical, mathematical, and computerknowledge.Their approach uses theorical concepts, computationalmodelling and experiment data to allowthe development of mathematical models of thecomplex molecular interaction networks (MINs).Moreover, this approach is emerging also in LifeSciences, with systems pathology guiding an understandingof the multidimensional aspects of diseasesystem fingerprints and systems pharmacology.This provides important insights into dynamic systemresponses upon multiple drug perturbations.Knowledge of the changes of system characteristicsduring the progression of a disease is mandatoryto create a conceptual framework for the design ofnew therapeutic strategies.AimThe aim of the VALAPODYN project is to set up thescientific and technological basis, for tasks withinthe following areas:• Pathway analysis: functional annotation of genesand proteins, investigation of structure anddynamics of signal transduction and transcriptionregulatory networks.• Predictive bioinformatics platform for dynamicmodelling: use of innovative biomathematics/bioinformatics to integrate experimental MINdata with biological tissue and pathologicalstates data obtained through the use of transcriptomicand proteomic approaches.• Bioinformatics: establishment of a highly specialiseddatabase on the genomics and proteomicsof MIN modelling.• Pathological tissue & animal models: analysis ofvalidated animal models of brain pathologies toevaluate gene/protein expression during initialcell death.• Microarrays: extensive multi-level global geneexpression profiling using the Affimetrix platform.• Proteomics: application of advanced quantitativeproteomics technologies (MALDI, ICAT, 2-DPAGE,Heavy Peptides isotopic dilution) for large-scaleproteome screening.• Neuroprotective molecules: characterization ofmolecules in the MIN of cell death the modulationof which should improve or cure neurodegenerativebrain disease.178

Key words: functional genomics, predictive dynamic models Molecular Interaction Networks,cell death and survival, neurodegenerationROLE OF SMEsThere are two SMEs in this consortium Biobase GmbH and Helios Biosciences SARL.The role of Biobase GmbH in the Valapodyn project is to provide high quality manually annotateddatabases to the consortium and applying them to the particular biological field inorder to systematically produce experimentally testable hypotheses. As Valapodyn isdevoted to study mechanisms of neurodegeneration, Biobase focuses on collecting relevantdata including regulation of cell cycle, apoptosis and mechanisms of neurodegeneration.BIOBASE, in collaboration with the other partners, plans to integrate data coming frompartners, and, provide this information to all partners. This activity is in the frame of WP3.Instead, Helios BioSciences will select and classify the therapeutic targets or combinationof therapeutic to cure neuro-degenerescence. Helios activity is at the cross-road ofthe different work-packages of the project as Helios has to integrate (with the help ofBiobase) Molecular Interaction Network and Biological data to build Dynamic Models ofMolecular Interaction Networks and select therapeutic targets which will be then validatedin vivo. In addition to that Helios will commercialize the validated therapeutic targets.Scientific coordinatorAntoine DepaulisGrenoble – Institut des NeurosciencesCentre de recherche Inserm U 836Université Joseph FourierBP170, 38042 Grenoble Cedex, FranceAntoine.depaulis@ujf-grenoble.frhttp://neurosciences.ujf-grenoble.fr/PartnersOlga Kel-MargoulisEdgar WingenderBiobase Wolfenbuettel GmbHGermanywww.biobase-international.com/pagesTodor VujasinovicHELIOS Biosciences SARLCréteil, Francewww.helios-bioscience.comDespina SanoudouFoundation of Biomedical Researchof the Academy of Athens FBRAAMolecular Biology DivisionCenter for basic researchAthens, GreeceExpected resultsThe VALAPODYN network is composed of leadingauthorities in the fields of genomics, proteomics,bioinformatics and neuroscience in Europe. Theyhave decided to join their efforts to develop a newinnovative System Biology approach to model thedynamics of Molecular Interaction Networks (MIN)related to cell death and survival in the brain. Thismodel will be dedicated to the selection of drugtargets for human brain.The project will first validate dynamic models forcell death through the characterisation of newpotential drug targets in an animal model forepilepsy where neurodegeneration is the initialstep of the development of epileptic seizures.Potential applicationsThe development of new and unique dynamic modellingtools will allow the consortium to participatein the process of applying integrative biology topathology research. This should significantlyimprove the quality of life for EU citizens, byadvancing the identification of new generations ofmore efficient drug targets; these drugs will beused to treat numerous diseases accounting formortality and several serious illnesses in the EU,such as cancer, cardiovascular diseases, neurologicaldiseases, etc. Dynamic models will form thebasis for the next generation of biological validationsfor novel therapeutic targets, instead of themethods currently in use, namely those involvinganimal models for drugs acting symptomatically atend receptors and effectors.VALAPODYN will also have a significant impact onthe ERA, by creating a new foundation for theexchange of fundamental research and know -ledge. The development of the internationalR&D network of SMEs in the biotechnology sector(HELIOS, BIOBASE and SynapCell throughINSERM during the project) will accelerate theemergence of the EU as a powerful contender inthe global technological market. The VALAPODYNconsortium will also allow for optimal use of theavailable EU resources and human potential.To disseminate the project results as widely aspossible, several different levels of informationdistribution are proposed. This will involve presentationsand forums for discussion, both ina scientific context (doctors, researchers, neurosciencestudents and collaborators in the field ofneurodegenerative disease research), and alsodirected towards pharmaceutical industrials andEuropean citizens.Edwin De PauwUniversity of Liege ULGDepartment of chemistryMass Spectrometry LaboratoryLiège, BelgiumHermona SoreqHebrew University of JerusalemDepartment of Biological ChemistryInstitute of Life SciencesJerusalem, IsraelRaffaella CatenaAlma Consulting GroupFrancewww.almacg.com179

