Alternative splicing in Ras transformed cells

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BACKGROUNDThrough a RNAi synthetic lethal screen we have identified a number of key mRNA splicing factors to be required for the viability of Ras mutant cancer cells.PURPOSEIn this project we aim to address the following questions: 1) the mechanism by which depletion of a subset of mRNA splicing factors causes synthetic lethality with Ras mutation; 2) which cellular proteins are differentially spliced in Ras mutant cells; 3) how the changes in mRNA splicing pattern in Ras mutant cells affect their viability compared to Ras wild type cells.SIGNIFICANT MATERIALS AND METHODS1) shRNAs that target splicing factors. 2) RNA-seq protocol for quantifying mRNA splicing pattern changes.FY2012 ACCOMPLISHMENTWe have validated shRNAs that target a number mRNA splicing factors that are identified to be synthetically lethal with KRAS. We have generated cell lines stably expressing rescue cDNAs to these factors. We have carried out RNA-seq experiments to characterize mRNA splicing patters in KRAS wild type and mutant cells with or without splicing factor knockdown. We have identified candidate genes whose proper splicing and expression are critical for the viability of KRAS mutant cells and we are currently investigate the mechanisms underlying such dependency.