Fig. 6: In vitro responses of endometrial organoids to ovarian hormones are similar to in vivo epithelial changes.

a, Experimental timeline of endometrial organoid cultures. Organoids were derived in ExM and then subjected to hormonal stimulation with estrogen (E2) followed by estrogen + progesterone (P4) + cAMP and prolactin (PRL). The time points at which organoids were collected for scRNA-seq are marked with an asterisk. b, UMAP projections of scRNA-seq data identify major cellular populations. c, UMAP representations colored by days after hormonal stimulation (top) or by treatments (bottom). d, Dot plot showing log₂-transformed expression of selected genes that distinguish the main cell populations. e, IHC to validate markers of the secretory population, SCGB2A2 and HEY1, and combined staining for FOXJ1 and acetylated α-tubulin in control (undifferentiated) and differentiated (hormonally stimulated) organoids. Black arrowheads indicate ciliated cells with FOXJ1-positive nuclei. Nuclei are counterstained with hematoxylin. Scale bars: 250 μm (red), 200 μm (black). Representative images of three endometrial organoids from three different donors. f, Predicted epithelial subsets of endometrial organoids using a logistic classifier. g, Heatmaps showing TFs differentially expressed in ciliated and secretory lineages. Color is proportional to log-transformed fold change, with asterisks highlighting TFs whose targets are also differentially expressed (that is, differentially activated TFs). h, Cells able to respond to progesterone derived from a clonal organoid culture (E001 individual) (Methods) are colored from left to right: (1) cluster labels as in Extended Data Fig. 8e; (2) Palantir pseudotime; (3) probability of cells to progress toward the ciliary lineage; and (4) probability that the cell differentiates toward the secretory lineage. NH, no hormone.