Large-scale loss of function RNAi screening has the greatest potential for the discovery of novel gene function and the identification of new protein targets with clinical relevance. Building upon our experience using synthetic siRNAs to down-regulate individual genes (ZO1 BC 010613) we have established robust RNAi screening formats using synthetic siRNAs. Developing an RNAi screening capability has required extensive optimization of the induction of RNAi by synthetic siRNAs in a manner compatible with a larger scale workflow that generates robust and reproducible data. Critical to establishing effective RNAi screening has been the development of optimized protocols, statistical analysis, and down-stream validation procedures. The scale of the RNAi screens we have conducted has started at a modest level but in FY10 we were able to move to screening several thousand genes simultaneously. Our independent and collaborative studies have established conditions for synthetic siRNA-mediated RNAi screening in several cancer cell lines, including those used for the study of breast, ovarian, colorectal cancer, multiple myeloma and Ewing's Sarcoma. Independent and collaborative RNAi screens to identify novel cancer-associated genes, including genes that can be exploited directly as anti-cancer molecular targets have been initiated. This hypothesis-generating approach has enabled us to identify a number of proteins that influence the growth of cancer cell lines and follow-up analysis of these specific proteins is on-going.
