Abstract 1226: Genomically encoded lineage plasticity drives resistance to EGFR targeted therapy in lung adenocarcinoma

Abstract EGFR-mutant lung adenocarcinoma (LUAD) represents 20% of all non-small cell lung carcinomas, with most patients presenting with incurable metastatic disease. Treatment with mutant-selective EGFR tyrosine kinase inhibitor (TKI) therapies such as osimertinib, the current standard of care for metastatic EGFR-mutant LUAD, results in greater overall and progression-free survival. However, all patients eventually relapse. Uncovering the mechanisms driving primary and acquired resistance to osimertinib is therefore critical to improving disease management. Here, we use clinical genomic sequencing (n=47) and single-nucleus RNA (snRNA) sequencing (n=62) to profile a cohort of unmatched treatment-naïve (n=26), on-treatment (n=6), and post-treatment relapsed (n=30) EGFR-mutant LUADs treated with osimertinib. Relapsed tumors are marked by increased tumor mutation burden, along with elevated rates of genome doubling and loss-of-heterozygosity. We derived expression-based signatures of LUAD, lung squamous cell carcinoma (LUSC), and small cell lung carcinoma (SCLC) and applied them to tumor cells across our cohort. Relapsed tumors had a marked decrease in LUAD gene signature expression compared to untreated tumors and accompanying increases in epithelial-mesenchymal transition (EMT) and stemness markers, consistent with dedifferentiation. Notably, tumors harboring secondary mutations to EGFR, MET, or other MAPK pathway genes and showing sustained MAPK signaling retained a more differentiated state. Patients lacking these secondary on-target or bypass mutations were more likely to experience relapse with histological transdifferentiation, marked by complete loss of LUAD signatures, and accompanying increases in LUSC or SCLC signatures. Phenotype matching of tumor cells to normal cells from the developing fetal lung revealed enrichment of airway progenitor populations in non-histologically transformed treatment-resistant patients, in contrast to a proportion of late bud-tip and club-like epithelial cells which predominated in treatment-naïve samples. In rare cases, we observed subpopulations of basal stem-like progenitors in otherwise well-differentiated pre-treatment tumors. In summary, single-cell mapping of histological and developmental phenotypes has revealed divergent evolutionary trajectories during the acquisition of resistance to osimertinib, defined by MAPK signaling reactivation or by loss of LUAD identity and histological transformation respectively. Citation Format: Matthew Zatzman, Alvaro Quintanal-Villalonga, Sohrab Salehi, Christina Falcon, Nicholas Ceglia, Sohrab P. Shah, Charles M. Rudin, Helena A. Yu. Genomically encoded lineage plasticity drives resistance to EGFR targeted therapy in lung adenocarcinoma abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts) ; 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84 (6Suppl): Abstract nr 1226.