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Abstract: SA-PO960

Single Nucleus Multiomic Sequencing of Human Kidney Identifies Potential Regulators of Fibrosis and Injury in CKD

Session Information

  • CKD: Pathobiology - II
    November 05, 2022 | Location: Exhibit Hall, Orange County Convention Center‚ West Building
    Abstract Time: 10:00 AM - 12:00 PM

Category: CKD (Non-Dialysis)

  • 2203 CKD (Non-Dialysis): Mechanisms

Authors

  • Ledru, Nicolas, Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Muto, Yoshiharu, 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
  • Wu, Haojia, Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Orlando, Giuseppe, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, United States
  • Waikar, Sushrut S., Boston Medical Center, Boston, Massachusetts, United States
  • Humphreys, Benjamin D., Washington University in St Louis School of Medicine, St Louis, Missouri, United States
Background

Chronic kidney disease (CKD) is a progressive and prevalent disease with disproportionate impact on BIPOC patients, representing a large source of both disease burden and disparities in health outcomes in the US. CKD is characterized by declining renal function and fibrosis. We have identified a proximal tubule subpopulation that fails to repair following acute kidney injury (AKI) and takes on pro-inflammatory and pro-fibrotic characteristics, implicating its potential role in transition to CKD. This failed repair state also increases in prevalence with both aging and disease, indicating that accumulation of this cell population may contribute to fibrosis and declining kidney repair capacity in CKD as well. Identification of regulatory elements associated with this proximal tubule state may lead to putative therapeutic targets in the treatment of CKD.

Methods

We performed single nucleus multiomic (simultaneous snRNA-seq and snATAC-seq) sequencing of eight healthy adult human kidneys in order to characterize the proximal tubule gene regulatory networks and the cis- and trans-regulatory elements underpinning the transition to the failed repair cell state. After quality control, we had 50,768 single cell transcriptomes and epigenomes. The latter identified 193,787 peaks.

Results

We applied a regularized regression analysis to generate a list of prioritized transcription factors and enhancer regions that regulate genes that change in expression along the healthy to failed repair trajectory. The findings were also integrated with CKD risk variants to provide putative mechanistic annotations. We used Cut&Run and siRNA knockdown in primary proximal tubule cell culture to validate our model’s predicted cis- and trans-regulatory elements of interest.

Conclusion

Our integrated single nucleus multiomic sequencing atlas allowed us to construct predictive parametric gene regulatory networks for genes that changed in expression along the healthy-failed repair proximal tubule trajectory. This identified several regulatory elements that, when therapeutically targeted, may allow for targeting of the failed repair population to reduce fibrotic and inflammatory signaling, while promoting repair mechanisms and return to a healthy proximal tubule state.

Funding

  • NIDDK Support