Abstract B014: Transcription factors governing the evolution of drug-tolerant persisters in KRAS-mutant non-small cell lung cancer

Rare tumor cell populations can evade cancer therapies, ultimately driving drug resistance and relapse. These resilient populations, termed “persisters,” display distinct molecular states compared to the bulk tumor. While some persisters acquire genetic mutations that confer growth advantage, others undergo non-genetic remodeling that enhances cellular plasticity and fitness. Previous studies suggest that stochastic gene activation promotes persister survival (Shaffer et al., Nature 2017; Goyal et al., Nature 2023), yet the master regulators of this plasticity remain undefined. Using DNA barcoding, we demonstrate that pre-determined, non-stochastic persisters exist in KRAS-mutant non-small cell lung cancer (NSCLC) treated with the KRAS G12C inhibitor sotorasib. These clones repopulate the tumor without harboring recurrent genetic alterations. By isolating single clones destined to persist or go extinct, and profiling their transcriptomes and chromatin accessibility, we found that persister clones activate an interferon-γ (IFNγ) transcriptional signature accompanied by increased chromatin accessibility at sites enriched for the transcription factors IRF1 and ZNF384. Functionally, ectopic ZNF384 expression converted the entire cell population into a resistant state, while IRF1 knockout prevented persister formation. Cleavage Under Targets & Release Using Nuclease (CUT&RUN) assays of ZNF384 and IRF1 revealed their binding to promoter and enhancer regions, including loci regulating IFNγ-responsive genes, thereby contributing to persister plasticity and survival. Together, our study identifies IRF1 and ZNF384 as tumor-intrinsic regulators linking IFNγ signaling to transcriptional plasticity, providing mechanistic insight into the evolution of drug tolerance and resistance in KRAS-mutant NSCLC. Citation Format: Chendi Li, Anahita Nimbalkar, Christopher J. Graser, Melissa Vieira, Mohammed U. Syed, Qian Qin, Barbara Karakyriakou, Sarah Clark, Anne Y. Saiki, Paul E. Hughes, Christopher Ott, Luca Pinello, Franziska Michor, Aaron N. Hata. Transcription factors governing the evolution of drug-tolerant persisters in KRAS-mutant non-small cell lung cancer [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 B014.