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Kidney Week

Abstract: FR-PO133

Single Cell Chromatin Accessibility Atlas During Murine Kidney Injury and Repair

Session Information

  • AKI: Mechanisms - II
    November 04, 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

  • Muto, Yoshiharu, Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Dixon, Eryn E., Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Wu, Haojia, Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Ledru, Nicolas, Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Wilson, Parker C., Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Kirita, Yuhei, Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Humphreys, Benjamin D., Washington University in St Louis School of Medicine, St Louis, Missouri, United States
Background

Recent single cell and single nucleus RNA-seq (snRNA-seq) studies revealed cell-specific molecular alterations in acute ischemic injury (AKI). We previously identified a failed-repair proximal tubular cell (FR-PTC) state with a persistent inflammatory signature after ischemic renal injury (IRI). However, the underlying epigenetic mechanisms driving the failed repair cell state is undefined.

Methods

We performed single nucleus ATAC-seq (snATAC-seq) on mouse kidneys after IRI: 4 hours, 12 hours, 2 days, 14 days, 6 weeks and sham (n = 3 for each) using the 10x Genomics platform. We integrated snATAC-seq data with the snRNA-seq data obtained from the same IRI mouse kidney samples, and a comprehensive bioinformatic analysis was performed on the dataset.

Results

We obtained 136,469 single-nucleus chromatin accessibility libraries with 193,731 peaks. We performed label transfer from snRNA-seq data to snATAC-seq using Seurat, and all major cell types (11 clusters) were identified. The proximal tubular cell (PT) cluster was further subclustered into 8 subtypes including FR-PTC, which showed specific promoter accessibilities on inflammatory molecules including Tnf, Ccl2 and Vcam1. Transcription factor motif enrichment analysis on accessible regions identified acute activation (4 hours after IRI) of NRF2 and AP1 in injured PT cells, although the most severely injured cells failed to activate NRF2, suggesting a potential therapeutic target. NF-kB transcription factors were activated specifically in FR-PTC to induce chronic inflammatory signatures. The most specifically accessible regions with NF-kB binding motifs in FR-PTC include potential distal enhancers for Ltbp2 and Edn1 that were up-regulated in FR-PTC. We constructed FR-PTC-specific cis-regulatory accessibility network to predict the cis interactions that shape these FR-PTC-specific gene expression signatures.

Conclusion

The first comprehensive snATAC-seq atlas of mouse IRI kidneys catalogued phase-specific and cell-specific activation of regulatory genomic regions and transcription factors that shape cell-specific responses to ischemic injury. Epigenetic mechanisms driving FR-PTC revealed in this study implicate potential novel therapeutic targets in AKI and its transition to chronic kidney disease.

Funding

  • NIDDK Support