Crispr Screening -sequencing results for pancreatic cancer cell lines treated with chemotherapeutic drugs

Pancreatic ductal adenocarcinoma (PDAC) harbors one of the worst prognoses of all common cancers with a five year survival rates remaining below 10% for the last three decades despite the use of multiple cytotoxic chemotherapies as first-line treatment. Large-scale genome sequencing and transcriptome profiling of PDAC patients has yet to produce successful targeted therapies for PDAC treatment and resistance to current chemotherapy regimens is common. We performed genome-wide CRISPR activation (CRISPRa) and CRISPR knock out (CRISPRko) screens for mechanisms of resistance to four cytotoxic chemotherapies (gemcitabine, 5-fluorouracil, irinotecan, and oxaliplatin) commonly used in the treatment of PDAC patients in two PDAC cell lines (BxPC3 and Panc-1). Drug-specific mechanisms of resistance tended to be relatively depleted for significant associations with PDAC patient survival suggesting they may be less clinically relevant than multi-drug mechanisms of resistance. We identified activation of ABCG2, a well-described efflux pump implicated in drug resistance, as the most consistent multi-drug resistance mechanism across drugs and cell lines. Small molecules inhibitors of ABCG2 restore sensitivity to chemotherapy. Our screen further revealed several novel pathways with relevance to resistance to multiple drugs. For example, activation of several members of the hemidesmisome complex and transcriptional repressor complexes are consistent mechanisms of multi-drug resistance. Finally we describe an approach for applying the results from our screen predict drug sensitivity in PDAC tumors and cell lines based on gene expression.