ACRONYMContract number: LSHM-CT-2006-037254 |EC contribution: € 1 955 856 | Duration: 24 monthsStarting date: 1 January 2007VASOPLUSwww.vasoplus.euSUMMARYThe Vasoplus project evaluates the potentialof PlGF as a pharmaceutical for majorchronic progressive ischemic cardiovasculardisorders (ischemic heart disease,heart failure) and arterial insufficiency(intermittent claudication and critical limbischemia) and as a biomarker for cardiovasculardisease. The project is based onbasic research on the VEGF-signalingpathway (via PlGF) performed over thelast five years (CTG, VIB-3), prototyperesearch performed with recombinantPlGF for pro-angiogenesis (GT and TG/TX),basic research on the association ofplasma PlGF and VEGF levels and humandiseases (IGB) and the development ofa diagnostic test to evaluate PlGF asa biomarker for cardiovascular disease.The comprehensive strategy encompassesthe validation of the ‘proof ofconcept’ observations made by the academicpartners of the consortium intotherapeutic concepts in new relevantsmall animal models, development ofindustrial scale GLP/GMP quality materialsand confirmation of their safety andefficacy in new, relevant large animalmodels. The strategy will be applied tothe development of pro-angiogenicrecombinant PlGF in ischemic heart diseasemodels and in peripheral arterialinsufficiency models. In parallel, thevalue of PlGF as a predictive biomarkerand as a diagnostic test for cardiovasculardisease will be explored in a collaborativeeffort with a large diagnosticcompany.The principal aim of the project is todevelop a new, safe and efficacious medicineto enhance the formation of bloodvessels and in doing so, to develop newtreatment paradigms for heart failureand critical limb ischemia.Placental Growth Factor (PlGF): new diagnosticand therapeutic applications in cardiovascular diseaseBackgroundIschemic heart disease (IHD) and peripheral arterialocclusive disease (PAOD) are the major causeof severe morbidity and mortality in Western societies.Patients who presently survive acute coronaryevents as a result of coronary intervention(angioplasty, stenting or coronary bypass surgery)or pharmacological coronary artery reperfusionoften develop congestive heart failure that is resistantto intervention or pharmacological treatment.Thus, the progress in the treatment of cardiovasculardisease has converted acute lethal syndromesinto a chronic debilitating disease. Therapeuticangiogenesis is a novel treatment paradigm butongoing clinical trials with the angiogenic proteinsVEGF and bFGF have not achieved convincing primaryendpoints of improved tissue perfusion andfunctional recovery. Therefore, current strategiesmust be reconsidered and alternative angiogenictargets validated.The pro-angiogenic drug candidate PlGF, unlikeVEGF, has in proof of concept studies been demonstratedto target pathological angiogenesis and notphysiological angiogenesis and to be devoid ofmost of the systemic side effects associated withadministration of VEGF. In initial proof of conceptstudies, PlGF levels in blood have been shown to bea distinct biomarker for cardiovascular disease.AimThe aim is threefold and summarised below.1. Determine the potential of PLGF as therapeuticfor major chronic progressive ischemic cardiovasculardisorders.• Determine the pro-angiogenic effects of PlGF on:– Revascularisation of ischemic limbs. This willbe studied in mice, rats and in rabbits.– Revascularisation of ischemic cardiac tissue.This will be investigated in mice. These modelswill be of critical importance as these diseasesare prevalent in patients eligible for therapeuticangiogenesis, and the limited success ofclinical trials with VEGF and basic fibroblastgrowth factor (bFGF) has indeed been in partattributed to refractoriness of such diseasegroups to angiogenic growth factors. Thesemodels and strategies will not only be of valuefor the present project but also for the developmentof pro-/anti-angiogenic medicines ingeneral.• Once the pro-angiogenic effect of PlGF will beestablished in rodent models, these effects needto be confirmed and validated in large animalmodels that are physiologically more closelyrelated to the situation in patients. Thereforenewly established models of cardiac ischemia inpigs and in baboons will be used. Demonstrationthat PlGF stimulates vessel growth in diseasesconditions closely related to the situation inpatients will markedly increase the likelihood ofsuccess in humans.2. Further development of the production process.• The production process has been transferred fromits original site of development to an industrialmanufacturer for further development so as to fitwith final production scale and GMP constraints.• State of the art application of ‘in process’ and‘final’ quality and stability control will requireadditional validation of new assays.• Discovery research will be performed on compoundimprovements, involving Cys-to-Gly substitutionfor improved stability and alternative isoforms(glycosylated PlGF-1 and PlGF-2 produced inChinese hamster ovary (CHO) cells).3. Determine the potential of PlGF as biomarker forcardiovascular disease.• Population study: A database, recently developedby IGB, holds the description of the health status,the genealogy and the genome-wide microsatellitemarker scan of approximately 4 000 individualsfrom genetically isolated villages in Italy. Thisdatabase will be studied to determine the contributionof PlGF and VEGF to specific humancardiovascular diseases and cancer.• Development of a reliable diagnostic test formeasurement of PlGF concentrations in humanblood samples based on compounds fromGeymonat and ThromboGencics/Thromb-X. It isintended to evaluate the degree of angiogenesis180

Key words: placental growth factor, PlGF, ischemia, cardiovascular diseaseROLE OF SMEsThree European SMEs based in Ireland, Belgium and Italy are involved. The project is led byThrombogenics/Thromb-X, an Irish biopharmaceutical company focused on the clinicaldevelopment of cardiovascular drugs in-licensed from academic institutions via its R&Daffiliate Thromb-X. Their research focuses on the preclinical development of biopharmaceuticalsfor innovative treatments of severe diseases as well as on the development of improvedtechnologies for transgenesis in mammalian species and for regenerative medicine. An Italianpharmaceutical SME, Geymonat SpA, has experience in translational biopharmaceuticalresearch and development. A Belgian biotech SME, Eurogentec S.A., will provide valuableexpertise in industrial development of recombinant PlGF compounds.These SMEs will receive 58 % of the project budget. There is a well-balanced integration ofthe industrial partners (three SMEs plusl a large company) and academic groups, orientatedtowards industrial exploitation of expected results.based on PlGF blood levels, together with otherbiomarkers of cardiovascular disorders, in a wellcharacterisedItalian cohort with the intent tostratify patients who might benefit from proangiogenictreatment.Expected resultsExpected results for the different objectives are asfollows.1. Determine the potential of PLGF as therapeuticfor major chronic progressive ischemic cardiovasculardisorders.