Fig. 3: Inflammatory PT cell states are associated with the fibrotic niche in human kidney disease.

a Density maps of cell type abundance overlayed on the same tissue section as in Fig. 2k. b Cell neighbourhoods in UUO samples (n = 5). Heatmap shows the mean enrichment (log2 scale, mean weighted by cell type abundance) of each cell type within a 25 µm radius of the reference cell type. Values greater or less than zero indicate enrichment or depletion of the cell type. cDC, classical dendritic cell. c Bar plots showing the enrichment ratio of myofibroblasts and myeloid cell types in proximity to inflammatory cell states in UUO samples (n = 5). Plots show means ± SEM. Paired two-sample Student’s t test. d Mean enrichment ratio of indicated transcripts adjacent to healthy, injured and inflammatory PT cell states relative to randomly sampled cells. x-axis: distance from centroids of all cells of that group, with transcripts quantified in 1 µm intervals. e Representative image of 5-plex immunofluorescence of obstructed nephrectomy tissue (from n = 4 samples), with insets showing higher magnification images. Scale bars: large image, 100 µm; small images, 20 µm. f 3-plex immunofluorescence demonstrating VCAM1⁺/ICAM1⁺ (arrow) and VCAM1⁺/ICAM1^- tubules (arrowhead) and the parietal epithelium of a glomerulus (*). Scale bar, 50 µm. g 5-plex immunofluorescence of healthy kidneys (from n = 2 samples), highlighting VCAM1⁺ tubular cell (arrow) and VCAM1⁺ parietal epithelial cells (arrowhead). Scale bar, 100 µm. h Immunofluorescence of obstructed kidney with CD68⁺ cells (arrows, left) in the lumen of ICAM1⁺ tubules. Arrowheads highlight CD68⁺ cells filopodia anchoring to ICAM1⁺ tubular cells (right). Scale bar, 20 µm. i Representative image of tubule (PanCK⁺), myofibroblast (FAP⁺) and macrophage (CD68⁺) segmentation. j Tubules were identified as FAP^-/CD68^-/PanCK⁺ and the proportion staining for VCAM1 and ICAM was determined. k UMAP of segmentation objects according to staining intensities of PanCK, VCAM1, ICAM1, FAP and CD68. l Enrichment of FAP and CD68 in proximity to VCAM1⁺/ICAM1^- or VCAM1⁺/ICAM1⁺ tubules. Violin plots of the percentage of the area covered (log2 scale) by FAP⁺ or CD68⁺ segmentations objects within a 25 µm radius of 6,304 tubule boundaries. Wilcoxon rank-sum test. Source data are provided as a Source Data file.