Fig. 7: WNT and NOTCH signatures dictate endometrial epithelial differentiation.

a, Experimental timeline of endometrial organoid cultures. Organoids were treated with inhibitors to either NOTCH (DBZ or DAPT) or WNT (IWP-2 or XAV939) upon initiation of hormonal stimulation. R-spondin-1 (RSPO-1) was omitted from ExM in the presence of WNT inhibitors. Collection time points for scRNA-seq are highlighted with asterisks. b, UMAP plots for scRNA-seq samples after either WNT or NOTCH inhibition. c, UMAP representations colored by inhibitor treatments (top) or hormonal stimulation (bottom). d, Bar plots showing enrichment of cells in ciliated and secretory clusters after NOTCH or WNT inhibition compared with untreated controls, analyzed with unpaired z-tests. e, IHC for acetylated α-tubulin (ciliary marker) and glycodelin (PAEP). Scale bars, 200 μm. Representative images of endometrial organoids derived from three different patients. Blue arrowheads indicate ciliated cells, orange arrowheads indicate secretory cells and green arrowheads indicate glandular secretions. f, Dot plot showing the log₂-transformed expression of genes characteristic of endometrial secretions in epithelial subsets. g, Radial representation of the cell type probabilities predicted by a logistic model trained on epithelial cells in vivo. The linear projection shows cells in each corner whenever a cell is predicted to belong to a given class with a probability of 1. h, Volcano plots representing differentially expressed genes within the secretory lineage in two comparisons: (1) cells cultured with and without WNT inhibitor; progesterone is present in the media; and (2) cells cultured with and without hormones; WNT inhibitor is present in the media. TFs that are significant in the in vivo dataset are highlighted. i, Heatmap showing differential activities of TFs significant in the in vivo analysis. Ctrl, control; NOTCHi, NOTCH inhibitor; WNTi, WNT inhibitor.