• Efficacy analysis of rhPlGF-1 for revascularisationof ischemic myocardium and limb muscle.• Comparative analysis of rhPlGF-1 efficacy forrevascularisation of ischemic tissue in rat andrabbit ischemia models.• Comparative analysis of rhPlGF-1 efficacy forrevascularisation of ischemic tissue in a mousemodel of ischemic cardiac failure.• Data on the percentage of animals that develop adysfunctional and ischemic myocardium versusthose that develop significant transmural necrosiscaused by acute occlusion of the stented segment.This will allow the project to determine thenumber of animals required to enter the study.• An evaluation of the size of dysfunctional but viablemyocardium by magnetic resonance imaging withdelayed enhancement as well as dobutaminestress echo and quantitation of global LV functionallowing power calculations for the NNT in order toobserve a significant increase in global LV function(increase in Ejection Fraction by 4-6%).• Perfusion studies to quantify the degree ofmyocardial perfusion both in the endo- and epicardialmyocardium. The effect of intervention onLV function will be expected within 1.5 years.2. Further development of the production process.• GLP qualified and GMP qualified rhPlGF-1.• High yield production of the mutein.• Stability of the mutein in solution and gel analysed.• Biological activity of the mutein verified by in vitroassays.• Small scale preparations available of CHO-producedrhPlGF-1, rhPlGF-2 and rhPlGF-1CG.• Validation for each assay development.• GLP compliant certification/recognition of theBelgian Monitoring authorities based on a fictiveGLP stability study with the aim to determine theshelf life and stability on rhPlGF-1.3. Determine the potential of PlGF as biomarker forcardiovascular disease.• Correlation of the plasma levels of VEGF and PlGF(-1 and -2) and health status of 2 800 samples byanalysis of the project database.• Definition of the VEGF and PlGF haplotypes in2 800 individuals.• Association analysis of VEGF and PlGF variants andhaplotypes with a trait or disease.• Status of PlGF assay development including preanalyticalconditions.• Completion of sample measurements using PlGFprototype assay, sCD40L and NT-pro-BNP diagnosticassays.• Correlation of plasma levels of PlGF, sCD40L, NTpro-BNP and health status of the study individuals.• Multi-variate analysis of the study completed.Potential applicationsTwo possible applications are being pursued withthis programme: a new, safe and effective medicineto enhance the formation of new blood vesselsin ischemic tissues and a new diagnostic tool forcardiovascular disease.Scientific coordinatorJ.M. StassenThromboGenics Ltd.14 Bridgecourt Office ParkWalkinstown AvenueDublin 12, Irelandjmstassen@thrombogenics.comwww.thrombogenics.comPartnersMauro BattistiGeymonat SpAAnagni, Italywww.geymonat.com/profilo.htmFlorence XhonneuxEurogentec S.A.Liege Science ParkSeraing, Belgiumwww.eurogentec.com/eu-home.htmlStefan JanssensKULeuvenLeuven, BelgiumMaria G. PersicoInstitute of Genetics and Biophysics A.B.T.Naples, ItalyPhilip BadenhorstUniversity of the Free StateBloemfontein, South Africawww.uovs.ac.zaGeorg HessRoche Diagnostics GmbHMannheim, Germanywww.roche.de/diagnostics/index.htmPlaceboPIGF treatment| More visible collateral vessels after 7 days ofPIGF treatment in rabbit hindlimb ischemia.181

ACRONYMContract number: LSHC-CT-2006-037874 |EC contribution: € 2 050 000 | Duration: 36 monthsStarting date: 1 January 2007VITALwww.cro.sanita.fvg.it/progetti/vital/index.htmSUMMARYTherapeutic vaccines targeting B cellnon-Hodgkin lymphoma (NHL) idiotype(Id) represent a promising approachagainst these malignancies. A broad useof Id-based vaccination, however, ishampered by the complexity and costsdue to the individualized production ofthese vaccines. Recent evidence indicatesthat these limitations may be overcome.In fact, distinct sets of stereotypedimmunoglobulins have been identified invarious B-NHL, suggesting that patientsshare Id with a higher frequency thanappreciated previously. Through thecomplementary and synergistic work ofacademic partners and three SMEs, weplan to exploit the molecular featuresof Id proteins of distinct B cell lymphomas/leukemias,particularly thosepathogenically associated with antigenstimulation and/or selection, to developpre-made, recombinant Id proteins tovaccinate subgroups of lympho-proliferativedisorders expressing molecularlycorrelated idiotypes. A database of Idsequences expressed by different B-NHLwill be constructed to identify subgroupsof tumors expressing molecularly correlatedId proteins. Selected Id proteins willbe characterized for their immunogenicityand, particularly, for the ability toinduce cross-reactive immune responsesagainst related Id proteins. B and T cellepitopes will be identified using innovativeapproaches and dedicated assaysfor immunomonitoring will be developed.Optimized versions of selected Idvaccines will be produced using newstrategies and validated in animal models.New adjuvants and delivery systemsfor improved Id vaccine formulations andadministration will be also evaluated andvalidated. The most promising Id proteinswill be produced and purified accordingto GMP standards and included in newvaccine formulations for innovative trialsof ‘cross-reactive’ immunotherapy.Development of optimized recombinant idiotypicvaccines for subset-specific immunotherapyof B cell lymphomasBackgroundNon-Hodgkin’s lymphomas (NHL) constitutea heterogeneous group of malignancies whoseincidence has significantly increased in recentdecades. In the year 2000, more than 145 000cases of NHL were diagnosed in developed countries,representing thus the sixth most commoncancer occurring among men and the eighthamong women. Low-grade B-cell NHLs, in particular,are incurable diseases characterized byrelatively slow growth and excellent initial responsivenessto chemotherapy but also by continuousrelapses. In particular, for patients with follicularlymphoma, median overall survival (7-10 years)has not improved over the past 30 years.Although in the vast majority of patients completeor partial remissions can be obtained with eithersingle agents or combination chemotherapy, theclinical course is characterized