High throughput RNAi based functional genomics in primary cells and in vivo

DESCRIPTION (provided by applicant): Completion of the HGP (human genome program) has opened the 'Genomic Era' in biomedical research and enables functional genomics analysis of various gene elements. The long-term goal of the ENCODE Project is to identifyand functionally characterize all of the sequence-based genomic elements. Functional elements that have been studied in ENCODE include transcribed sequences, regulators of transcription, and regulators of RNA transcripts themselves. The function of more than 50% of transcribed gene sequences is unknown. Most of them are expressed in specialized cells and thus their functions can only be studied in a biologically relevant context (i.e. primary cells, in vivo). In this propoal we plan to develop and commercialize a new RNAi platform that enables gene studies in a biologically relevant context with a long term goal of building a functional map of human genome. Introduction of small interfering RNAs (siRNAs) into cells with transfection reagents results in efficient gene silencing. siRNA-based functional genomics is widely used in established cell lines in vitro, but its applicability to primary cells and in vivo target validatin has been limited because of lack of efficient and non-toxic delivery systems. In collaboration with RXi pharmaceuticals we have developed a novel class of RNAi compounds - self deliverable RNAs. These small, asymmetric, hydrophobically modified RNA compounds enter cells and tissues without requirement for delivery formulation and efficiently silence genes in vitro and in vivo, enabling functional genomics studies in primary cells, embryonic cells, tissues, ex vivo, and in vivo. The major technical hurdle, which impedes wide spread use of this platform by scientific community is the complex and costly process of compound identification, synthesis and validation. The focus of this fast-track proposal is optimization of compound discovery process (Phase I) and development of a panel of 200-1000 functionally validated sdRNAs (Phase II), Completion of this proposal will build a commercially available product platform that will revolutionize functional genomics studies in biologically relevant systems such as primary cells, stem cells, tissue and organ models and eventually in vivo.