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Kidney Week

Abstract: FR-OR03

Single-Cell and Spatial Transcriptomics Reveal Distinct Subpopulations of Kidney Resident Macrophages in AKI

Session Information

Category: Acute Kidney Injury

  • 103 AKI: Mechanisms

Authors

  • Cheung, Matthew David, The University of Alabama at Birmingham, Birmingham, Alabama, United States
  • Erman, Elise, The University of Alabama at Birmingham, Birmingham, Alabama, United States
  • Lever, Jeremie M., The University of Alabama at Birmingham, Birmingham, Alabama, United States
  • Agarwal, Anupam, The University of Alabama at Birmingham, Birmingham, Alabama, United States
  • George, James F., The University of Alabama at Birmingham, Birmingham, Alabama, United States
Background

Macrophages are important in renal homeostasis and the response to acute kidney injury (AKI). Kidney resident macrophages (KRMs) are a unique, self-renewing F4/80HiCD11bInt population that originate from the fetal yolk sac and fetal liver during embryogenesis. Preliminary data suggests that the KRM population consists of a number of undescribed subpopulations with distinct functions, but the transcriptional signatures and spatial organization of these subsets in the kidney tissue remain unknown. Here, we combined scRNAseq and spatial transcriptomics to identify and localize KRM subpopulations during homeostasis and injury.

Methods

Fluorescence activated cell sorting was used to isolate KRMs from C57BL/6J mice without treatment and at one and six days after bilateral ischemia-reperfusion injury (BIRI). Single-cell RNA sequencing was performed using the 10X Genomics platform. For spatial transcriptomics, kidney sections were placed on 10X Visium Spatial Gene Expression slides, imaged, and then sequenced. scRNAseq and spatial gene expression data were integrated and analyzed using the R package, Seurat 4.0.

Results

UMAP plots of integrated data from injured and control mice revealed 6 major clusters of KRMs with unique transcriptional profiles. Spatial transcriptomics revealed that these clusters reside in distinct cellular compartments within the kidney. Following IRI, these subpopulations appear in cellular compartments distinct from those occupied in the controls. Gene ontology analysis (Biologic Process) indicated that the largest subpopulations changing location expressed transcripts associated with locomotion and chemotaxis. It also indicated that the transcriptomic profiles of each subpopulation were associated with distinct functions.

Conclusion

Transcriptionally distinct subpopulations of KRMs reside within specific kidney microenvironments and change location as a function of injury. Gene expression data suggests that they are physically migrating from one compartment to another. This indicates that resident macrophages in the kidney are not static with respect to transcriptional profiles and location. Therefore, further study of the temporal and spatial characteristics and signaling pathways of these subpopulations in the context of homeostasis and injury is warranted.

Funding

  • NIDDK Support