Abstract 419: Chromosomal instability and oncogene dosage variations underlying KRAS G12C inhibition therapy resistance in lung cancer

Abstract KRAS G12C inhibitors (G12Ci), including the FDA-approved Sotorasib and Adagrasib, represent a significant advancement in targeted cancer therapies. As their use in non-small cell lung cancer patients expands, addressing the pervasive challenge of drug resistance is critical. Resistance mechanisms can be innate, acquired, or both, often coexisting within complex scenarios. Recent studies have highlighted various resistance mechanisms to G12Ci, such as oncogene amplification, activation of alternative signaling pathways, additional mutations in KRAS or its associated networks, and adaptive processes like epithelial-to-mesenchymal transition. Identifying the primary drivers and predominant mechanisms of resistance is crucial for developing effective countermeasures. To tackle these challenges, we developed Oligo-CALL, an innovative cellular barcoding technology that employs antisense oligonucleotide-inducible CRISPRa for lineage labeling. This technique allows for precise clonal tracking and the retrospective isolation of clones. Using Oligo-CALL, we analyzed tumor clonal heterogeneity and traced the evolution of resistance in lung cancer cells treated with G12Ci. Treatment with Sotorasib resulted in reduced clonal diversity, indicative of strong selective pressure. Similar clonal compositions across different replicates suggest that intrinsic mechanisms significantly contribute to G12Ci resistance. Notably, about 30% of resistant clones showed increased expression of the Kras G12C allele, primarily due to genomic gains, pointing to chromosomal instability (CIN) as a key factor in resistance development. Comprehensive analyses including fluorescent karyotyping, whole-genome, and transcriptome sequencing of isolated tumor clone pairs, revealed extensive genomic complexity and increased heterogeneity under G12Ci treatment. Resistant clones exhibited specific increases in copy number variations, chromosomal structure variations, and additional single nucleotide mutations, further underscoring CIN as a driving force behind G12Ci resistance. Clones that underwent drug treatment displayed higher CIN scores compared to their treatment-naïve counterparts. Intriguingly, cells resistant to G12Ci demonstrated increased sensitivity to PARP inhibitors, suggesting that targeting DNA repair pathways could induce synthetic lethality, offering a potential strategy to overcome resistance in lung cancer cells. Citation Format: Dingcheng Gao, Yingzhuo Liu, Yi Ban. Chromosomal instability and oncogene dosage variations underlying KRAS G12C inhibition therapy resistance in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 419.