Fig. 9: Imaging-based single-cell spatial transcriptomics reveals the presence of ISG-T cells in close proximity to plasmacytoid dendritic cells in inflamed kidneys. | Nature Communications

Fig. 9: Imaging-based single-cell spatial transcriptomics reveals the presence of ISG-T cells in close proximity to plasmacytoid dendritic cells in inflamed kidneys.

From: Type I interferon drives T cell cytotoxicity by upregulation of interferon regulatory factor 7 in autoimmune kidney diseases in mice

Fig. 9

a Kidney tissue was analyzed using imaging-based single-cell spatial transcriptomics. b UMAP plot showing different cell clusters. c–e Representative images of kidney tissues under different conditions: H&E-stained tissue overview (far left), magnified view of the indicated area (top middle), DAPI-stained image overlaid with cell boundaries and specific marker genes (top right), segmented cells color-coded by cell type annotation using the same color scheme as in (b) (bottom middle), and segmented cells showing only ISG-T cells and pDCs in color with other cells shown in transparent (bottom right). These findings were confirmed in more than three areas and representative images were chosen. f Heatmap showing ISG expression levels in different T cell subtypes. g Dot plot showing the frequency of ISG-T cells among all T cells (Control, n = 6; ANCA-GN, n = 32; Lupus nephritis, n = 19). h Cell proximity analysis showing the median distances between ISG-T cells and different non-lymphocyte cell types. i Bar graph showing the distances between ISG-T cells and pDCs in different conditions (Control, n = 414; ANCA-GN, n = 2429; Lupus nephritis, n = 952). P values were calculated by one-way ANOVA with Tukey’s multiple comparison test. Cell type abbreviations: pDC plasmacytoid dendritic cell, podo podocyte, MC mesangial cell, PEC parietal epithelial cell, EC endothelial cell, FIB fibroblast, fib. MC fibrotic mesangial cell, PT proximal tubule, VSM/P vascular smooth muscle cell/pericytes, DCT distal convoluted tubule, CNT connecting tubule, TAL thick ascending limb of loop of Henle, ATL ascending thin limb of loop of Henle, DTL descending thin limb of loop of Henle, PC principal cell, and intercalated cell (IC) of collecting duct, PapE papillary tip epithelial cells abutting the calyx, NEU neuronal cell, N neutrophil, MAC macrophages, Mono monocytes, MDC monocyte-derived cell, PL plasma cell, cDC conventional dendritic cell, cycling mononuclear phagocyte, NKC/T natural killer cytotoxic T cell, cycNKC/T cycling natural killer cytotoxic T cell. Source data are provided as a Source Data file.

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