Abstract B019: SOX2 induction and ΔNp63-high subpopulations mark adaptive responses to EGFR inhibition in lung adenocarcinoma

Abstract EGFR-mutant non-small cell lung cancers (NSCLCs) initially respond to EGFR tyrosine kinase inhibitors (TKIs) such as osimertinib, but tumors eventually develop resistance. While genetic mutations explain many instances of resistance, an increasing body of evidence points to transcriptional and cell state changes as another route by which tumor cells evade therapy. The dynamics that shape these adaptive responses and the non-genetic mechanisms involved in facilitating them remain incompletely understood. We investigated transcriptional programs activated in EGFR-mutant LUAD cells following TKI treatment and observed robust induction of SOX2, a transcription factor involved in promoting stemness and lineage plasticity, within a day of drug exposure. In parallel, we investigated the role of APOBEC cytidine deaminases (APOBEC3A and APOBEC3B), which have been linked to mutagenic processes in cancer. While both enzymes have been implicated in drug resistance, the individual contributions of the two enzymes remain ill studied. Using competition assays with single gene knockouts of either APOBEC3A or APOBEC3B, we observed that loss of APOBEC3A leads to a more profound reduction in the survival of drug-tolerant cells following TKI therapy. These results highlight a functional role for APOBEC activity in sustaining early drug-tolerant populations under therapeutic pressure. Over the course of long-term osimertinib treatment, we also identified distinct subpopulations of cells with elevated ΔNp63, an isoform of TP63 that serves as a marker of squamous cell trans-differentiation. These ΔNp63-high cells emerge during the acquisition of drug resistance, and evidence suggests that this subpopulation may rely on CDK4, a cell cycle-regulating kinase, to sustain growth under therapeutic pressure. Pharmacological inhibition of CDK4 with palbociclib reduced the survival of ΔNp63-high cells, highlighting a potential therapeutic vulnerability in this proliferative subpopulation. Together, our findings demonstrate that adaptive resistance in EGFR-mutant NSCLC is driven by several non-genetic resistance mechanisms, including SOX2 induction, ΔNp63-driven squamous cell transdifferentiation, and APOBEC-mediated promotion of drug-tolerant persister cells. Citation Format: Sharan Srinivasan, Jessica N. Becerra, Nina M. Garcia, James V. Alvarez. SOX2 induction and ΔNp63-high subpopulations mark adaptive responses to EGFR inhibition in lung adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Cancer Evolution: The Dynamics of Progression and Persistence; 2025 Dec 4-6; Albuquerque, NM. Philadelphia (PA): AACR; Cancer Res 2025;85(23_Suppl):Abstract nr B019.