Exploiting synthetic lethality to enhance KRAS inhibitor therapy of cancer

New York University School Of Medicine, New York NY

Investigators

Abstract

PROJECT SUMMARY/ABSTRACT KRAS is among the most frequently mutated genes in human cancer with most mutations affecting codon 12. KRASG12C (G12C) is especially common in non-small cell lung cancer (NSCLC), comprising ~half of all KRAS mutations in this disease (~15% of NSCLC overall). Approximately 40% of colorectal carcinoma (CRC) cases are KRAS-mutated (~10% G12C), while ~1-2% of pancreatic ductal adenocarcinomas (PDAC) have this mutation. Mutant KRAS had long been viewed as “undruggable”, until pioneering chemical biology and medicinal chemistry studies resulted first in G12C-specific inhibitors (G12Cis), and later in a plethora of agents targeting other mutant alleles or even wild type (WT) KRAS and most/all mutants (“pan-KRAS”). Thus far, two small- molecule G12Cis, sotorasib and adagrasib, have been FDA-approved as second-line agents for NSCLC. While the magnitude of the conceptual advance provided by G12Cis and other RAS inhibitors (RASi) cannot be overstated, the clinical response to single-agent G12Cis has been modest. Specific co-mutations (e.g., KEAP1) can impair the response of G12C-mutated NSCLC, while as single agents, G12Cis have minimal activity in G12C-mutated CRC. Even when tumors initially respond, resistance emerges rapidly via multiple mechanisms. Early results suggest that intrinsic and/or emergent resistance will also limit the clinical impact of other RASis. Whether the same resistance mechanisms will plague other KRAS inhibitors remains unclear, yet what does seem likely is that durable responses and, ultimately cures, of KRAS-mutated NSCLC will require drug combinations, potentially including conventional chemoradiation and immune therapies. Rapidly and efficiently devising such strategies would address a major unmet medical need. We recently reported the results of a genome-wide CRISPR/Cas9 “dropout” screen for adagrasib synthetic lethal (SL) genes in four (4) KRASG12C;STK11-co-mutated cell NSCLC lines, three (3) of which are also KEAP1-mutated. We identified ~40 genes that were SL in at least 3 lines, including three (3) serine/threonine kinases (STKs), and ~330 that were SL in at least two lines. Although our screens focused on SL (i.e., dropout) genes, we also identified 30 enriched “resistance hits” in at least 2 lines. Functional studies provided initial validation of the three STKs, as well as ROCK1,2 (which emerged from studies of other recurrent SL genes), but more complete evaluation, including mechanistic and in vivo efficacy studies, was lacking, as was the applicability of screen “hits” to other G12C malignancies and other RASis. We propose to tackle these key gaps via a combined biochemical, genetic, and functional genetic approach. Specfically, we will 1) evaluate four STK family members as SL targets more broadly and in vivo and clarify the mechanistic basis of synthetic lethality, and 2) use CRISPR/Cas9 “mini-libraries” to define the synthetic lethality/resistance landscape for G12Cis and other RASis. Our results will address a critical unmet need in medical oncology by credentialling new targets for RASi combinations.