Abstract: TH-OR083

DNA Methylation Changes in Human Kidney Development and Disease Revealed by Whole Genome Bisulfite Sequencing of Tissue Samples

Session Information

Category: Developmental Biology and Inherited Kidney Diseases

  • 401 Developmental Biology

Authors

  • Park, Jihwan, University of Pennsylvania, Philadelphia, Pennsylvania, United States
  • Li, Szu-Yuan, University of Pennsylvania, Philadelphia, Pennsylvania, United States
  • Seasock, Matthew J, University of Pennsylvania, Philadelphia, Pennsylvania, United States
  • Bryer, Joshua S, University of Pennsylvania, Philadelphia, Pennsylvania, United States
  • Shrestha, Rojesh, University of Pennsylvania, Philadelphia, Pennsylvania, United States
  • Susztak, Katalin, University of Pennsylvania, Philadelphia, Pennsylvania, United States
Background

Numerous epidemiologic studies have confirmed the associations between “fetal programming” and development of chronic kidney disease (CKD) and hypertension. The epigenetic system is not only heritable but also under the influence of the environment, therefore proposed to mediate the environmental “programming effect”. Cytosine methylation is important epigenetic signal, however limited data is available in kidneys of different conditions. In addition, most prior reports have examined epigenetic changes in only < 1% of about 1 billion cytosines in the genome.

Methods

Here, we generated base pair resolution methylome maps of early (11.5 weeks) and late (18.5 weeks) human fetal kidneys and microdissected tubules from healthy and CKD adult subjects (n=12). Our whole genome bisulfite sequencing (WGBS) data cover 96~98% of all CpGs with 15x mean genome coverage. Computational analysis included WGBS alignment and methylation extract followed by differential methylation analysis and PCA. Functional regions were mapped using histone modification ChIP-Seq datasets.

Results

In fetal kidneys we identified low methylated regions (LMRs) and unmethylated regions (UMRs) which are enriched in enhancers and promoters, respectively inferring their functional activity. Transcription factor motif analysis indicates enrichment for CTCF in early and SIX1 in late fetal kidneys in the LMRs. We also identified differentially methylation regions (DMRs) in adult CKD tubule samples when compared to the controls. DMR-genes were associated with immune and Notch signaling (VEGFA, TNF, STAT5A and NOTCH1). We finally compared fetal and adult kidneys, and found that (1) PC1 separates fetal from adult kidneys and (2) PC2 separates early fetal and adult fibrosis from late fetal and normal kidneys. The DMRs between the groups separated by PC2 are associated with developmental genes such as HNF1B, MTSS1, NOTCH1, PAX2 and SIX1. HNF1 binding motif is highly enriched in the DMRs and expression of HNF1B and its potential target, MTSS1, are reduced in fibrosis samples of human and mouse CKD models.

Conclusion

Our study provides a novel comprehensive epigenome map of human fetal kidneys and identified common DNA methylome changes in normal development and fibrosis, which offers new insight into injury repair processes in CKD.

Funding

  • NIDDK Support