Fig. 3: Single-cell transcriptome analysis delineates the landscape of T-cell population in the immune microenvironment of IMN.

A UMAP plot showing the distribution of cell types in the IMN ecosystem from the integrated scRNA-seq datasets included in this study. B Violin plots showing the selected marker genes that were used to identify the cell types in this study. The relative expression level of these genes was compared between IMN samples and healthy kidneys. Case, IMN; Control, healthy kidney. C t-SNE projections of sub-clustered T cells, labeled in different colors. D Boxplots illustrating the fraction of T-cell subtypes in IMN (n = 9) and healthy kidney (n = 6), respectively. The two groups were labeled in different colors. Case, IMN; Control, healthy kidney. The P-value was calculated by the Wilcoxon test. The error bars represent the error margins. E Heatmap indicating the expression of selected gene sets in T-cell subtypes, including naive, resident, inhibitory, cytokines, co-stimulatory, transcriptional factors (TF), and cell types. F Pseudotime-ordered analysis of T-cell subtypes from IMN and healthy samples. T cell subtypes are labeled by colors. G Heatmap showing the dynamic changes in gene expression of T-cell subtypes along the pseudotime (lower panel). The distribution of T-cell subtypes during the transition (divided into 4 phases), along with the pseudo-time. Subtypes are labeled by colors (upper panel). IMN idiopathic membranous nephropathy, PT proximal tubule cells, LOH loop of Henle cells, IC intercalated cells, PC principal cells, Mes mesangial cells, Pod podocytes, DT distal tubule cells, PEC parietal epithelial cells, Mac macrophages, Mono monocytes, EC endothelial cells, Treg regulatory T cell.