Uncovering genetic mechanisms of kidney aging through transcriptomics, genomics, and epigenomics

Kidney Int. 2019 Mar;95(3):624-635. doi: 10.1016/j.kint.2018.10.029.


Nephrons scar and involute during aging, increasing the risk of chronic kidney disease. Little is known, however, about genetic mechanisms of kidney aging. We sought to define the signatures of age on the renal transcriptome using 563 human kidneys. The initial discovery analysis of 260 kidney transcriptomes from the TRANScriptome of renaL humAn TissuE Study (TRANSLATE) and the Cancer Genome Atlas identified 37 age-associated genes. For 19 of those genes, the association with age was replicated in 303 kidney transcriptomes from the Nephroseq resource. Surveying 42 nonrenal tissues from the Genotype-Tissue Expression project revealed that, for approximately a fifth of the replicated genes, the association with age was kidney-specific. Seventy-three percent of the replicated genes were associated with functional or histological parameters of age-related decline in kidney health, including glomerular filtration rate, glomerulosclerosis, interstitial fibrosis, tubular atrophy, and arterial narrowing. Common genetic variants in four of the age-related genes, namely LYG1, PPP1R3C, LTF and TSPYL5, correlated with the trajectory of age-related changes in their renal expression. Integrative analysis of genomic, epigenomic, and transcriptomic information revealed that the observed age-related decline in renal TSPYL5 expression was determined both genetically and epigenetically. Thus, this study revealed robust molecular signatures of the aging kidney and new regulatory mechanisms of age-related change in the kidney transcriptome.

Keywords: aging; epigenome; genetics; kidney; transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Aging / genetics*
  • Aging / pathology
  • Computational Biology
  • DNA Methylation / genetics
  • Epigenomics
  • Female
  • Gene Expression Profiling
  • Genetic Variation
  • Glomerular Filtration Rate / physiology
  • Humans
  • Intracellular Signaling Peptides and Proteins / genetics
  • Lactoferrin / genetics
  • Male
  • Middle Aged
  • Muramidase / genetics
  • Nephrons / pathology*
  • Nephrons / physiopathology
  • Nuclear Proteins / genetics
  • RNA-Seq
  • Renal Insufficiency, Chronic / genetics*
  • Renal Insufficiency, Chronic / pathology
  • Renal Insufficiency, Chronic / physiopathology
  • Transcriptome / genetics*


  • Intracellular Signaling Peptides and Proteins
  • LTF protein, human
  • Nuclear Proteins
  • PPP1R3C protein, human
  • TSPYL5 protein, human
  • Muramidase
  • Lactoferrin