CRISPR-Drug Combinatorial Screening Identifies Effective Combination Treatments for MTAP-deleted Cancer

Abstract CDKN2A/MTAP co-deletion occurs frequently in non-small cell lung cancer and other solid tumors, including glioblastoma and pancreatic ductal adenocarcinoma. Lung cancer remains the leading cause of cancer-related mortality, and fewer than 15% of glioblastoma or pancreatic cancer patients survive 5 years, underscoring the need for more effective therapies. PRMT5 is a synthetic-lethal dependency in MTAP-null tumors and an attractive therapeutic target for CDKN2A/MTAP-deleted cancers. A new revolutionary class of inhibitors, referred to as MTA-cooperative PRMT5 inhibitors, has shown promising results in ongoing early phase clinical trials. Nonetheless, effective cancer treatment typically requires therapeutic combinations to improve response rates and defeat emergent resistant clones. Thus, we sought to determine whether perturbation of other pathways could improve the efficacy of MTA-cooperative PRMT5 inhibitors. A paralog and single gene targeting CRISPR library was used to screen MTAP-deleted cancers in the presence or absence of MTA-cooperative PRMT5 inhibitors. Loss of several genes sensitized to PRMT5 inhibition, including members of the MAPK pathway. Chemical inhibition of MAPK pathway members using KRAS, MEK, ERK, and RAF inhibitors synergized with PRMT5 inhibition to kill CDKN2A/MTAP-null, RAS-active tumors. Further, MTA-cooperative PRMT5 inhibitors combined with either KRAS or RAF inhibitors led to complete responses in vivo, emphasizing the potential benefit for patients. Lastly, cell lines resistant to KRAS inhibition were not resistant to MTA-cooperative PRMT5 inhibitors and vice versa, suggesting non-cross-reactive mechanisms of resistance. Overall, this study identifies therapeutic combinations with MTA-cooperative PRMT5 inhibitors that may offer significant benefit to patients.