Environmental chemical mixtures reprogram mammary epithelial development to epigenetic states associated with breast cancer

Environmental exposures occur as complex mixtures, yet the mechanisms by which they alter human tissue development and confer cancer susceptibility remain poorly defined. Here, we establish a physiological 3D human breast organoid high-content screening (3D-HCS) platform that quantitatively links exposure-induced developmental disruption to cancer-relevant cell states. Screening of structurally diverse environmental chemicals as single agents but also as mixtures reveals heterogeneous but reproducible developmental responses, indicating that distinct environmental chemicals perturb different aspects of mammary morphogenesis. Focusing on bisphenols, we show that a physiological-dose mixture (BPA, BPS, and BPF; 3BPX) disrupts organoid development and induces transcriptional programs characterized by extracellular matrix remodeling, epithelial plasticity, and partial epithelial–mesenchymal transition (EMT), accompanied by widespread DNA methylation remodeling. The 3BPX exposure signature maps to ER⁺ luminal breast cancers and is preferentially enriched in invasive lobular carcinoma (ILC), a subtype characterized by epithelial plasticity and stromal interaction. Genome-wide DNA methylation profiling revealed that the 3BPX-associated methylation signature is detectable in primary tumors and adjacent normal tissue and is enriched in Normal-like tumors and ILC. Together, these findings demonstrate that environmentally relevant chemical exposures induce heterogeneous developmental perturbations that converge on conserved transcriptional and epigenetic programs associated with epithelial plasticity, tissue remodeling, and cancer susceptibility. These exposure-induced states persist as molecular “scars” that map to defined epithelial and stromal compartments in human breast cancers, supporting a model in which developmental exposures establish a field of increased oncogenic potential.