Fig. 4: Predicted ligand–receptor interactions and role of macrophages in endometrial repair and regeneration.

a, Left, UMAP projections of scRNA-seq data for 32,322 immune cells colored by cell type. Right, UMAP projections of snRNA-seq data for 24,820 immune cells/nuclei colored by cell type. b, Beeswarm plot of the distribution of log fold change between the proliferative and secretory phases in neighborhoods containing immune cells from different cell types in scRNA-seq data. Differentially abundant neighborhoods at log fold change > 2.5 and spatial FDR < 0.1 are colored. c, Dot plot showing normalized, log-transformed and variance-scaled expression of genes (y axis) in uNK and uM cell states (x axis) in scRNA-seq data. Asterisk denotes significantly upregulated expression at FDR < 0.05. d, Dot plots showing normalized, log-transformed and variance-scaled expression of signaling molecules and receptors (y axes) upregulated in uNK, uM and stromal cell states (x axes) in scRNA-seq data. Asterisk denotes significantly upregulated expression at FDR < 0.05. The predicted cell–cell communication between uNK, uM and stromal cell states, including its likely role, is shown by differently colored arrows. e, Dot plot showing normalized, log-transformed and variance-scaled expression of pro-angiogenic signaling molecules (y axis) upregulated in uNK and uM cell states (x axis) in scRNA-seq data. Asterisk denotes significantly upregulated expression at FDR < 0.05. f, Schematic illustration of macrophage and stromal cell signaling during the menstrual and proliferative phases, likely involved in macrophage cell recruitment, increasing wound healing abilities and dampening inflammation in stromal cells. g, Schematic illustration of macrophage, endothelial cell and PV cell signaling likely involved in macrophage recruitment and angiogenesis. Cells from donors on hormones and donors with endometriosis were excluded from analyses shown in b–e of this figure. Asterisk denotes significantly upregulated expression FDR < 0.05. cDC, conventional dendritic cells; FDR, false discovery rate; ILC3, innate lymphoid cell type 3; pDC, plasmacytoid dendritic cell; T_reg, regulatory T cells.