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Kidney Week

Abstract: SA-PO956

The Cell-Type and Region-Specific Chromatin Landscape of the Kidney

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

  • Gisch, Debora L., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Lake, Blue, University of California San Diego, La Jolla, California, United States
  • Basta, Jeannine M., Washington University in St Louis, St Louis, Missouri, United States
  • Robbins, Lynn, Washington University in St Louis, St Louis, Missouri, United States
  • Pherson, Michelle, Saint Louis University, Saint Louis, Missouri, United States
  • Barwinska, Daria, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Parikh, Samir V., The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
  • Rovin, Brad H., The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
  • Cheng, Ying-Hua, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Zhang, Kun, University of California San Diego, La Jolla, California, United States
  • El-Achkar, Tarek M., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Mollah, Shamim, Washington University in St Louis, St Louis, Missouri, United States
  • Dagher, Pierre C., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Jain, Sanjay, Washington University in St Louis, St Louis, Missouri, United States
  • Rauchman, Michael I., Washington University in St Louis, St Louis, Missouri, United States
  • Eadon, Michael T., Indiana University School of Medicine, Indianapolis, Indiana, United States

Group or Team Name

  • KPMP
Background

Activation or repression of gene transcription is regulated by changes in the chromatin landscape, including post-translational modifications of histones and DNA methylation. In an integrated multi-omic approach, we characterized the regulation of reference transcript expression for the podocyte, proximal tubule (PT), and thick ascending loop of Henle (TAL) cells.

Methods

Using human nephrectomy and biopsy tissue, we developed quality (QC) standards for whole genome bisulfite sequencing (WGBS, N=30) of dissected glomeruli (GLOM) and tubulointerstitium (TI), Cleavage Under Targets & Release Using Nuclease (CUT&RUN) in bulk (N=12) with H3K27ac and H3K27me3 antibodies and single cell Multiome (combined snRNAseq and scATACseq, N=12) to comprehensively define epigenomic features of accessible chromatin regions in the kidney. Peak alignment in genomic regions (promoter, exon, CpG island, etc) was determined by Fisher’s exact test. In identical specimens, proteomic, transcriptomic, and KPMP/HubMAP snRNAseq atlas (>200,000 nuclei) phenotypes were compared.

Results

QC measures for batch correction, controls, and reproducibility are optimized for human kidney. We describe the methylome for 22,156,845 CpGs. After genomic feature modeling (promoter, etc), WGBS inversely correlated with mRNA (R=0.61) and protein (R=0.55). Peaks of WGBS, CUT&RUN, and the Multiome were aligned for cell-specific expressed genes, comparing podocytes to GLOM, and TAL/PT to TI or Bulk. Glom/TI WGBS valleys aligned with scATACseq peaks (p<9x10-11). CUT&RUN H3K27ac peaks aligned with TI WGBS valleys (p<0.03). CUT&RUN H3K27ac and scATAC-seq peaks coincided in TAL and PT (both p<0.001). A tensor factorization network analysis identified consistent regulation of ESRRG, a gene associated with TAL injury in a snRNAseq atlas, showing consistent WGBS, H3K27ac, H3kme3, and scATACseq regulation in its promoter and introns 1 and 3.

Conclusion

These studies integrate histone modification and DNA methylation, which contribute to chromatin accessibility in the kidney. This epigenomic reference atlas is a first step to assess downstream expression changes in multiple kidney cell types and will be valuable to characterize CKD GWAS variants that map to distal enhancers.

Funding

  • NIDDK Support