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Abstract: FR-PO574

Epigenetic Age Is Accelerated in ADPKD Kidneys and Is Regulated by Autophagy-Mediated DNA Methyltransferase

Session Information

Category: Genetic Diseases of the Kidneys

  • 1201 Genetic Diseases of the Kidneys: Cystic

Authors

  • Li, Lu, Mayo Clinic Department of Internal Medicine, Rochester, Minnesota, United States
  • Li, Xiaoyan, Mayo Clinic Department of Internal Medicine, Rochester, Minnesota, United States
  • Harris, Peter C., Mayo Clinic Department of Internal Medicine, Rochester, Minnesota, United States
  • Calvet, James P., University of Kansas Medical Center Department of Biochemistry and Molecular Biology, Kansas City, Kansas, United States
  • Li, Xiaogang, Mayo Clinic Department of Internal Medicine, Rochester, Minnesota, United States
Background

The epigenetic clock (DNA methylation age) is characterized by changes in DNA methylation (DNAm) levels across specific CpG sites that are associated with chronological age, diseases and mortality. Epigenetic age acceleration (EAA), the residual variation in DNAm age, indicates whether individuals and specific organs are aging faster or slower than their chronological age in response to endogenous and exogenous factors. Whether epigenetic age is regulated by autophagy and accelerated in ADPKD kidneys remains unknown.

Methods

To investigate an association between epigenetic clock/EAA and autophagy in ADPKD, we performed single cell RNA sequencing (scRNA-seq), whole-genome bisulfite sequencing (WGBS), Western blot and qRT-PCR analysis.

Results

We found that 353 human and 329 mouse CpG dinucleotide DNA methylation markers correspond to 309 human genes and 224 mouse genes. Our scRNA-seq analysis indicated that the numbers of dysregulated epigenetic clock associated genes were 48, 33 and 70 in collecting duct cells; 8, 14 and 44 in macrophages; and 2, 14 and 57 in fibroblasts in day 7, 14 and 21 Pkd1 homozygous kidneys compared to the same cell types in age matched Pkd1 heterozygous kidneys. The differential methylation status of these epigenetic genes and the specific methylation sites on these genes were identified in ADPKD kidneys compared to normal individuals as examined by WGBS. The dysregulation of epigenetic clock genes is associated with a gradual upregulation of DNA methyltransferase1 (DNMT1), the only DNMT responsible for maintaining DNA methylation, in day 7, 14 and 21 Pkd1 homozygous kidneys. DNMT1 interacted with ATG7, a key player of autophagy. Treatment with the autophagy inhibitor, Lys05, increased DNMT1 protein, whereas treatment with autophagy inducer decreased DNMT1 protein in kidneys, supporting that autophagy is involved in DNMT1 mediated epigenetic age acceleration in ADPKD. We also found that the methylation status of four epigenetic clock genes, including Apoe, Cldn4, Mgp and Slc38a2, are potential biomarkers that indicate epigenetic age acceleration in ADPKD kidneys.

Conclusion

Autophagy is a key player of DNMT1 mediated epigenetic age and cyst growth in ADPKD kidneys. Targeting DNMT1 and inducing autophagy should have a synergistic effect on decreasing cyst growth and epigenetic age acceleration.