Research Report 2010 - MDC

Stefan KempaStructure of the GroupGroup LeaderStefan KempaScientistsGuido MastrobuoniGraduate StudentMatthias PietzkeUndergraduate StudentChristin HessTechnical AssistantJulia DiesbachSecretariatSabrina DeterStart of group: April 2009Integrative metabolomics andproteomicsWithin the past decades biochemical data of single processes, metabolic and signalingpathways has been collected. Advances in technology led to improvements of sensitivityand resolution of bioanalytical techniques. These achievements build the basis of so-called‘genome wide’ analyses.High throughput techniques are the tool for such largescale “-omics” studies allowing the obtainment of acomplete picture of a determinate cell state, concerningits metabolites, transcripts and proteins. For exampletwo-dimensional gas chromatography coupled to timeof-flightmass spectrometry (GCxGC-TOF-MS) is a promisingtechnique to overcome limits of complexmetabolome analysis using one dimensional GC-TOF-MS. However, single level study of a living organism(transcripts, proteins or metabolites) cannot give acomplete understanding of the mechanism regulatingbiological functions. The integration of transcriptomics,proteomics and metabolomics data in the newlyemerging field of System Biology, combined with existingknowledge, allows connecting biological processeswhich were treated as independent so far. In this contextthe aim of our group is to apply metabolomics andproteomics techniques for absolute quantification andanalysis of turnover rates of proteins and metabolitesusing stable isotopes; in addition, the further developmentof workflows for data analysis and integrativestrategies will be in the focus of our interest.Functional analysis of cancer metabolismMatthias Pietzke, Julia Diesbach, Markus Landthalerand Jana WolfBeside the enormous diversity of cancers, all tumor cellsseem to share the same metabolic disorder. Already in1924 the famous Nobel Prize biochemist Otto Warburgdescribed an anaerobic type of metabolism performedby cancer tissues. This phenomenon, called Warburgeffect, is still under investigation and the benefit forcancer cells from this metabolic behavior is stillobscure; but it might stem from the onset of cancerogenesis.To unravel the regulatory mechanisms inducingthis metabolic disorder we perform integrativetranscriptomic, proteomic and metabolomic studies.These analyses will allow understanding the molecularprocesses leading to the observed metabolic alterationsof cancer cells and could help to improve anti cancertherapies.Planaria as model organismGuido Mastrobuoni, Julia Diesbach, SebastianMackowiak and Catherine Adamini (Rajewsky Group)The planarian Schmidtea mediterranea is a well-establishedmodel organism at BIMSB. These freshwater flatwormscan regenerate all lost body tissue after amputationdue to a population of pluripotent somatic stemcells called neoblasts that constitute up to 30 percentof the total organism cells.In parallel to other studies carried at BIMSB, aimed tounderstand the role of small RNAs in the planariandevelopment and regeneration of their germ cells, ourgroup is involved in collaborative projects for the functionalannotation of Planaria genome using proteomicdata (figure 1).Once a full genome has been assembled, the main challengelies in its annotation, i.e., in identifying the protein-codinggenes and other functional units that areencoded in the genome. Whole-genome annotation196 Berlin Institute of Medical Systems Biology