PDF file: EURASNET Annual Report 2008

12. Mis-splicing and DiseaseWorkpackage description (month 37-54)Workpackage number 12 Starting day or starting event 0 monthParticipant id 4 7 10 11 12 12 16 19 25 26 27 32a a cPerson months 8 42 8 8 8 8 8 8 8 8 6 8Objectives• Identifying the connection between derangements in RNA splicing and disease• Dissemination of splicing technology and knowledge to patient care through the establishment of a taskforce to bring to the attention of practicing clinicians the role of RNA splicing derangements in disease. TheHuman Genetic Societies meetings and other relevant gatherings will be the target of this activity. WP 16 and 21can assist with this.• Setting up best practice protocol for the interpretation of nucleotide changes seen in diagnosticsequencing.Description of workThe study of mis-splicing in disease can be schematically divided into three work phases:1. Identification of aberrant splicing. This will be done by direct evaluation of patient’s RNA samples. WhenRNA is not available, or when it has a tissue-specific expression, appropriate experimental models (minigene andin vitro splicing assays) will be produced. These will be useful also for diagnostic purposes and for subsequentelucidation of the basic mechanism(s) as described in point 2. Dedicated databases and in silico prediction toolswill be created in parallel.2. Elucidation of the basic mechanism(s) that cause mis-splicing. This phase will be done in close cooperationwith WP7, WP9 and WP11. This includes several complementary activities:a. The identification of common classes of regulatory elements disrupted by the mutations (enhancer,silencer, composite elements etc.),b. The investigation of the role of secondary structure determinants and trans-acting splicing factors inmis-splicingc. The identification of pathological splicing mechanisms.3. Initial evaluation of the potential therapeutic effect of compounds developed by high throughput screening andthe study of changes in the expression of trans-acting splicing factors by means of RNAi (see also WP14).We expect some time-frame overlapping among the work-phases due to differential progress of one activityand/or discovery of new mechanisms.Deliverables211 In depth characterization of trans-acting factors of particular interest with regards to their functionality,biochemical properties, and general importance for the cellular metabolism particularly in the development oftumors (Biamonti) (month 42)267 GROUP 16 (CARMO-FONSECA) is planning to identify cancer-specific splicing factor gene expressionsignatures and novel cancer-specific alternative splicing events (planned for month 48).329 GROUP 7 (F. BARALLE) will continue to focus on the relationship between mutations-trans-acting factorsand disease. In particular, they will continue in the analysis of the effect of splicing mutations in a variety of genes(NF-1, ATM, Herg, BRCA1, CFTR) and in the collaboration with other groups to identify disease-mutationsaffecting the splicing process. In addition, one line of research that will be substantially increased in the nearfuture will regard the investigation of nuclear factor TDP-43 and its relationship with neurodegenerative diseases.This will be performed using a new Drosophila melanogaster transgenic animal model that is currently developedat ICGEB obtained by engineering the knockout of TBPH (TDP-43 homologue in Drosophila). This model will beused to characterize the potential defects in genes known to be important for neuronal development and theireventual relationship with the human situation. In parallel, the group will focus on better characterizing the265