Integrative Transcriptional and Chromatin Analyses Reveal Enhancer-Mediated Regulatory Programs Driving Breast Cancer Metastasis

Breast cancer metastasis remains the leading cause of disease-related mortality, yet the regulatory mechanisms enabling tumor cells to adapt to distant tissue environments remain poorly defined. Here, we generated a multi-omic resource integrating transcriptomic (RNA-seq) and chromatin accessibility (ATAC-seq) profiles from estrogen receptor-positive primary breast tumors and matched liver and lung metastases obtained from the same patients, including diagnostic and postmortem specimens. This design enabled direct intra-patient comparisons of primary and metastatic regulatory landscapes. We identified extensive reprogramming of chromatin accessibility and gene expression in metastatic lesions relative to primary tumors, indicating widespread regulatory remodeling. Peak-to-gene correlation analysis uncovered thousands of metastasis-associated enhancer-gene linkages, with metastatic samples exhibiting significantly increased enhancer connectivity. These rewired enhancer networks preferentially targeted clinically relevant genes, including RIPK4 , ISYNA1, and RAB3D, which were associated with three or more enhancers in metastases but not in primary tumors. Furthermore, ATAC-seq footprinting combined with gene expression analysis revealed distinct, tissue-specific transcription factor activity profiles in liver and lung metastases, including ESR1, that were not explained by transcription factor expression levels alone. Together, these data provide a resource of metastasis-specific regulatory elements and their cognate transcription factors, revealing new regulatory vulnerabilities that may be therapeutically exploitable. Implications: These findings support a model in which breast cancer metastasis is driven by enhancer regulatory reprogramming, allowing tumor cells to adapt to a variety of microenvironments.