by a high relapserate. After relapse, both the response rate andrelapse-free survival after subsequent salvagetreatment regimens steadily decrease, resultingin a median survival of only 4-5 years after the firstrelapse. These clinical findings, coupled with thesubstantial toxicities of standard treatments,have stimulated the search for novel and moretumor-selective therapies. Therapeutic vaccinestargeting B cell lymphoma idiotype (Id) representa promising immunotherapeutic approach fora better clinical control of these malignancies.This strategy is based on the observation thatimmunoglobulins (Ig) expressed by neoplastic Blymphocytes carry unique determinants in theirvariable regions (idiotypes), which can be recognizedas tumor specific-antigens. Indeed, bothprotein- and dendritic cell-based vaccines thatuse the patient-specific Id have resulted in clinicallysignificant tumor-specific cellular responseswith very little toxicity. A broad use of Id-basedvaccination for B cell lymphomas, however, ishampered by the fact that these approaches arepatient-specific so that the vaccine must be individuallyproduced for each patient. On thesegrounds, new strategies obviating the need toproduce customized vaccines would further simplifyclinical applications of idiotypic vaccines.AimThe objective of VITAL is the development andproduction of optimized recombinant idiotypicvaccines for the treatment of subgroups of lymphoproliferativedisorders expressing molecularlycorrelated idiotypes. These vaccines will beincluded in new formulations for innovative trialsof immunotherapy potentially targeting a largefraction of lymphoma/leukemia patients.Expected results• Establishment of a large database includingsequences of idiotypic VH and VL genesexpressed by a variety of lympho-proliferativedisorders, including low grade B-NHL, autoimmunity-associatedlympho-proliferations, andchronic lymphocytic leukemia. This will allowthe identification of candidate Id proteins for‘cross-reactive’ immunotherapy.• Pre-clinical characterization of the immunogenicityof selected natural Id proteins, with particularregard to their ability to induce immuneresponses against lymphoma cells expressingmolecularly correlated Id proteins. The characterizationwill include the identification of B cellepitopes and HLA Class I-restricted cytotoxic Tcell epitopes using innovative approaches andwill allow the development of dedicated assaysfor immunomonitoring.• Design and validation of optimized Id vaccines.• Evaluation and validation of new adjuvants andinnovative delivery systems for improved Idvaccine formulations and administration.• ‘Clinical-grade’ production and purification ofoptimized Id proteins for patient vaccination.The SMEs are an integral part in the project inmaking the new diagnostic and therapeutic toolsavailable, not only for Europe but also for theworld market. The close integration between clinicaland research activities at several university182

Key words: lymphoma, leukaemia, vaccine, idiotype, immunotherapyROLE OF SMEsThree SMES, out of seven participants, play a key role in the research activities of the project.In particular, PEPSCAN will be responsible for design, preparation and screening of syntheticpeptide libraries and for the reconstruction of interaction sites in the complexesincluded in VITAL. It will coordinate the mapping of B cell epitopes and test the efficacy ofnew adjuvants.ProImmune Ltd. will be involved in the identification of HLA Class I-restricted CTL epitopes.It will do so by using its Pro5® MHC Pentamers and ProVE MHC Pentamer Libraries. In closecollaboration with PEPSCAN, optimised versions of selected Id vaccines will be producedusing different new strategies to enhance both humoral and cellular immune responses.Areta International will, through process development and manufacturing of tailored-madebatches, produce the most promising Id proteins according to GMP standards. If necessary, itwill define innovative technological approaches for GMP scale-up production and purificationof selected recombinant Id proteins.Scientific coordinatorRiccardo DolcettiCentro di Riferimento Oncologico – IRCCSNational Cancer InstituteVia Franco Gallini, 233081 Aviano, Italyrdolcetti@cro.itPartnersBjarne BogenUniversity of Oslo andRikshospitalet University HospitalOslo, NorwayMaria MasucciKarolinska InstitutetStockholm, SwedenAntonio RosatoDepartment of Oncologyand Surgical SciencesUniversity of PadovaPadova, ItalyHans PetrusMaria LangedijkPepscan Therapeutics B.V.Lelystad, The Netherlandswww.pepscan.nlhospitals and Cancer Centers with the SMEs willform new centres of excellence where EuropeanSMEs will benefit from close collaboration at thesame time as new diagnostic and therapeuticproducts will be developed to the benefit ofpatients with lymphoid malignancies.Nikolai SchwabeProImmune LimitedOxford, United Kingdomwww.proimmune.com/ecommerceMaria Luisa NolliAreta International S.r.l.Gerenzano (VA), Italywww.aretaint.comPotential applicationsThe results obtained in the present project willallow the design and activation of phase I/II clinicaltrials aimed at validating the use of optimized,pre-made vaccines for the treatment ofa relatively broad spectrum of lymphoid malignancies.The proposed Id vaccination may be beneficialalso for patients with pre-neoplastic B-celllymphoproliferations, such as mixed cryoglobulinaemia.These vaccines, in fact, may be usedwith the purpose to alleviate the symptoms and,ultimately, to prevent the possible evolutiontowards an overt B cell malignancy. Once validatedas drugs, the vaccines will have the advantageto be easily distributed to all Hematologyand Oncology Departments, including those ofperipheral Hospitals/Universities. Thus, resultsobtained in the present project will have animportant strategic impact in solving, at least inpart, the dramatic social and health problemrepresented by NHL.| Flow chart, outlining the main expectedresults, leading from identificationof shared idiotypes to the developmentof optimized vaccines for the treatmentof B-cell lymphoproliferations.183

