Abstract PR08: Combinatorial CRISPR-Cas9 reveals many cancer synthetic lethal interactions are private to cell type

We developed a systematic approach to map human genetic networks by combinatorial CRISPR-Cas9 perturbation coupled to robust analysis of growth kinetics. We targeted all pairs of 73 cancer genes with multiplexed guide RNAs in two cell lines, testing 23,652 combinations. Numerous therapeutically relevant interactions were identified, most private to one cell line. These patterns replicated with combinatorial drugs at 80% precision. Thus, cellular context will be critical to synthetic-lethal therapies.Here, we combined multiplex targeting with array-based oligonucleotide synthesis to create dual-gRNA libraries covering up to 105 defined gene pairs. We conducted genetic interaction screens by transducing the dual-gRNA lentiviral library into a population of cells stably expressing Cas9, maintaining these cells in exponential growth over the course of four weeks, then sampling the relative changes in gRNAs at days 3, 14, 21 and 28 post-transduction. To robustly quantify gene fitness and genetic interactions, we developed a computational analysis framework that integrates all samples across the multiple days of the experiment.Using this method we evaluated all pairwise gene knockout combinations among a panel of 73 genes divided between tumor-suppressor genes (TSG) and cancer-relevant drug targets (DT), a subset of which were also verified oncogenes. Experiments were performed in two cancer cell lines: HeLa, a cervical cancer cell line driven by Human Papilloma Virus (HPV); and A5...
Source: Molecular Cancer Therapeutics - Category: Cancer & Oncology Authors: Tags: Other Topics: Oral Presentations - Proffered Abstracts Source Type: research