Fig. 1: Identification of the cell subtypes in kidney allograft biopsies by single-cell RNA seq.

a Experimental Approach. Kidney allograft biopsies were used for scRNAseq (n = 16 biopsies from 14 patients). b Uniform Manifold Approximation and Projection (UMAP) plot of 35,152 cells passing QC filtering. The main kidney cell types are represented, including loop of Henle (LOH), podocytes, vascular smooth muscle and pericytes (vSMp), proximal tubule (PT), intercalated cells (IC), three endothelial cell subsets comprising vasa recta (ECvr), glomerular (ECg) and peritubular capillaries (ECptc), myeloid cells, and lymphoid cells. c Schematic of a juxtamedullary nephron showing relevant cell types and associated vasculature. d Dot plot showing average gene expression values of canonical lineage markers (log scale) and percentage of major cell types represented in the whole dataset and UMAP plot. e Relative proportions of the 18 different cell types identified in the kidney transplant biopsies. f Polar plot of the 16 biopsies²². The biopsies were reclassified into 4 groups: non-rejecting donor-specific antibody (NR DSA)-negative (NR DSA-), NR DSA-positive (NR DSA+), T cell-mediated rejection (TCMR), DSA-positive antibody-mediated rejection (ABMR DSA+). g Spearman’s correlation coefficient represented by a dot with 95% confident interval represented by the error bars of the correlation between inflammation severity (radius on the polar plot)²² and the frequency of the different immune cells as a proportion of the total population. Panels a and c were created using biorender.com.