A Single-Cell Transcriptome Atlas of the Mouse Glomerulus

Abstract

Three different cell types constitute the glomerular filter: mesangial cells, endothelial cells, and podocytes. However, to what extent cellular heterogeneity exists within healthy glomerular cell populations remains unknown. We used nanodroplet-based highly parallel transcriptional profiling to characterize the cellular content of purified wild-type mouse glomeruli. Unsupervised clustering of nearly 13,000 single-cell transcriptomes identified the three known glomerular cell types. We provide a comprehensive online atlas of gene expression in glomerular cells that can be queried and visualized using an interactive and freely available database. Novel marker genes for all glomerular cell types were identified and supported by immunohistochemistry images obtained from the Human Protein Atlas. Subclustering of endothelial cells revealed a subset of endothelium that expressed marker genes related to endothelial proliferation. By comparison, the podocyte population appeared more homogeneous but contained three smaller, previously unknown subpopulations. Our study comprehensively characterized gene expression in individual glomerular cells and sets the stage for the dissection of glomerular function at the single-cell level in health and disease.

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

“…This dataset comprised 23,108 cells, including 11,851 cells from cold-and 11,257 cells from warm-dissociated kidneys (see Methods). These cells were then annotated using scMatch [29] by comparing their expression to reference gene expression profiles extracted from three previously published single-cell or single-nucleus RNA-seq studies of adult mouse kidneys [26,30,31]. The inferred identities were then used to calculate cell-type-specific gene expression signatures and further refine the annotations (see Methods and Supplementary Fig.…”

“…Reference dataset. To construct the reference dataset for scMatch [29], we obtained gene counts and cell types reported in three single-cell (or single-nuclei) adult mouse kidney studies [26,30,31]. Counts were normalised to cell library size and averaged within each cell type to derive reference vectors ( Supplementary Fig.…”

Single Cell Profiling Reveals Sex, Lineage and Regional Diversity in the Mouse Kidney

“…For example, female mice and humans are more resistant to ischemia or ER-stress-invoked renal injury (Hodeify, 2013;Park et al, 2004;Aufhauser et al, 2016). Single nucleus and single cell RNA-sequencing (scRNA-seq) have provided new insight into the cellular make-up of mammalian organ systems including the kidney (Wu et al, 2019;Habib et al, 2017;Macosko et al, 2015;Adam et al, 2017;Chen et al, 2017;Park et al, 2018;Karaiskos et al, 2018;Han et al,2018). However, kidney studies have been largely male-centered and lack insight into higher order organization of cell types critical to kidney function.…”

Understanding the Biology and Pathogenesis of the Kidney by Single-Cell Transcriptomic Analysis

“…Mouse glomeruli have just been analyzed by scRNAseq at a large scale with a total of 13,000 glomerular cells being sequenced, resulting in mouse glomerular singlecell transcriptome atlas [80]. In this work, the authors identified three subpopulations of podocytes as well as a subset of endothelial cells exhibiting proliferative property as shown by expression of proliferation marker genes.…”

“…This approach gave rise to more precise dissection of cell types or subtypes compared with scRNA-seq of whole kidney, as described in the work by Park et al [79]. Another example is the scRNA-seq of mouse glomeruli by Karaiskos et al [80]. They resolved three subpopulations of podocytes in contrast with Park et al's [79] work based on scRNA-seq of entire kidney.…”