The Kidney in High Definition

Researchers at UHN’s Toronto General Hospital Research Institute (TGHRI) and Ajmera Transplant Centre have constructed a detailed, single cell-level map of the healthy human kidney. By profiling gene expression in individual cells that make up the organ, the team has gained deep insights into how it functions—and how cells that comprise the kidney differ between males and females.

One in 10 Canadians has some form of kidney disease and, in many cases, the mechanisms underlying disease development and progression are unclear.

“Characterizing the individual molecular states of cells in healthy organs is a critical first step for defining disease processes and developing targeted treatments,” explains Dr. Sarah Crome, a Scientist at TGHRI and the Ajmera Transplant Centre and co-senior author of the study.

Using single-cell RNA sequencing—a technique for measuring gene expression within individual cells— the team analyzed biopsied tissue from 19 living kidney donors.

With data from over 27,000 healthy kidney cells, the team built a detailed map of the diverse cell populations and the genes that are active within these cells.

“Because there are clear sex-based differences in many kidney diseases, we designed the study to uncover differences in molecular pathways that contribute to the observed sex differences to better understand the underlying causes of kidney disease,” says Dr. Ana Konvalinka, a TGHRI Senior Scientist, Transplant Nephrologist at the Ajmera Transplant Centre and co-senior author of the study.

The team discovered that cells from male donors had greater expression of genes related to aerobic metabolism and oxidative stress, whereas those from females had greater expression of genes involved in protection against oxidative stress.

Dr. Caitríona McEvoy, currently a Transplant Nephrologist at Tallaght University Hospital in Ireland and co-first author of the study, says that the sex-based differences in gene expression were linked to functional differences in a particular cell type in the kidney, which plays a pivotal role in regulating fluid-electrolyte balance and pH. “Male cells had higher baseline metabolic activity, which could explain why males are more susceptible to certain metabolism-related kidney injuries.”

The researchers also examined the presence of immune cells, which are relevant for understanding immune-mediated diseases, such as fibrosis and transplant rejection.

“We identified immune cells in the kidney that are distinct from their counterparts in the blood and identified unique features of the immune niche in the healthy kidney,” says Julia Murphy, a PhD candidate in Dr. Crome’s laboratory and co-first author of the study. “These immune cells could play an important role in immune homeostasis—promoting beneficial immune responses that are necessary to fight infection while reducing harmful responses, such as unchecked inflammation, that can damage healthy tissue.”

Drs. Crome and Konvalinka say the team’s insights into the healthy organ provide an important reference for studying the factors that govern kidney health and disease. These findings will help scientists model the kidney, identify what goes wrong in acute and chronic diseases, and test new drugs and regenerative medicine therapies to treat them.

This work was supported by the Canadian Institutes of Health Research, the Canada First Research Excellence Fund, the Kidney Foundation of Canada, the Canada Foundation for Innovation and the UHN Foundation. Dr. Sarah Crome is a Scientist at TGHRI and the Ajmera Transplant Centre and an Assistant Professor in the Department of Immunology at the University of Toronto (UofT). Dr. Ana Konvalinka is a TGHRI Senior Scientist, a Transplant Nephrologist at the Ajmera Transplant Centre, and an Assistant Professor in the Departments of Medicine and Laboratory Medicine and Pathobiology (LMP) and the Institute of Medical Science at UofT. Other key contributors to this study include Drs. Bo Wang, a TGHRI Scientist and an Assistant Professor in the Department of LMP at UofT; Sonya MacParland, a TGHRI Scientist, an Associate Professor in the Departments of LMP and Immunology at UofT, and a Tier 2 Canada Research Chair in Liver Immunobiology; and Gary Bader, a Princess Margaret Cancer Centre Affiliate Scientist and a Professor at the Donnelly Centre for Cellular and Biomolecular Research at UofT.

McEvoy CM, Murphy JM, Zhang L, Clotet-Freixas S, Mathews JA, An J, Karimzadeh M, Pouyabahar D, Su S, Zaslaver O, Röst H, Arambewela R, Liu LY, Zhang S, Lawson KA, Finelli A, Wang B, MacParland SA, Bader GD, Konvalinka A, Crome SQ. Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity. Nat Commun. 2022 Dec 10. doi: 10.1038/s41467-022-35297-z.