Fig. 4: Role of Runx1 in myofibroblast differentiation.

a Diffusion map showing sub-clustering of fibroblasts. Colors refer to sub-cell-types and arrow represents differentiation trajectory from fibroblast to myofibroblast. Pe pericyte, Fib fibroblast, MF myofibroblast. b Line plots showing cell proportion from the day after UUO along the trajectory. c Pseudotime heatmap showing gene activity (left) and TF motif activity (right) along the trajectory. d Footprinting profiles of Runx1 and Twist2 binding sites along the trajectory. e Immuno-fluorescence (IF) staining of Runx1 (red) in PDGFRb-eGFP mouse kidney. In sham-operated mice, Runx1 staining shows a reduced intensity in PDGFRb-eGFP+ cells compared to remaining kidney cells (arrows). f Immuno-fluorescence (IF) staining of Runx1 (red) in PDGFRb-eGFP mouse kidney at 10 days after UUO as compared to sham. Arrows indicate Runx1 staining in expanding PDGFRb-eGFP+ myofibroblasts. g Quantification of Runx1 nuclear intensity in PDGFRb-eGFP+ cells in sham vs. UUO mice. Error bars represent the SD of the intensity. Data are presented as mean ± SD. Statistical significance was assessed by a two-tailed Student’s t-test with p < 0.05 being considered statistically significant (n = 3 mice). h Performance of top-performing imputation methods on the prediction of Runx1 target genes measured with AUPR. i Peak-to-Gene links (top) predicted on scOpen matrix and associated to Tgfbr1 in fibroblast cells. The height of links represents its significance. Dash line represents the threshold of significance (FDR = 0.001). ATAC-seq tracks (below) were generated from pseudo-bulk profiles of fibroblast/myofibroblast cells with increasing pseudo time (0–20, 20–40, 40–60, 60–80, and 80–100). Binding sites of Runx1 (B1–B4) supported by ATAC-seq footprints and overlapping to peaks are highlighted on the bottom. j Scatter plot showing gene activity of Tgfbr1 and normalized peak accessibility from raw (upper) or scOpen imputed matrix (lower) for peak-to-gene link B4. Each dot represents cells in a given pseudotime and the overall correlation is shown in the left-upper corner. Scale bars in e and f represent 50 μm. For details on statistics and reproducibility, see the “Methods” section. Source data for Fig. 4 are provided as a Source Data file.