Arid1a directs lineage specification in mammary epithelial cells

Epigenetic regulation is essential for mammary gland development, yet the specific chromatin remodelers that govern mammary epithelial cell fate remain poorly defined. Mutations in SWI/SNF chromatin remodeling complex subunits occur in more than 20% of human cancers, with ARID1A being the most frequently altered. In breast cancer, ARID1A loss of function mutations are enriched in metastatic estrogen receptor-positive (ER⁺) disease and associated with endocrine therapy resistance. To define the developmental role of Arid1a in vivo, we generated mice with mammary epithelium specific Arid1a deletion. These animals displayed disrupted ductal branching and aberrant terminal end bud formation. Mammary organoids derived from Arid1a deficient tissue further revealed abnormal cystic morphology and impaired differentiation. To dissect the molecular consequences of Arid1a loss, we performed single cell multiomic profiling that combine single nucleus RNA and chromatin accessibility sequencing from the same cells, together with H3K27ac and BRG1 CUT&RUN-seq. Arid1a loss caused a collapse of normal mammary epithelial lineage architecture, with single cell analyses showing failure to maintain basal, luminal progenitor, and alveolar identities. Instead, Arid1a deficient cells were restricted to an undifferentiated luminal hormonal like state characterized by reduced estrogen receptor signaling competence. Chromatin profiling revealed profound remodeling, including decreased accessibility and impaired SWI/SNF targeting at lineage defining transcription factors (TF) such as Foxa1, Gata3, and Sox9. A CRISPR/Cas9 pooled loss of function screen identified Foxa1 and Meis1 as essential regulators whose deletion recapitulated the Arid1a null phenotype, positioning them as downstream effectors required for mammary cell fate specification. Notably, Meis1 emerged as a previously unrecognized regulator of luminal hormonal identity. Our work provides a framework for understanding how Arid1a rewires the chromatin landscape and transcriptional network in normal mammary development. By identifying lineage specific TF motifs and critical regulators like Meis1, we identify new opportunities for targeted therapeutic intervention.