Fig. 4: Within different MEs, Fibroblasts have distinct gene expression patterns, with a subset of Fibroblasts representing acute response to injury.

A Left - coordinates plot showing the composition of four MEs enriched in AKI samples. Middle-spatial locations of each of the MEs in one AKI sample. Right - expression of marker genes of each ME in all fibroblasts in the sample. B Differentially expressed genes within fibroblasts between the different MEs. The heatmap shows the mean expression of each of the genes, calculated for fibroblasts within each ME as well as for all fibroblasts in control and AKI. The depicted MEs represent four enriched in AKI (ME-5,15,9,16) and five enriched in control (ME-1,3,7,8,12). C Top – sub-clusters of Fibroblasts based on gene expression presented in Umap space. Clusters were calculated using Leiden clustering. Bottom – same ME and marker genes as in (A), presented on Umap space. D Mean expression score for the DE genes shown in panel (B) calculated within fibroblast populations in a time course snRNAseq data following injury in a mouse model of AKI. The scores were calculated for individual fibroblasts using Seurat and averaged for each mouse. The data presented in the heatmap shows the average of all mice in each condition. The minimum values were subtracted for each score such that minimum score = 0. N = 3 mice per time point. E The same calculation as in (D) was performed on a dataset of samples collected from patients who have undergone AKI (n = 11), exhibit CKD (n = 13), and are compared to normal kidney biopsies (n = 14). F Vcam1 antibody-staining with Clcf1, Crlf1 and Npr3 expression measured using RNAscope on control sample. The image is of one representative control sample out of two. G Same as in (F) on the AKI sample. The image is of one representative AKI sample out of three.