Lineage identity governs oncogene dependence in murine NSCLC models of KRAS inhibitor resistance [ATAC-Seq]

Primary and acquired resistance to targeted therapy represent significant challenges to durable treatment responses in cancer. In lung cancer and other cancer types, allele- specific and pan-KRAS inhibitors offer new promise, but these are hampered by incomplete responses as well as genetic and non-genetic mechanisms of acquired resistance. To model these mechanisms, we treat genetically engineered mouse models of KrasG12C-driven lung cancer with sotorasib, a KRASG12C inhibitor, until the emergence of drug resistance. The initial response to sotorasib was rapid, but incomplete. Residual tumor burden transcriptionally resembled the alveolar type II cell, phenocopying residual disease signatures identified in patients treated with EGFR inhibitors. After continued sotorasib treatment, we observed diverse mechanisms of drug resistance in vivo, including genetic MAPK reactivation and lineage transformation from adenocarcinoma to squamous histology. Focusing mechanistic studies on squamous transformation, we showed that expression of the basal transcription factor ∆Np63 is sufficient to rewire transformed alveolar organoids to a squamous state in vitro, conferring insensitivity to KRAS inhibition. In vivo, either ectopic expression of Sox2 or loss of Nkx2-1, which are tolerated during Kras-driven tumorigenesis, poised tumors for squamous lineage commitment upon KRAS inhibition. Squamous- transformed tumors did not exhibit evidence of KRAS/MAPK reactivation, underscoring the role for lineage transcription factors and histologic transformation in mediating oncogene independence.