ACRONYMContract number: LSHG-CT-2006-037220 |EC contribution: € 1 739 000 | Duration: 36 monthsStarting date: 1 January 2007ZF-TOOLSbiology.leidenuniv.nl/ibl/S1/research/ZF-TOOLSSUMMARYThe ZF-TOOLS project comprises the coordinatedefforts of three research laboratoriesand three SMEs aimed to achievethe following two main objectives: First,a genomic-based marker discovery forbiomedical screens in zebrafish and, secondly,the use of high-throughput markeranalysis and tumour cell implants forthe identification of tumour growth andmetastasis factors and organismaldefence factors.High-throughput Tools for BiomedicalScreens in ZebrafishBackgroundHuman disease research and drug developmentrely heavily on the use of animal models. Amongthese, the mouse model is the most intensivelystudied. However, over the last decade thezebrafish has emerged as an attractive alternativemodel and has progressively gained importance.This is due to the fact that the zebrafish offersexciting novel research opportunities because ofthe optical transparency of its embryos and itsamenability to genetics. To date, the value ofzebrafish in pharmacological studies has not yetbeen extensively explored and exploited. However,findings emphasise the potential of using zebrafishin several phases of drug discovery processes andin toxicological screens.The ZF-TOOLS project is focused on the incorporationof zebrafish into the preclinical drug screeningpipelines. The small size of zebrafish embryos andthe large numbers in which they can be obtainedmake them particularly suitable for high-throughputdrug screens. Furthermore, drugs can be easilyapplied to zebrafish embryos through dilution inthe embryo medium and absorption through skinand gills.AimThe project aims to develop a case study for an antitumourdrug screening system, based on theimplantation of fluorescently labelled tumour cellsinto zebrafish embryos. This innovative tumour cellimplantation system is currently being developedby one of the SME partners and has the majoradvantage that it does not involve the use of transgenicanimals. Growth and metastasis properties ofimplanted tumour cells can be efficiently monitoredby fluorescence microscopy during the developmentof the transparent zebrafish embryos. Thissystem resembles the natural situation of tumourgrowth, as the tumour cells are derived fromzebrafish cell cultures of embryonic origin andimplanted back into zebrafish embryos. It is envisagedthat a powerful screening system can arise bycombining high-throughput marker analysis withthe possibility to visualise tumour growth andmetastasis in an optically transparent vertebratemodel organism.However, for the realisation of this complex screeningsystem, the identification of relevant diseasemarker genes in zebrafish represents a crucial step.In ZF-TOOLS, different genomics approaches will beused to discover novel markers, which will be suitablefor application in the ZF-TOOLS tumour screeningsystem and will also have a broader utility fordisease research in the zebrafish model. The experimentaldesign of this genomics approach isexpected to result in the identification of twoclasses of markers, namely markers correlatingwith growth and metastasis of tumour cells andmarkers correlating with the immune or otherdefence responses of the organism towards tumourcells. The project will concentrate on both classesof markers because the interactions betweendeveloping tumours and the tumour microenvironmentare decisive for tumour survival or rejection.Expected resultsThe strategic aim of ZF-TOOLS is the developmentof a zebrafish embryo screening system as aninnovative genomics tool. This system will beemployed for high-throughput effectiveness testingof pharmaceutical compounds that have thepotential to influence disease processes, includingtumour growth, metastasis and immune defenceresponses. This zebrafish screening tool offerssome unique features that make it very attractive incomparison with existing tools. First, it combinesthe power of genomic analysis of disease markergenes with the power of in vivo monitoring of diseaseprocesses in a transparent vertebrate modelorganism. Secondly, it has the potential for highthroughputapplication due to the small size ofzebrafish embryos, to the high numbers with whichembryos can be obtained, and to the choice ofhigh-throughput molecular screening tools thatwill be developed within the project.In order to establish the zebrafish screening tools,the project will undertake a multidisciplinaryfunctional genomics approach which integratesdifferent global expression profiling techniquesand bioinformatics. Based on this approach, the184

Key words: zebrafish embryo model, oncogenic cell implants, anti-tumor drug discovery, reporter cell lines, tumor markers,immune response markers, expression profilingROLE OF SMEsThree research intensive SMEs, ZF-screens B.V, BaseClear B.V and ZenonBio Ltd., play a crucialrole in the ZF-TOOLS project.The activities of ZF-Screens B.V. are focused on the development and application of the tumourimplantation system, including drug screens and the identification and exploitation of noveltumour factors. Zebrafish embryo-based screens, integrated at an early phase in the drug discoverypipeline, can likely increase efficiency of further tests in a rodent system. It is expectedthat a proof-of-principle of the tumour implant screening system would open up a fast market,not only for contract research in screens for new therapeutics but also for licensing of the noveltechnology that ZF-Screens has developed and will further strengthen during this project.The main role of BaseClear B.V. in the project is the development of high-throughput expressionanalysis tests, based on the use of MLPA (Multiplex Ligation-dependent Probe Amplification)technology. MLPA has been an important breakthrough in DNA diagnostics and is also extremelyvaluable to increase efficiency of mRNA expression profiling (RT-MLPA). BaseClear has beenactive in custom molecular services and contract research projects since 1993. Currently, thecompany serves more than 2 400 customers from 450 national and international companies anduniversity research departments. BaseClear intends to exploit the experience gained fromthe ZF-TOOLS project to add MLPA and RT-MLPA custom services to their portfolio. In addition,RT-MLPA probe sets developed in the project will be sold for research purposes.ZenonBio Ltd. is the main bioinformatics partner in the project, responsible for analysis and integrationof genomic data sets. The company markets state-of-the-art diagnostic systems inHungary and previously developed software for signal and image processing. Their bioinformaticsexpertise, further strengthened by the project, will be directed towards development ofservices. A potentially good market for new entrepreneurial activities of ZenonBio Ltd. lies in theSouth-Eastern European region, including Hungary, Serbia-Montenegro, Romania and Bulgaria.Scientific coordinatorAnnemarie H. MeijerLeiden UniversityInstitute of BiologyClusius LaboratoryWassenaarseweg 642333 AL Leiden, The