Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes

Bing He,Gül Gizem Korkut,Katja Möller-Hackbarth,Dina Dabaghie,Marie Jeansson,Emmanuelle Charrin,Mark Lal,Ping Chen,Annika Wernerson,Thomas Benzing,David Unnersjö‐Jess ,Patrik Ernfors,María Bintanel-Morcillo ,Christer Betsholtz,Rickard Sandberg,Sonia Zambrano,Yizhou Hu,Lars Wennberg,Anna Witasp,Bernhard Schermer,Jaakko Patrakka

doi:10.1038/s41467-021-22331-9

Abstract

Molecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, however, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), are missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we use Smart-seq2 to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. The analysis reveals genetic programs for all four glomerular cell types (podocytes, glomerular endothelial cells, MCs and PECs) as well as rare glomerulus-associated macula densa cells. Importantly, we detect heterogeneity in glomerulus-associated Pdgfrb-expressing cells, including bona fide intraglomerular MCs with the functionally active phagocytic molecular machinery, as well as a unique mural cell type located in the central stalk region of the glomerulus tuft. Furthermore, we observe remarkable species differences in the individual gene expression profiles of defined glomerular cell types that highlight translational challenges in the field and provide a guide to design translational studies.

Highlights

Molecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research
We further identified a unique mural cell type located in the stalk/root of the glomerulus tuft
To investigate cell types and expression patterns in mouse and human kidney glomeruli, we dissociated the isolated glomerular tissues followed by FACS single-cell sorting, and subjected them to Smart-seq[2], a scRNA-seq method that is more sensitive in gene detection compared to droplet-based methods[9] (Fig. 1a)

Summary

Introduction

Molecular characterization of the individual cell types in human kidney as well as model organisms are critical in defining organ function and understanding translational aspects of biomedical research. Previous studies have uncovered gene expression profiles of several kidney glomerular cell types, important cells, including mesangial (MCs) and glomerular parietal epithelial cells (PECs), are missing or incompletely described, and a systematic comparison between mouse and human kidney is lacking. To this end, we use Smartseq[2] to profile 4332 individual glomerulus-associated cells isolated from human living donor renal biopsies and mouse kidney. A validation of the anatomical position of the cells described as MCs and evidence that these cells represent the unique cell type intrinsic to the glomerular tuft was missing Another scRNA-seq study on human whole kidneys reported podocyte transcriptomes but lacked properly annotated MCs and GECs6. A bridge connecting the gap between two species is required for translational studies

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Conclusion