Mechanisms of genetic and non-genetic resistance to KRAS inhibition - PROJECT SUMMARY KRAS is the most frequently mutated oncogene in lung adenocarcinoma (LUAD) and colorectal cancer (CRC). In the US alone, cancers carrying KRAS mutations account for almost 100,000 deaths per year. New mutant- selective and pan-KRAS inhibitors have recently emerged as a potent and effective strategy to block KRAS- mediated oncogenic signaling, however early clinical signs suggests that drug resistance is not only possible, but a common outcome to KRAS-targeted treatment. Defining the mechanism/s underlying acquired resistance to KRAS targeted therapies will drive more effective treatment stratification for patients and guide the development of combination or second-line therapies to prevent or reverse drug resistance. Drug resistance can arise through both genetic changes and non-genetic cellular adaptations that either reduce drug exposure or bypass a tumor's dependence on the drug target. Using matched patient biopsies from a recent KRAS inhibitor clinical trial, and KRAS-driven pre-clinical model systems, we identified the induction of inflammatory gene expression as a conserved response to KRAS inhibition that emerges prior to the known resistance drivers. In parallel, through the use of CRISPR base editing (BE) screens, we identified a subset of cancer-associated mutations that enable resistance to KRAS inhibition and are associated with elevated inflammatory signaling. Finally, our data show that targeting inflammatory mediators JAK and/or TBK1 can reduce the emergence of KRAS resistance. Together with published prior work, our data suggest model whereby resistance to KRAS inhibition can be triggered by a cell intrinsic inflammatory transcriptional programs – induced by drug exposure - that promote progression to previously described drug-resistant states. In AIM 1 we will determine whether the induction of an inflammatory transcriptional response in cancer cells following KRAS inhibition is the trigger that drives the genesis of lineage reprogramming and drug resistance. Further, we will directly test whether targeting key signaling nodes in the drug-induced inflammatory response can prevent lineage reprogramming and/or drug resistance. In AIM 2 we will use focused cancer-associated BE screens and BE-PerturbSeq profiling to identify those genetic changes that promote an enhanced inflammatory response and/or lineage reprogramming and determine whether multiple distinct cancer-associated mutations converge on a common cellular response to drug treatment. In particular, we will determine whether mutations in CIC, SMAD4, and TGFBR2 that are enriched in drug resistant populations, drive resistance through the engagement of specific inflammatory signaling programs. Together, work in this proposal aims to provide mechanistic understanding of how specific genetic and non- genetic changes drive resistance to KRAS inhibition. This work will help define the patient populations and tumor context where KRAS inhibitors are most effective and catalyze the development of combination strategies to prevent drug resistance and improve outcomes for patients with KRAS mutant cancer.