Netherlandsa.h.meijer@biology.leidenuniv.nlwww.biology.leidenuniv.nl/ibl/about.shtmlPartnersHerman P. SpainkZF-screens B.V.The Netherlandswww.zf-screens.comNicholas Simon FoulkesForschungszentrum KarlsruheKarlsruhe, Germanywww.fzk.deBas ReichertBaseClear B.V.The Netherlandswww.baseclear.comTamás ForraiZenon Bio Ltd.Hungarywww.zenonbio.huMátyás MinkSzeged UniversityDepartment of Geneticsand Molecular BiologyHungarywww.u-szeged.hu/indexe.htmlZF-TOOLS project expects to achieve the followingresults:• knowledge of tumour growth and metastasisfactors and organismal defence factors;• high-throughput tools for quantitative analysisof disease marker sets;• a collection of constitutive and inducible, oncogenicand non-oncogenic reporter cell lines usefulfor basic disease research and for applicationin screening systems;• case study results of a novel anti-tumour drugscreening system, based on the implantation offluorescently labelled tumour cells into zebrafishembryos.Potential applicationsThe ZF-TOOLS project aims to reinforce Europeancompetitiveness by generating strategic know -ledge, thanks to its multidisciplinary researchapproach. The developed tools and technologywill be exploited for basic research on vertebratedisease and for strategic research and serviceactivities on behalf of three high-tech SMEs.The ZF-TOOLS objectives are focused on the incorporationof the zebrafish embryo model into thepreclinical drug screening pipelines. The use ofmice for in vivo monitoring of disease processessuch as tumourigenesis, metastasis and immuneresponse to tumours is limited by costs andthroughput level. Introducing a high-throughputzebrafish embryo model could potentially contributeto cost-effective and more efficient methodsin the anti-tumour drug discovery process.Moreover, acceleration of drug lead time benefitseconomy as well as quality of life of cancer patients.The lack of basic knowledge of disease markergenes is the current bottleneck for biomedicalresearch in zebrafish and for genomics-based compoundscreens in this model organism. The ZF-TOOLS project uses multidisciplinary functionalgenomics approaches to discover novel diseasemarkers. The expected identification of factorsimportant for tumour growth and metastasis andorganismal defence responses will generate fundamentalknowledge relevant to human health andwill open the door to the establishment of zebrafishbasedbiomedical research and screening tools.| Transparent zebrafish embryo.185

ACRONYMContract number: LSHB-CT-2006-037244 | EC contribution: € 2 326 567 | Duration: 36 monthsStarting date: 1 December 2006PREGENESYSwww.pregenesys.net/mainSUMMARYPreeclampsia is a multi-system disorderthat complicates 5-7% of all pregnancies,is responsible for 18% (the second largestcause) of maternal deaths during pregnancy,and for a third of premature births.This complex disorder is expressed asa newly onset hypertension and proteinloss in urine (proteinuria) that develops inthe mother after the 20 th week of gestation,in association with varying degreesof end-organ damage. It may be coupledto potentially life-threatening complicationsof the kidney, liver, blood systemand brain, and can result in convulsions/seizures(eclampsia).Concerning the baby, preeclampsia isresponsible for approximately 7-9 % ofneonatal morbidity and mortality. Majormotor and cognitive disabilities, blindnessand life-long complications can taketheir toll.While clinically diagnosed in the secondhalf of pregnancy, the underlying pathophysiologyis associated with deleteriousalterations of implantation and placentation,which already begin in the firsttrimester.There is no ‘gold standard’ for an effectivepreventive therapy and the only currentlyaccepted treatment of establishedpreeclampsia is (premature) delivery. Thisis often done at the expense of foetal wellbeing(excess neonatal morbidity andmortality).The Pregenesys research project is cofinancedby and carried out within Priority 1of FP6. It aims to develop early (1 st trimesterof pregnancy) non-invasive biomarkersand means for the diagnosis and monitoringof preeclampsia and its progression,that would help to tailor appropriate putativetherapies, thus optimising them forthe prevention of preeclampsia or thereduction of its severity.Development of Early Non-Invasive Biomarkersand Means for the Diagnosis and ProgressionMonitoring of Preeclampsia and TailoringPutative TherapiesROLE OF SMEsDiagnostic Technologies Ltd. (DTL) is the project coordinator. It is a medical diagnostic andbiotechnology company at the forefront of placental protein molecular biology and biochemistryincubated at the Technion-Israel Institute of Technology (Haifa, Israel) in 1994and emerged as an independent company in 2001.ImunoSTAR – Research and Commercialisation of Bio-diagnostic Products S.A. – aims atpromoting and commercialising innovative immunology tests and diagnostic servicesfor application in biomedical and health market. It specialises in the Obstetrics andGynaecology field.| Confocal microscopy of normal term placental villi.Placental villi from a normal term placenta stained for PP13(red) and actin (green) are shown. Nuclei were counterstained with DAPI. Shown is an overlay of a stack of 20single images. (Courtesy of B. Huppertz, Graz.)Scientific coordinatorHamutal MeiriDiagnostic Technologies Ltd.2 Ha’Carmel St.,Building B, 4th floorYokneam 20692, Israelhamutal.meiri@pregenesys.comhamutalmeiri@hotmail.comThe project is undertaken by a consortiumconsisting of 10 members from 9 differentcountries, including universities, hospitals,private research organisations, SMEs anda large industrial company.186

SME CALLIndexby projectnumber• LSHP-CT-2005-037912FASTEST-TB . . . . . . . . . . . . . . . . . 66• LSHP-CT-2006-036871INNOVAC . . . . . . . . . . . . . . . . . . 88• LSHM-CT-2006-036534NEOBRAIN . . . . . . . . . . . . . . . . . 120• LSHB-CT-2006-036813PROLIGEN . . . . . . . . . . . . . . . . . 142• LSHM-CT-2006-037050INDABIP. . . . . . . . . . . . . . . . . . . . 86• LHSB-CT-2006-037168EXERA . . . . . . . . . . . . . . . . . . . . 62• LSHP-CT-2006-037200MUNANOVAC . . . . . . . . . . . . . . . . 112• LSHB-CT-2006-037212Diagnosis . . . . . . . . . . . . . . . . . . 44• LSHP-CT-2006-037217TB-DRUG . . . . . . . . . . . . . . . . . . 170• LSHG-CT-2006-037220ZF-TOOLS . . . . . . . . . . . . . . . . . . 184• LSHG-CT-2006-037226MEGATOOLS . . . . . . . . . . . . . . . . 104• LSHM-CT-2006-037227CVDIMMUNE . . . . . . . . . . . . . . . . 38• LSHG-CT-2006-037231SYSCO . . . . . . . . . . . . . . . . . . . . 160• LSHB-CT-2006-037244PREGENESYS . . . . . . . . . . . . . . . 186• LSHB-CT-2006-037245NanoSense . . . . . . . . . . . . . . . . . 