Extended Data Fig. 7: Origin of myofibroblast in mouse kidney.
From: Decoding myofibroblast origins in human kidney fibrosis
a, Representative image of COL1α1 in-situ hybridization in a Pdgfrb-creER;tdTomato kidney after UUO surgery. Scale bar, 10 μm. b, c, Quantification of αSMA+ cells in PDGFRβtdtom+ kidneys from UUO day 10. n = 3. Data are mean ± s.d. d, Scaled expression of the top 10 genes by specificity in each cell cluster depicted in Fig. 3e. All cells from each cell cluster are averaged in one column. e, Expression of select genes in all 10 cell clusters from Fig. 3e. f, ECM score visualized on the same UMAP embedding from Fig. 3e. g, Distribution of ECM score, collagen score, glycoprotein score and proteoglycan score per cell cluster. h, Immuno-fluorescence staining in sham and UUO (day 10) mouse kidney showing PDGFRα expression in a subset of Pdgfrb-creER;tdTomato positive cells (arrows). i, RNA ISH showing co-localization of Col1a1 expression in PDGFRα PDGFRβ double-positive cells. COL1α1 PDFGRα PDGFRβ triple-positive cells (arrows) occur solely in the kidney interstitium. j, Left, COL1α1 expression and ECM score in CD10− cells (Fig. 1b) stratified according to PDGFRα and PDGFRβ expression. Right, percentage of COL1α1+ and COL1α1− cells in the same data, stratified in the same way. COL1α1− cells occur mostly in PDGFRα PDGFRβ double-negative cells whereas COL1α1+ cells occur predominantly in PDGFRα PDGFRβ double-positive cells (n = 51,849). Group comparisons: (other genes) vs (a/b): P = 2.618674 × 10−317, (a) vs (a/b): P = 5.277528 × 10−53, (b) vs (a/b): P = 1.243014 × 10−233, (other genes) vs (a): P = 1.531528 × 10−177, (b) vs (a): P = 6.344322 × 10−64, (other genes) vs. (b): P = 8.89697 × 10−152. Bonferroni corrected P values based on a two-sided Wilcoxon rank sum test. k, Distribution of immunofluorescence/TA score over 62 patients and representative image of a trichrome stained human kidney tissue microarray (TMA) stained by multiplex RNA ISH using PDGFRA, PDGFRB and COL1A1 probes with nuclear counterstain (DAPI) of 62 kidneys (patient data in Supplementary Table 2) (left), average scaled COL1α1 expression in the ISH data stratified by PDGFRα PDGFRdetection in the same data (middle) and percentage of COL1α1-positive and -negative cells in the same data stratified in the same way (right). Group comparison: (α/β) vs (COL1α1): P ≈ 0, (α/β) vs (β): P ≈ 0, (α−) vs (α): P ≈ 0. Bonferroni corrected P values based on a two-sided Wilcoxon rank sum test. l–p, A diffusion map embedding of pericytes and matrix-producing cells with annotation of the different time points in m, cell cluster annotation in n and scaled expression of selected genes in o–q. q, The surgery type per cell (sham versus UUO) visualized on the same UMAP embedding from Fig. 4c (top), or with colours representing the cell types/states (bottom). r, Expression of select genes on the same UMAP embedding from Fig. 3j. s, ECM and collagens score distribution for the four main cell types (top) and for mesenchymal clusters (bottom). Scale bars, 50 μm (b, h, i), 10 μm (k). For details on statistics and reproducibility, see Methods.
