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Kidney Week

Abstract: TH-PO140

Lineage Tracing and Single Cell Multiomics Reveal Long-Term Effects of Adaptive and Maladaptive Repair After AKI

Session Information

  • AKI: Mechanisms - I
    November 03, 2022 | Location: Exhibit Hall, Orange County Convention Center‚ West Building
    Abstract Time: 10:00 AM - 12:00 PM

Category: Acute Kidney Injury

  • 103 AKI: Mechanisms

Authors

  • Gerhardt, Louisa Maria Sophie, Keck School of Medicine of the University of Southern California, Los Angeles, California, United States
  • Koppitch, Kari A., Keck School of Medicine of the University of Southern California, Los Angeles, California, United States
  • Cho, Sam, Keck School of Medicine of the University of Southern California, Los Angeles, California, United States
  • McMahon, Andrew P., Keck School of Medicine of the University of Southern California, Los Angeles, California, United States

Group or Team Name

  • McMahon Lab, USC Stem Cell
Background

Acute kidney injury (AKI) triggers a proliferative response as part of the intrinsic repair program that can result in adaptive or maladaptive repair of proximal tubule cells (PTCs). Maladaptive PTCs contribute to disease progression from AKI to chronic kidney disease (CKD), but the cellular and molecular understanding underlying the adaptive and maladaptive repair trajectories is limited.

Methods

We used genetic fate-mapping to label and trace proliferating (Ki67+) cells after ischemia-reperfusion injury. Combined snRNA- and ATAC-seq of lineage-traced cells isolated by FACS at 4 weeks and 6 months after AKI and controls was performed to generate a final dataset of 83,315 high-quality nuclei (after quality control and doublet removal). Published snRNA-seq data was used to assess transcriptomic changes early after AKI.

Results

Labeling Ki67+ cells early after AKI revealed a broad proliferative response in kidney epithelial and non-epithelial cells, which was preceded by cell type-specific and global gene expression changes, such as downregulation of genes involved in transmembrane transport processes and upregulation of immediate early response genes. A heterogeneous population of maladaptive PTCs derived from all proximal tubule segments persisted until 6 months after AKI, although decreasing in abundance in time post AKI. Combined profiling of gene expression and chromatin accessibility in the same cell showed a specific activation of the transcription factors Rbpj, Klf6, Runx1 and Creb5 as well as of members of the NF-kB and the AP-1 family in maladaptive PTCs, accompanied by corresponding changes in target gene expression. Regulatory factors of adaptively repaired PTCs, such as Maf and Hnf4a, were downregulated in maladaptive PTCs. Comparison of adaptively repaired PTCs with control PTCs suggested long-term effects of AKI on the transcriptional state of PTCs, including reduced expression of genes encoding critical transmembrane transport proteins.

Conclusion

This study provides the first combined snRNA- and snATAC-seq atlas of healthy and injured kidney tissue, defines the regulatory landscape of PTCs after adaptive and maladaptive repair and reveals long-term effects of AKI on PTCs even following adaptive repair.

Funding

  • NIDDK Support