Fig. 2: Heterogeneity of nephron and mesenchymal cell types in untransplanted and transplanted kidney organoids.

a UMAP visualization of a total of 10,198 high-quality nephron cells obtained from untransplanted (3116 cells from d7+13, 3963 from d7+20) and transplanted (1816 cells from d7+13, 1303 from d7+20) kidney organoids, color-coded by condition (left) and by cluster (n = 16; right). b Expression-level scaled heatmap of the top 20 marker genes in nephron subclusters. Scale: z-score of the gene expression level. Abbreviations: G1S-S: proliferative nephron cells G1S-S, G2M-M: proliferative nephron cells G2M-M, NPC: nephron progenitor cells, NPC-pod: podocyte-committed progenitors, immature pod; immature podocytes, early pod #1: early podocytes #1, early pod #2: early podocytes #2, late pod: late podocytes, late pod (stress): late podocytes (stress-induced), hypoxic pod: hypoxic podocytes, mesenchymal: mesenchymal-like nephron cells, PTA/RV: pretubular aggregate/renal vesicle, PT #1: proximal tubules #1, PT #2: proximal tubules #2, LoH-like: loop of Henle-like, DT/CD: distal tubules/collecting duct. c Hierarchical clustering of nephron cell types, color-coded according to P-value from multiscale bootstrap resampling analysis on all highly variable genes. d Relative cluster quantification of the nephron cell types in transplanted versus untransplanted kidney organoids (d7+13 and d7+20). Source data are provided as a source data file. e UMAP visualization of a total of 5748 high-quality mesenchymal cells obtained from untransplanted (1028 cells from d7+13, 2607 from d7+20) and transplanted (653 cells from d7+13, 1460 from d7+20) kidney organoids, color-coded by condition (left) and by cluster (n = 12; right). f Expression-level scaled heatmap of the top 20 marker genes in mesenchymal subclusters. Scale: z-score of the gene expression level. Abbreviations: G1S-S: proliferative mesenchymal cells G1S-S, G2M-M: proliferative mesenchymal cells G2M-M, mural cells: unspecified mural cells, per/mesang: pericytes/mesangial cells, SMCs: smooth muscle cells, mes prog: mesenchymal progenitors, chon like cells: chondrocyte-like cells, neural prog: neural progenitors. g Hierarchical clustering of mesenchymal cell types, color-coded according to P-value from multiscale bootstrap resampling analysis on all highly variable genes. h Relative cluster quantification of the mesenchymal cell types in transplanted versus untransplanted kidney organoids (d7+13 and d7+20). The color legend for this figure is the same as the one in (e). Source data are provided as a source data file. i Staining of PDGFRβ + stromal cells in untransplanted and transplanted kidney organoids reveals abundant PDGFRβ + stromal cells in the periphery of untransplanted organoids (asterix and first magnification) and scarce PDGFRβ + cells in the center (second magnification). Transplantation induces the appearance of perivascular stromal cells (PDGFRβ+, arrowhead and magnifications) supporting perfused blood vessel (LCA+). Magnifications of boxed areas are shown. Scale bars 200 µm.