Abstract 1428: Dissecting a triple-negative breast cancer super enhancer: insights into oncogenic gene regulation

Abstract Triple Negative Breast Cancer (TNBC) is an aggressive and therapeutically challenging subtype of breast cancer, characterized by significant intra-tumoral heterogeneity and the absence of actionable molecular markers. This study addresses the urgent need for targeted therapies by investigating the role of non-coding regulatory elements, specifically super enhancers (SEs), in TNBC pathogenesis. SEs are large clusters of enhancers with high transcription factor occupancy and enhancer RNA (eRNA) production, regulating key genes involved in cell identity and cancer progression. Using Chromatin Immunoprecipitation sequencing (ChIP-seq) and Global Run-On sequencing (GRO-seq) across 13 cancer cell lines, we identified a novel TNBC-specific, transcriptionally active SE on chromosome 17, located upstream of the ITGA3 gene. To elucidate its functional role, we conducted CRISPR-interference (CRISPRi) assays coupled with RNA sequencing in TNBC cells, revealing genome-wide SE target genes. Integration with high-throughput chromosome conformation capture (Hi-C) data established direct chromatin interactions linking the SE to its target genes, which collectively form a gene signature predictive of poor clinical outcomes. Perturbation of this SE via CRISPR significantly impaired tumor cell proliferation, highlighting its role as a potential driver of oncogenic phenotypes. These findings provide new insights into enhancer-target gene interactions in TNBC and identify this SE and its associated gene network as promising therapeutic targets. Citation Format: Natalia Maldonado Vázquez, Nicole Zaragoza Rodríguez, Hector Franco. Dissecting a triple-negative breast cancer super enhancer: insights into oncogenic gene regulation [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 1428.