Cell lineage analysis by comprehensive single-cell RNA-sequencing in IMN and control subjects

(A) Schematic of the scRNA-seq pipeline. kidney (n=6) samples from patients with IMN or healthy control subjects (n=2) were collected at the time of clinically indicated renal biopsy or live kidney donation, respectively. Kidney biopsies were enzymatically disaggregated into single-cell suspensions and loaded onto a microfluidic device for cell barcoding, cell lysis, reverse RNA transcription, and then scRNA-seq as well as various analysis. (B)Seventeen distinct cell clusters were visualized by UMAP plotting, with each cell color-coded for its associated subtypes. The color of the cells represented group origin. (C) UMAP plot of cell clusters from different subjects of IMN patients and control. The color of cells reflected the individual origin. (D) Bar plots of the percent contribution of cell clusters in kidneys from different subjects. Blocks represented different subjects, and block height was in proportion to the number of cells. (E) Heatmap of the top 20 most differentially expressed genes in each cluster to identify mutually exclusive gene sets, which were then used to determine the cell lineage of each cluster. Each column represented a cell cluster, and each row corresponded to a marker gene for the individual cluster. Transcript abundance ranges from low (purple) to high (yellow). (F) Violin plot of selected marker genes that identified the clusters generated by UMAP plotting. It was colored by different cell subtypes.

Abbreviations were as follows: PT, proximal tubule cells; LOH, loop of Henle cells PC, principal cells; IC, intercalated cells; DT, distal tubule cells; EC, endothelial cells; Pod, podocytes; MC, mesangial cell; DC, dendritic cells; Mac, macrophages; Mono, monocytes; Fib, fibroblasts; Per, pericyte.