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Abstract: PO2226

Integrated Analysis of the DNA Methylome, Transcriptome, and Proteome in Human Glomerular and Tubulointerstitial Compartments

Session Information

Category: Pathology and Lab Medicine

  • 1601 Pathology and Lab Medicine: Basic

Authors

  • Parikh, Samir V., The Ohio State University Wexner Medical Center, Columbus, Ohio, United States
  • Collins, Kimberly S., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Melo ferreira, Ricardo, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Cheng, Yinghua, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Barwinska, Daria, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Ferkowicz, Michael J., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Dunn, Ken, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Kelly, Katherine J., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Sutton, Timothy A., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Shapiro, John P., 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
  • Dagher, Pierre C., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • El-Achkar, Tarek M., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Eadon, Michael T., Indiana University School of Medicine, Indianapolis, Indiana, United States
Background

The interplay between the human DNA methylome, transcriptome, and proteome in the kidney glomerulus and tubulointerstitium is incompletely understood. Promoter sequence methylation is often thought to contribute to gene and protein expression regulation. We hypothesized that promoter sequence methylation would explain differential protein expression between the glomerulus and tubulointerstitium.

Methods

Nine reference nephrectomies underwent laser microdissection of the glomeruli and tubulointerstitium. DNA methylation sequencing, RNA sequencing, and mass spectrometry quantification of peptides was completed for both compartments in the samples. Datasets were dimensionally reduced to match expressed proteins (N = 4600). Regions of hypermethylation in promoter sequences, introns, and exons were assessed and compared to corresponding protein and mRNA expression.

Results

At least three patterns of hypermethylation were observed across the methylome: promoter sequence, intronic, and exonic methylation. In many cases, promoter sequence or exonic methylation of the tubulointerstitium correlated with a higher glomerular to tubulointerstitial protein and mRNA expression ratio. Likewise, increased tubulointerstitial protein or mRNA expression was associated with glomerular hypermethylation of promoter or exonic regions. For example, Uromodulin (UMOD) protein and mRNA expression were higher in the tubulointerstitium than the glomerulus. The strongest regions of uromodulin hypermethylation were observed in exons 9 and 10 of the glomerular compartment, although hypermethylation was also observed in the promoter sequence and two intronic regions of the tubulointerstitium. In contrast, regions of hypermethylation of Apolipoprotein L1 (APOL1) were exclusively confined to the tubulointerstitium, distributed in all three patterns.

Conclusion

Promoter sequence methylation alone does not explain differential expression patterns between the glomerular and tubulointerstitial compartments. Hypermethylation of exonic regions also contributes to expression regulation.

Funding

  • NIDDK Support