Abstract 5065: Single-cell transcriptomic profiling of longitudinal patient tumors and PDX models reveals resistance mechanisms in ALK- and EGFR-mutant LUAD

Abstract Resistance to EGFR and ALK tyrosine kinase inhibitors (TKIs) in lung adenocarcinoma (LUAD) remains a major barrier to effective treatment. Tumor adaptation frequently involves dynamic cellular state transitions, altered signaling networks, and interactions within the tumor microenvironment (TME). Understanding the mechanisms driving resistance in EGFR- and ALK-mutant tumors is critical to developing strategies to improve patient outcomes. This study investigates transcriptomic changes underlying TKI resistance and persistance, combining patient data with functional insights from PDX models. Tumor biopsies from 11 LUAD patients were collected across three treatment stages: baseline (n=6), minimal residual disease (MRD, n=4), and relapse (n=1). Patient-derived xenograft (PDX) models were generated from pretreated tumors with EGFR and ALK mutations. Tumors were grafted into five mice per model, with three receiving treatment until stable residual disease emerged and two serving as untreated controls. Single-nucleus RNA sequencing was performed on both patient tumor samples and PDX models to comprehensively profile transcriptomic changes. Transcriptomic changes were observed in both patient tumor samples and PDX models during TKI treatment. In patients, at MRD, a novel subpopulation expressing mesenchymal and neuronal markers was identified, accompanied by altered cell-cell communication involving neuronal signaling (RELN), stromal remodeling (FGFRs), and survival pathways (MAPK). At relapse, signatures of epithelial-mesenchymal transition (EMT), ECM remodeling, and immune evasion were enriched. In PDX models, most persister cells were arrested in the G1 phase and showed suppression of canonical cancer pathways, while notable upregulation of the ciliated pathway was observed across models. This study provides a high-resolution transcriptomic map of TKI-treated LUAD tumors. Resistance mechanisms in EGFR- and ALK-mutant tumors include neuronal, EMT, MAPK signaling, ECM remodeling, and activation of the ciliated pathway. These findings offer novel therapeutic targets to combat resistance, leveraging the integration of patient-derived data and functional insights from PDX models. Citation Format: Naomi Mfonfu, Floriane Brayé, Galina Boldina, Matteo Cesaroni, Luc Fibroulet, Sergey Nikolaev, Andrey Yurchenko. Single-cell transcriptomic profiling of longitudinal patient tumors and PDX models reveals resistance mechanisms in ALK- and EGFR-mutant LUAD [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 5065.