Genome-wide RNAi synthetic lethality profiling to identify enhancers of Enzastaurin response

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The genetic aberrations acquired during the development of tumors represent both the drivers of disease and the opportunities for tailored therapeutics in cancer. Patients with genes and pathways altered in specific tumor types may respond differently to targeted therapies. Understanding these genetic determinants of drug sensitivity early in the discovery process can help to improve and accelerate decisions regarding clinical indications, patient stratification and combination studies. To this end, we employed a cell-based druggable genome-wide (~7000 targets) siRNA screen to determine enhancers of drug response for Enzastaurin (LY317615), a late stage clinical candidate undergoing trials in various cancers. Assay development, validation, high throughput screening, hit selection and prioritization and follow-up studies were performed in cell line models - Calu6 (lung), HCT116 (colon), U87MG (glio) and MCF7 (breast) - representing different tumor types and varied genetic backgrounds. In the final step, 4 siRNAs per target were picked for validation among all 4 cell lines, where cell proliferation, cell death and qPCR assay readouts were collected and analyzed. ~50 sensitizers have thus been identified that potentiate drug effect by synthetic lethal chemogenetic interactions in a dose responsive fashion in 1 or more cell lines. Integrative analyses of single or multiple genes with orthogonal datasets or published data have shed light on their application as clinically useful biomarkers and/or targets for combination therapy. In particular, to identify patient stratification opportunities, gene(s) with underlying genetic alterations that demonstrated differential sensitivity in model systems were of marked interest and have been followed up to guide clinical development. HDAC2 is an example that is currently being investigated. In conclusion, we have demonstrated that RNAi based synthetic lethality screening is a powerful cellular pharmacogenomics approach that can be used to identify functionally relevant genetic determinants of Enzastaurin response. These enhancers of drug response have translational utility and when successfully implemented, would provide a novel opportunity to tailor therapy and improve clinical success of targeted agents.