Systematic analyses of CRISPR-Cas9 screens reveal clinically relevant modulators of gemcitabine sensitivity

Chemotherapies targeting the fundamental process of DNA replication have remained the foundation of numerous cancer treatment regimens for decades. However, the efficacy of DNA replication-targeting therapies is hindered by tumor heterogeneity and the limited predictive markers available to identify patient populations that would benefit most from therapy. Chemical genetic CRISPR-Cas9 screens provide powerful platforms to reveal factors that modulate the sensitivity of clinically relevant therapies in diverse cell backgrounds in an unbiased manner. To systematically assess the prognostic potential of sensitizers and resistance genes from CRISPR-Cas9 screens on cancer patient outcomes, we performed chemogenomic screens with the DNA replication stress-inducing agent gemcitabine on four different cell backgrounds including pancreatic ductal adenocarcinoma (PDAC), a highly aggressive cancer type where gemcitabine is a frontline treatment. We tested the predictive potential of 52 rationally selected genes from the CRISPR-Cas9 screens on overall survival of PDAC patients and show that 38 of the 52 genes accurately provided prognostic value in the patient cohorts, yielding a 73% validation rate. We identified unappreciated roles for several prognostic gemcitabine sensitivity modulators in PDAC including DCAF8L2, CCNF, EXO1, HROB, BRD9, and C1orf109, and define essential roles for mitochondrial function and RNA processing in promoting gemcitabine cytotoxicity. Together, our work provides a rich resource of cellular mediators of the response to therapeutic DNA replication stress and presents a systematic analysis of the impact of CRISPR-Cas9 screen hits on cancer patient survival outcomes, promoting the rational use of chemogenomic screens for treatment biomarker identification.