High-throughput identification of genes involved in single and multi-drug resistance in pancreatic cancer with pooled CRISPR screening

Chemoresistance is the norm in pancreatic ductal adenocarcinoma (PDAC) leading to an abysmal five-year survival rate of less than 10%. We performed genome-wide CRISPR activation (CRISPRa) and CRISPR knock out (CRISPRko) screens to identify mechanisms of resistance to four cytotoxic chemotherapies (gemcitabine, 5-fluorouracil, irinotecan, and oxaliplatin) used to treat PDAC patients in two PDAC cell lines. Mirroring patient treatment outcomes, we found that multi-drug resistance genes were more likely to be associated with patient survival. We identified activation of , a well-described efflux pump, as the most consistent resistance gene in four drugs and two cell lines. Small molecule inhibitors of ABCG2 restored sensitivity to chemotherapy. Our screen demonstrated that activation of members of the hemidesmisome complex and transcriptional repressor complexes conferred resistance to multiple drugs. Finally, we describe an approach for applying our results to predict drug sensitivity in PDAC tumors and cell lines based on gene expression.