Abstract 3220: Integrated epigenomic profiling reveals distinct transcription factor networks driving therapy resistance in estrogen receptor positive metastatic breast cancer

Abstract Background: Endocrine therapy resistance in estrogen receptor positive metastatic breast cancer remains poorly understood, with many resistant tumors lacking actionable genomic alterations. Emerging evidence suggests epigenetic reprogramming drives resistance through transcription factor regulatory network rewiring, yet comprehensive epigenomic characterization of resistant tumors remains limited. Methods: We performed integrated ATAC-seq and RNA-seq profiling in clinically relevant models of therapy-resistant and sensitive estrogen receptor positive metastatic breast cancer, including patient-derived xenografts harboring diverse genomic alterations, along with sensitive breast cancer cell lines. We applied unsupervised clustering to chromatin accessibility and gene expression data to identify non-genomic clusters. Master regulators were identified by integrating transcription factor binding motif enrichment in accessible chromatin regions with downstream target gene expression networks. Results: We identified five distinct epigenomic clusters of therapy-resistant estrogen receptor positive metastatic breast cancer, each driven by unique master transcription factor regulatory programs. Cluster 1, comprising all sensitive models such as patient-derived xenografts and cell lines, retained luminal hormone-responsive identity. Therapy resistant tumors segregated into four distinct programs: Cluster 2 showed pioneer factor dominance with enhanced chromatin remodeling while maintaining partial luminal features. Cluster 5 represented an ESR1-mutant luminal HER2 hybrid state with ERBB2 amplification, combining altered estrogen receptor signaling with receptor tyrosine kinase activation. Cluster 4 displayed mesenchymal resistance via epithelial-mesenchymal transition. Cluster 3 represented the most dedifferentiated phenotype, an inflammatory cancer stem cell state with FOXA1 loss. Conclusion: Our integrated epigenomic approach reveals that therapy-resistance in estrogen receptor positive metastatic breast cancer is orchestrated by four distinct transcription factor-driven regulatory programs that emerge through non-genetic rewiring rather than genomic alterations alone. These clusters span a spectrum from pioneer factor-mediated chromatin remodeling and hybrid luminal-HER2 states to mesenchymal plasticity and inflammatory stem-like networks. Importantly, these epigenetic clusters may explain mutation-negative resistance and reveal subtype-specific therapeutic vulnerabilities. This molecular framework provides a roadmap for precision medicine approaches tailored to the epigenomic state of resistant metastatic breast cancer. Citation Format: Gizem Yayli-Vokshi, Sandra Cohen, Weiling Li, Hong Shao, Sydney Bowker, Elisa de Stanchina, Pedram Razavi, Sarat Chandarlapaty, Ekta Khurana. Integrated epigenomic profiling reveals distinct transcription factor networks driving therapy resistance in estrogen receptor positive metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3220.