118• LSHC-CT-2006-037251CAPPELLA . . . . . . . . . . . . . . . . . . 26• LSHM-CT-2006-037254VASOPLUS . . . . . . . . . . . . . . . . . 180• LSHP-CT-2006-037276RespViruses . . . . . . . . . . . . . . . . 148• LSHG-CT-2006-037277VALAPODYN . . . . . . . . . . . . . . . 178• LSHB-CT-2006-037293QuAGSIC . . . . . . . . . . . . . . . . . . 144• LSHB-CT-2006-037319IBDchip . . . . . . . . . . . . . . . . . . . 80• LSHB-CT-2006-037325BacAbs . . . . . . . . . . . . . . . . . . . . 18• LSHB-CT-2006-037386ANGIOSTOP . . . . . . . . . . . . . . . . . 12• LSHM-CT-2006-037400IMMUNATH . . . . . . . . . . . . . . . . . 82• LSHG-CT-2006-037415SMARTER . . . . . . . . . . . . . . . . . . 154• LSHG-CT-2006-037457SysProt . . . . . . . . . . . . . . . . . . . 162• LSHG-CT-2006-037462ChILL . . . . . . . . . . . . . . . . . . . . . 28• LSHB-CT-2006-037479MYOAMP . . . . . . . . . . . . . . . . . . 116• LSHC-CT-2006-037489Immuno-PDT . . . . . . . . . . . . . . . . 84• LSHP-CT-2006-037494PRIBOMAL . . . . . . . . . . . . . . . . . 138• LSHB-CT-2006-037499liintop . . . . . . . . . . . . . . . . . . . . 96• LSHG-CT-2006-037517TargetHerpes . . . . . . . . . . . . . . . 166• LSHG-CT-2006-037543TEMPO. . . . . . . . . . . . . . . . . . . . 174• LSHB-CT-2006-037545ENLIGHT . . . . . . . . . . . . . . . . . . . 56• LSHM-CT-2006-037554AGLAEA . . . . . . . . . . . . . . . . . . . . 10• LSHC-CT-2006-037555MAMMI . . . . . . . . . . . . . . . . . . . 100188

• LSHC-CT-2006-037559CancerGrid . . . . . . . . . . . . . . . . . . 22• LSHB-CT-2006-037560USDEP . . . . . . . . . . . . . . . . . . . . 176• LSHB-CT-2006-037575COMICS . . . . . . . . . . . . . . . . . . . . 36• LSHG-CT-2006-037586STREPTOMICS . . . . . . . . . . . . . . 158• LSHP-CT-2006-037587PlasmodiumdUTPase . . . . . . . . . . 134• LSHP-CT-2006-037651EPIVAC . . . . . . . . . . . . . . . . . . . . 58• LSHB-CT-2006-037653OMVac . . . . . . . . . . . . . . . . . . . . 126• LSHB-CT-2006-037661GLYFDIS . . . . . . . . . . . . . . . . . . . 70• LSHB-CT-2006-037681DiaNa . . . . . . . . . . . . . . . . . . . . . 48• LSHG-CT-2006-037683FGENTCARD . . . . . . . . . . . . . . . . 68• LSHM-CT-2006-037692NPARI . . . . . . . . . . . . . . . . . . . . 124• LSHB-CT-2006-037702Mimovax . . . . . . . . . . . . . . . . . . 108• LSHC-CT-2006-037737HI-CAM . . . . . . . . . . . . . . . . . . . . 72• LSHB-CT-2006-037739Drop-Top . . . . . . . . . . . . . . . . . . 50• LSHP-CT-2006-037785TB-trDNA . . . . . . . . . . . . . . . . . . 172• LSHG-CT-2006-037793OptiCryst . . . . . . . . . . . . . . . . . . 128• LSHP-CT-2006-037796SERO-TB. . . . . . . . . . . . . . . . . . . 152• LSHM-CT-2006-037833MYASTAID . . . . . . . . . . . . . . . . . 114• LSHM-CT-2006-037846RATstream. . . . . . . . . . . . . . . . 146• LSHC-CT-2006-037852LIGHTS . . . . . . . . . . . . . . . . . . . . 94• LSHM-CT-2006-037870EACCAD . . . . . . . . . . . . . . . . . . . 54• LSHC-CT-2006-037874VITAL . . . . . . . . . . . . . . . . . . . . . 182• LSHG-CT-2006-037897AUTOSCREEN . . . . . . . . . . . . . . . . 16• LSHE-CT-2006-037899MANASP . . . . . . . . . . . . . . . . . . 102• LSHG-CT-2006-037939BioBridge . . . . . . . . . . . . . . . . . . 20• LSHM-CT-2006-037950cNEUPRO . . . . . . . . . . . . . . . . . . 32• LSHM-CT-2006-037957MagRSA . . . . . . . . . . . . . . . . . . . 98• LSHM-CT-2006-037965INTELLIMAZE . . . . . . . . . . . . . . . . 90• LSHB-CT-2007-036644DIALOK . . . . . . . . . . . . . . . . . . . . 46• LSHB-CT-2007-037241SAGE . . . . . . . . . . . . . . . . . . . . . 150• LSHB-CT-2007-037283EURO-PHARMACO-GENE . . . . . . . . 60• LSHG-CT-2007-037291MODEST . . . . . . . . . . . . . . . . . . 110• LSHP-CT-2007-037301HIVSTOP . . . . . . . . . . . . . . . . . . . 78• LSHB-CT-2007-037303DeZnIT . . . . . . . . . . . . . . . . . . . . 42• LSHP-CT-2007-037304CILMALVAC . . . . . . . . . . . . . . . . . 30• LSHB-CT-2007-037365TargetScreen2 . . . . . . . . . . . . . . 168• LSHM-CT-2007-037472TAMAHUD . . . . . . . . . . . . . . . . . . 164• LSHB-CT-2007-037590Net2Drug . . . . . . . . . . . . . . . . . . . 122• LSHB-CT-2007-037636InVitroHeart . . . . . . . . . . . . . . . . . . 92• LSHC-CT-2007-037642HighReX . . . . . . . . . . . . . . . . . . . . 74• LSHM-CT-2007-037669PHECOMP . . . . . . . . . . . . . . . . . . 130• LSHB-CT-2007-037703STEMDIAGNOSTICS. . . . . . . . . . . . . 156• LSHB-CT-2007-037730COBRED . . . . . . . . . . . . . . . . . . . . 34• LSHB-CT-2007-037740PRISM . . . . . . . . . . . . . . . . . . . . . 140• LSHP-CT-2007-037760HIVResInh. . . . . . . . . . . . . . . . . . . . 76• LSHM-CT-2007-037765PHOTOLYSIS . . . . . . . . . . . . . . . . . 132• LSHM-CT-2007-037831MEMORIES . . . . . . . . . . . . . . . . . . 106• LSHC-CT-2007-037834DEPPICT . . . . . . . . . . . . . . . . . . . . 40• LSHM-CT-2007-037862ARTEMIS. . . . . . . . . . . . . . . . . . . . . 14• LSHB-CT-2007-037933POC4life . . . . . . . . . . . . . . . . . . . . 136189

SME CALLIndexby coordinator• Allaer Didier . . . . . . . . . . . . . . . . . . . . . . 28Diagenode S.A.• Amaral Margarida D. . . . . . . . . . . . 168University of Lisboa• Anné Jozef. . . . . . . . . . . . . . . . . . . . . . . . . 158Catholic University of Leuven• Bágyi István . . . . . . . . . . . . . . . . . . . . . . . 22AMRI Hungary• Benlloch Jose M a . . . . . . . . . . . . . . . . 100Consejo Superior deInvestigaciones científicas• Berrih-Aknin Sonia . . . . . . . . . . . . . . 114Université Paris Sud (UPS)• Bill Roslyn . . . . . . . . . . . . . . . . . . . . . . . . 128Aston University• Birch Mike . . . . . . . . . . . . . . . . . . . . . . . . 124F2G Ltd.• Bois Emmanuel . . . . . . . . . . . . . . . . . . 136Cezanne SAS• Brandt Remco . . . . . . . . . . . . . . . . . . . . . 30Cilian AG• Campadelli-Fiume Gabriella . . . 166University of Bologna• Caricasole Andrea. . . . . . . . . . . . . . . . 164Siena Biotech SpA• Cattaneo Antonino . . . . . . . . . . . . . . . 106European Brain Research Institute• Collins Andrew . . . . . . . . . . . . . . . . . . . . 36University of Oslo• Costi Maria Paola . . . . . . . . . . . . . . . . . 94University of Modenaand Reggio Emilia• Cutting Simon M. . . . . . . . . . . . . . . . . . 88Royal Holloway University of London• Dammann Olaf . . . . . . . . . . . . . . . . . . . 120Hannover Medical School• Danielsson Mats . . . . . . . . . . . . . . . . . . 74Sectra Mamea AB• Daura Xavier . . . . . . . . . . . . . . . . . . . . . . . 18Universitat Autònoma de Barcelona• Depaulis Antoine . . . . . . . . . . . . . . . . . 178UMR 704 Inserm-UniversitéJoseph Fourier• Di Lorenzo Diego . . . . . . . . . . . . . . . . . 64Ospedale Civile di Brescia• Dickinson Anne . . . . . . . . . . . . . . . . . . . 