Fig. 6: Human milk contains several subsets of macrophages.

a,b, UMAP and corresponding heatmap of mean marker expression (a) showing immune cells in human milk (collected on days 4–63 pp and pregated on CD45⁺ cells) and graphs showing percentage of immune cell populations among CD45⁺ cells in human milk (b) (n = 13), analyzed by flow cytometry. Representative UMAP is shown from one of four independent experiments, n = 4. Two-tailed unpaired Student’s t test was performed. ****P < 0.0001. c, Seurat guided clustering and dimensionality reduction by UMAP showing seven immune cell populations including B cells, T cells, three populations of macrophages (Mac 1–3), monocytes (Mo), DC2/DC3 and unidentified clusters termed ‘Rest’ in scRNA-seq analysis of immune cells (CD45⁺) sorted from human milk samples (n = 6). d, Dot plot showing expression of selected genes in the three human macrophage subsets, monocytes and DC2/DC3 as in c. Dot size represents percentage of cells in a cluster expressing each gene; dot color reflects expression level. e, Heatmap showing the expression of liMac signature genes (as in Fig. 2c) by human milk macrophages (Mac 1, Mac 2 and Mac 3) and T cells as in c. f, Prediction similarity scores of mouse mammary gland macrophages applied to human milk macrophage subsets as in c. Each dot represents a cell. g, UMAP of the MoMac-VERSE compendium with annotated clusters⁴² (left) and Mac 1, Mac 2, Mac 3, monocytes (Mo) and DC2/DC3 (as in c) projected on the MoMac-VERSE (right). h, UMAP and frequencies of the MoMac-VERSE populations projected on human milk Mac 1, Mac 2, Mac 3, monocytes (Mo) and DC2/DC3 (as in c). i, Dot plot showing expression of selected ‘TREM2 signature’ genes^22,42,45 in the human macrophage clusters Mac 1, Mac 2, Mac 3 as in c. Dot size represents percentage of cells in a cluster expressing each gene; dot color reflects expression level (as indicated on legend).