Resident Macrophage Subpopulations Occupy Distinct Microenvironments in the Kidney
Dataset ID: STDS0000151
29,920 Spots
32,285 Genes


Dataset information
The kidney contains a population of resident macrophages from birth that expands as it grows and forms a contiguous network throughout the tissue. Kidney resident macrophages (KRMs) are important in homeostasis and the response to acute kidney injury (AKI). While the kidney contains many microenvironments, it is unknown whether KRMs are a heterogeneous population differentiated by function and location. We combined single-cell RNA sequencing (scRNAseq), spatial transcriptomics, flow cytometry, and immunofluorescence imaging to localize, characterize, and validate KRM populations during quiescence and following 19 minutes of bilateral ischemic kidney injury. scRNAseq and spatial transcriptomics revealed seven distinct KRM subpopulations, which are organized into zones corresponding to regions of the nephron. Each subpopulation was identifiable by a unique transcriptomic signature suggesting distinct functions. Specific protein markers were identified for two clusters allowing analysis by flow cytometry or immunofluorescence imaging. Following injury, the original localization of each subpopulation is lost, either from changing locations or transcriptomic signatures. The original spatial distribution of KRMs is not fully restored for at least 28 days post-injury. The change in KRM localization confirms a long hypothesized dysregulation of the local immune system following acute injury and may explain the increased risk for chronic kidney disease.
Overall design
Single-cell RNA sequencing of kidneys leukocytes and spatial transcriptomics of whole kidneys obtained mice before and after bilateral ischemia reperfusion injury. There are five timepoints (quiescent/day 0, day 1, day 6, and day 28 with n=3 per timepoint for both single-cell and spatial transcriptomics
10x visium, scRNA
Illumina NovaSeq 6000 (Mus musculus)
Mus musculus
Organ parts
Kidney-resident macrophages (KRMs)
Cheung MD, Erman EN, Moore KH, et al. Resident macrophage subpopulations occupy distinct microenvironments in the kidney. JCI Insight. 2022;7(20):e161078. Published 2022 Oct 24. doi:10.1172/jci.insight.161078
Submission date: 2022-04-04Update date: 2022-09-07
Sample number: 15Section number: 15

Cheung, Matthew D; Erman, Elise N; Moore, Kyle H; Lever, Jeremie M; Li, Zhang; LaFontaine, Jennifer R; Ghajar-Rahimi, Gelare; Liu, Shanrun; Yang, Zhengqin; Karim, Rafay; Li, Zhang; Yoder, Bradley K; Agarwal, Anupam; George, James F

GEO Series Accessions: GSE200115