Abstract 5684: Drug-anchored in vitro and in vivo CRISPR screens to identify targetable vulnerabilities and modifiers of response to MRTX849 in KRASG12C-mutant models
Authors: Engstrom Lars D. , Waters Laura , Gatto Sole , Fernandez-Banet Julio , Aranda Ruth , Pavlicek Adam , Christensen James G. , Olson Peter 
Published: September 2020

MRTX849 is a recently described covalent KRASG12C inhibitor in active clinical development in non-small cell lung cancer (NSCLC) and other cancers harboring this mutation. Additional genetic alterations in hallmark pathways are co-incident with KRASG12C mutations in NSCLC and several of these alterations have been shown to contribute to the oncogenic phenotype. The impact of co-occurring genetic alterations on KRAS dependency or response to KRAS targeted therapy is unknown. Evaluation of MRTX849 across a panel of cell and patient-derived xenograft models demonstrated strong single agent activity in the majority of models tested, however, a subset of models were less responsive. A focused sgRNA library targeting ~1,000 genes was tested in MRTX849-anchored CRISPR/Cas9 screens in vitro and in vivo in multiple KRASG12C-mutant cell lines. Several genes that act either upstream or downstream of KRAS were depleted with MRTX849 treatment which illuminated specific targetable vulnerabilities in the context of KRASG12C inhibition. These data provided a catalogue of putative combination targets. sgRNAs targeting EGFR, PTPN11 (SHP2), SOS1, mTOR, CDK1/2/4/6 were all depleted in MRTX849-treated (or vehicle-treated) cell lines or xenograft models. Furthermore, treatment with small molecules targeting selected vulnerabilities confirmed these genetic data. Finally, targeting FGFR1 exhibited context-dependent dropout that may conditionally address receptor tyrosine kinase reactivation following MRTX849 treatment. This observation was further confirmed utilizing the FGFR family inhibitor BGJ398. Further evaluation of dependencies utilizing an integrated analysis of RNAseq data also revealed KRAS regulates and is critically dependent on specific pro-survival genes BCL2L1, MCL1 and BIRC5 (Survivin) for cancer cell viability. On the other hand, loss of tumor suppressors including KEAP1, NF1, CBL, RB1 and PTEN conferred a growth advantage and partial resistance to MRTX849 treatment in selected models. sgRNAs targeting the RAS pathway genes SPRY2 and NRAS were also enriched providing additional insight into the wiring of KRAS mutant tumors and adaptive response to KRASG12C inhibition. These data provide key insight into the genes that mediate the mechanism of action of, as well as confer partial resistance to, MRTX849, and identify combination targets that augment the anti-tumor effect of MRTX849.

Citation Format: Lars D. Engstrom, Laura Waters, Sole Gatto, Julio Fernandez-Banet, Ruth Aranda, Adam Pavlicek, James G. Christensen, Peter Olson. Drug-anchored in vitro and in vivo CRISPR screens to identify targetable vulnerabilities and modifiers of response to MRTX849 in KRASG12C-mutant models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5684.