Layered Single-Cell Heterogeneity in Hormone Receptor Signaling Across Mouse Organoids and Human ERα+ Cancer Cells

Abstract

Hormone receptor signaling is often interpreted through receptor abundance as a proxy for hormone responsiveness, yet the determinants of single-cell variability in hormone response remain unclear. Using murine mammary organoids, we mapped estrogen (E2) and progesterone (P4) responses at single-cell resolution. Despite controlled 3D culture conditions, basal cell-derived organoids exhibit striking variability in hormone-induced transcriptional responses, with ER cells varying in the fraction of responsive genes engaged. This variability is not explained by receptor abundance alone. Instead, response magnitude correlates with expression of transcriptional co-regulators including Ncoa1, Ncor1, and Ncor2, suggesting that co-regulator balance contributes to variation in endocrine response magnitude. Organoids exhibit a mixed basal-luminal enhancer landscape and growth factor-dependent remodeling of ER and PR protein abundance. MCF7 cells show delayed activation kinetics and reach a lower response plateau. Together, these findings reveal that hormone response magnitude varies independently of receptor abundance in mammary organoids and follows distinct activation dynamics in human ER+ cancer cells.