156University of Newcastle upon Tyne• Dolcetti Riccardo . . . . . . . . . . . . . . . . . 182National Cancer Institute• Einsele Hermann . . . . . . . . . . . . . . . . 102University of Wuerzburg• Ekström Björn . . . . . . . . . . . . . . . 56Olink AB• Ellerbrok Heinz . . . . . . . . . . . . . . . . . . 176Robert Koch-Institut• Falciani Chiara . . . . . . . . . . . . . . . . . . . . . 66Philogen• Finn Paul . . . . . . . . . . . . . . . . . . . . . . . . . . . 68InhibOx Ltd.• Fiorini Carlo . . . . . . . . . . . . . . . . . . . . . . . 20Politecnico di Milano• Frostegård Johan . . . . . . . . . . . . . . . . . 38Karolinska University Hospital• Gauguier Dominique . . . . . . . . . . . . . 68University of Oxford• Gilbert Ian. . . . . . . . . . . . . . . . . . . . . . . . . 134University of Dundee• Goudsmit Jaap . . . . . . . . . . . . . . . . . . . . 138Crucell Holland B.V.• Hartmann Marcus . . . . . . . . . . . . . . . . . 30Cilian AG• Holthofer Harry. . . . . . . . . . . . . . . . . . . . 48Haartman Institute• Hotter Georgina . . . . . . . . . . . . . . . . . 142Instituto de InvestigacionesBiomédicas de Barcelona190

• Huet Jacqueline . . . . . . . . . . . . . . . . . . 112PHUSIS• Huggett Jim . . . . . . . . . . . . . . . . . . . . . . . 172University College London• Imhof Axel . . . . . . . . . . . . . . . . . . . . . . . 154Ludwig Maximilians Universityof Munich• Jensen Sanne . . . . . . . . . . . . . . . . . . . . . 26Evolva S.A.• Kel Alexander . . . . . . . . . . . . . . . 122/160BIOBASE GmbH• Keri György . . . . . . . . . . . . . . . . . . . . . . . 170Vichem Chemie Research Ltd.• Kuijper Ed J. . . . . . . . . . . . . . . . . . . . . . . . 54Leiden University Medical Center• Kulikowski Tadeusz . . . . . . . . . . . . . . . 76Instytut Biochemii iBiofizyki PAN• Leiser Robert-Matthias . . . . . . . . . . 44Agrobiogen GmbH• Lenas Petros . . . . . . . . . . . . . . . . . . . . . . . 14Complutense Universityof Madrid (UCM)• Lévi Francis. . . . . . . . . . . . . . . . . . . . . . . . 174INSERM U776• Lipp Hans-Peter . . . . . . . . . . . . . . . . . . . 90NewBehavior AG• Ludwig Bernard . . . . . . . . . . . . . . . . . . . 10ADDEX Pharmaceuticals France SAS• Maes Tamara . . . . . . . . . . . . . . . . . . . . . 86C. S. O. Oryzon genomics• Maldonado Rafael . . . . . . . . . . . . . . 130Universitat Pompeu Fabra (UPF)• Malik Arif . . . . . . . . . . . . . . . . . . . . . . . . . 162MicroDiscovery GmbH• Mandenius Carl-Fredrik . . . . . . . . . . 92Linköping University• Mandler Markus . . . . . . . . . . . . . . . . . 108Affiris GmbH• Martinsson-Niskanen Titti. . . . . . . . 12BioInvent International AB• Meijer Annemarie H. . . . . . . . . . . . . 184Leiden University• Meinke Andreas . . . . . . . . . . . . . . . . . . 126Intercell AG• Meiri Hamutal . . . . . . . . . . . . . . . . . . . 186Diagnostic Technologies Ltd.• Mouly Vincent . . . . . . . . . . . . . . . . . . . . 116INSERM• Müller-Hartmann Herbert . . . . . . . 110AMAXA GmbH• Ochoa Gorka . . . . . . . . . . . . . . . . . . . . . . . 50Progenika Biopharma• Ogden David . . . . . . . . . . . . . . . . . . . . . . 132CNRS UMR 8118• Overduin Michael . . . . . . . . . . . . . . . 140University of Birmingham• Palme Klaus . . . . . . . . . . . . . . . . . . . . . . . 16University of Freiburg• Pâques Frédéric . . . . . . . . . . . . . . . . . 104CELLECTIS S A• Pasterkamp Gerard . . . . . . . . . . . . . . 82University Medical Center Utrecht• Porgador Angel . . . . . . . . . . . . . . . . . . . . 70Ben-Gurion University of the Negev• Reinerio Gonzalez. . . . . . . . . . . . . . . . . 84Philogen• Riess Olaf . . . . . . . . . . . . . . . . . . . . . . . . 146Eberhard-Karls-Universität Tübingen• Robertson Graeme . . . . . . . . . . . . . . . . 40Siena Biotech SpA• Roca Josep . . . . . . . . . . . . . . . . . . . . . . . . . 20Institut d’InvestigacionsBiomèdiques August Pi i Sunyer• Sans Miquel . . . . . . . . . . . . . . . . . . . . . . 80Hospital Clínic/IDIBAPS• Schildgen Oliver . . . . . . . . . . . . . . . . . . 148Institute for Medical Microbiology,Immunology, and Parasitology• Schillberg Stefan . . . . . . . . . . . . . . . . . . . 150Fraunhofer-Institut für Molekularbiologie undAngewandte Oekologie IME• Schrenzel Jacques . . . . . . . . . . . . . . . . . . 98Geneva University Hospitals• Singh Mahavir . . . . . . . . . . . . . . . . . . . . . . . 66LIONEX Diagnostics& Therapeutics GmbH• Skjeltorp Guri . . . . . . . . . . . . . . . . . . . . . . . 118Dalen Diagnostics AS• Smith C. I. Edvard . . . . . . . . . . . . . . . . . . . 60Clinical Research Center• Stanescu Ioana . . . . . . . . . . . . . . . . . . . . . 58FIT Biotech Plc• Stassen J.M. . . . . . . . . . . . . . . . . . . . . . . . . 180ThromboGenics Ltd.• Takacs Laszlo . . . . . . . . . . . . . . . . . . . . . . . . 34BioSystems International• van Holst Gerrit-Jan . . . . . . . . . . . . . . . . . 78Viruvation B.V.• Veuskens Jack . . . . . . . . . . . . . . . . . . . . . . . 46KREATECH Biotechnology B.V.• Weisbuch Claude . . . . . . . . . . . . . . . . . . . 144Genewave SAS• Weldingh Karin . . . . . . . . . . . . . . . . . . . . . 152Statens Serum Institut• Wiltfang Jens . . . . . . . . . . . . . . . . . . . . . . . . . 32University of Erlangen-Nuremberg• Zucco Flavia . . . . . . . . . . . . . . . . . . . . . . . . . 96Istituto di Neurobiologia e MedicinaMolecolare191

European CommissionEUR 23457 — Synopses of projects funded through the SME call for “Life sciences,genomics and biotechnology for health”Luxembourg: Office for Official Publications of the European Communities2008 — 191 pp. — 21.0 x 29.7 cmISBN 978-92-79-08803-2DOI 10.2777/13756

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KI-NA-23457-EN-CSMEs in Health research, synopses of projects fundedthrough the SME call for “Life sciences, genomics andbiotechnology for health”Hundreds of research-intensive small and medium sized enterprises (SMEs) areactive in the health sector. In recognition of their innovative potential, scientificstrength and strategic importance, a special effort was made to involve them in theSixth Framework Programme (FP6), where a very successful ‘SME call’ was publishedwith a budget of € 200 million.As a result of this call, 270 SMEs in the health and biotech sector, acceded toa leading role as key players and driving forces in the research activities of86 EU-funded projects, receiving more than 40 % of the EU contribution.This publication presents those 86 projects and aims to illustrate the EU’s commitmentto health research, bringing together transnational and multidisciplinaryexpertise from both industry and academia.