Epigenetic clock and DNA methylation analysis of porcine models of aging and obesity

Kyle M. Schachtschneider, Lawrence B. Schook, Jennifer J. Meudt, Dhanansayan Shanmuganayagam, Joseph A. Zoller, Amin Haghani, Caesar Z. Li, Joshua Zhang, Andrew Yang, Ken Raj, Steve Horvath*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

11 Citations (Scopus)


DNA-methylation profiles have been used successfully to develop highly accurate biomarkers of age, epigenetic clocks, for many species. Using a custom methylation array, we generated DNA methylation data from n = 238 porcine tissues including blood, bladder, frontal cortex, kidney, liver, and lung, from domestic pigs (Sus scrofa domesticus) and minipigs (Wisconsin Miniature Swine (TM)). Samples used in this study originated from Large White X Landrace crossbred pigs, Large White X Minnesota minipig crossbred pigs, and Wisconsin Miniature Swine (TM). We present 4 epigenetic clocks for pigs that are distinguished by their compatibility with tissue type (pan-tissue and blood clock) and species (pig and human). Two dual-species human-pig pan-tissue clocks accurately measure chronological age and relative age, respectively. We also characterized CpGs that differ between minipigs and domestic pigs. Strikingly, several genes implicated by our epigenetic studies of minipig status overlap with genes (ADCY3, TFAP2B, SKOR1, and GPR61) implicated by genetic studies of body mass index in humans. In addition, CpGs with different levels of methylation between the two pig breeds were identified proximal to genes involved in blood LDL levels and cholesterol synthesis, of particular interest given the minipig's increased susceptibility to cardiovascular disease compared to domestic pigs. Thus, breed-specific differences of domestic and minipigs may potentially help to identify biological mechanisms underlying weight gain and aging-associated diseases. Our porcine clocks are expected to be useful for elucidating the role of epigenetics in aging and obesity, and the testing of anti-aging interventions.

Original languageEnglish
Pages (from-to)2467-2483
Number of pages17
Issue number5
Publication statusPublished - Oct 2021

Bibliographical note

Funding Information:
This work was supported by the Paul G. Allen Frontiers Group (SH).

Publisher Copyright:
© 2021, The Author(s).


  • Aging
  • DNA methylation
  • Development
  • Epigenetic clock
  • Minipigs
  • Pig
  • Porcine


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