Fig. 4: Inflammatory cell states in the kidney across disease aetiologies.

a Workflow to spatially quantify 1,000 transcript species on the CosMx platform in nephrectomy samples from patients with chronic pyelonephritis (n = 4) and renal biopsies from patients with minimal change disease (n = 3) or IgA nephropathy (n = 6). b Left: UMAP visualisation of 246,055 cells across all samples coloured by cell annotations. PEC parietal epithelial cell, PT proximal tubular cell, LOH-DCT Loop of Henle and distal convoluted tubule, CD Collecting Duct, SMC Smooth muscle cell. Right: Representative images of nephrectomy and biopsy samples, showing cells coloured by annotation key in UMAP. c Representative spatial plot of pyelonephritic kidney. Dots represent individual cells coloured by their niche cluster. d Higher resolution of the rectangular inset in (c). highlighting inflammatory (arrows) and injured (arrowhead) tubular epithelia. Left: Cells coloured according to activation state and broad cell lineage. Right: Cells coloured according to granular annotation. e Higher resolution of areas indicated in (d) highlighting inflammatory (arrow) and injured (arrowhead) epithelia. Dots show the location of injury-associated (red) or inflammatory-associated (yellow) transcripts with cells coloured by activation state and broad lineage. f Dotplot of expression of injury and inflammatory markers identified by snRNA-seq (Fig. 2c) in the CosMx (1000-plex) dataset. Dot colours show the averaged gene expression (log scale) and size indicates proportion of cells expressing the gene. g Mean enrichment ratio of transcripts in healthy, injured and inflammatory PT cell states relative to randomly sampled cells. x-axis: distance from centroids of all cells of the respective group, with transcripts quantified in 1 µm intervals. h Bar plots showing enrichment of myofibroblasts and myeloid cell types in proximity to PT cell states. Plots show means ± SEM. Paired two-sample Student’s t test. i Correlation between percentage of inflammatory PT cells and the proportions of myofibroblasts, monocytes and classical dendritic cells (cDC) in biopsy samples. Graph shows linear regression slope with Pearson co-efficient. j Correlation between percentage of inflammatory PT cells and estimated glomerular filtration rate (eGFR) in biopsy samples. Linear regression slope with Pearson co-efficient.