Single cell sequencing unravels molecular identity of rare renal cell types

Kidney tissue is very heterogenous with >30 different distinct cell types. This has made it difficult to define molecular fingerprints of individual renal cell types as expression levels obtained through analysis of whole kidney tissue generates data averaged across large populations of cells. To overcome this challenge, researchers from the have developed single cell RNA-sequencing protocols in mouse and human kidney tissue, with a special focus on the ultrafiltration unit of the kidney, the glomerulus.

What are the most important results in the published study?

We detected previously unknown heterogeneity in glomerular mural cells (mesangial cells). This is very interesting as mesangial cell injury is known to play a key role in the development of most chronic kidney diseases. Our study re-writes the definition of the mesangial cell and significantly renew our knowledge on this unique cell type. Another major finding in our study was that human kidney cells had very different molecular signatures from their corresponding mouse cells. For instance, many disease-associated human cell-specific genes were not expressed by same cell types in mouse. These differences can explain many translational challenges in the field and our data can hopefully guide the choice of animal models in future studies.

What is your/your group’s and KI:s part in the study?

Our group had an overall responsibility for running the project. We optimized and performed single cell capture, performed downstream analyses, validation experiments and functional studies. Bioinformatic analyses were performed together with professor Rickard Sandberg´s group at the Department of Cell and Molecular Biology. Human renal biopsy material was collected at the Division of Pathology at Karolinska University Hospital. High resolution imaging of renal tissue was done in collaboration with Scilifelab in Solna and University of Cologne in Germany.

What happens now, what is the next step?

Obviously, single cell transcriptomics can be applied to study many different biological and clinical questions in nephrology. One outstanding question is about reno-protective drugs: why do they preserve kidney function? Currently used drugs are based largely on repurposing of existing therapeutics and are neither kidney target–based nor designed to address the underlying molecular mechanisms. Single cell profiling of kidneys treated with these drugs can unravel which cell type(s) and mechanisms are mediating their reno-protective effects. This can open up possibilities to develop novel, more targeted kidney therapeutics.

We also want to apply single cell profiling to study regeneration in kidney tissue. This is a highly controversial topic as we still do not know whether some major renal cell types can be regenerated or not. I believe that single cell profiling of potential progenitor populations can give answers to some important pending questions in this field.

scRNA-seq analysis of isolated mouse and human glomerulus-associated cells

Fig. 1

a Summarized study design and experimental procedure. b Projection of mouse and human single cells onto 2-D UMAP space coloured by assigned cell types. Cell numbers in each population are shown in parenthesis. c The expression of known cell type marker genes in mouse and human principal glomerular cells. The markers include Nphs1/NPHS1 for podocytes, Pdgfrb/PDGFRB for mesangial-like cells (MLCs) and Pecam1/PECAM1 for ECs. The colour intensity of dots represents the expression level. The colour scale is defined by log2(mean RPKM). d Mouse and human podocyte, glomerular EC, and MLC enriched active regulons constructed by SCENIC. Regulons active in >50% of cells in one cell type but not in other two cell types were considered as cell-type enriched regulons. Binary activity scores are shown in the heatmap with black indicating ‘ON/active’ and white indicating ‘OFF/inactive’. CD collecting duct, DCT distal convoluted tubule, PTC proximal tubule cell, EC endothelial cell, MLC mesangial-like cell, MNP mononuclear phagocyte, PEC glomerular parietal epithelial cell, cTAL cortical thick ascending limb; colour dots indicate diverse cell types.


He B, Chen P, Zambrano S, Dabaghie D, Hu Y, Möller-Hackbarth K, Unnersjö-Jess D, Korkut GG, Charrin E, Jeansson M, Bintanel-Morcillo M, Witasp A, Wennberg L, Wernerson A, Schermer B, Benzing T, Ernfors P, Betsholtz C, Lal M, Sandberg R, Patrakka J. (2021) Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes. Nat Commun 12(1):2141. [article]

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