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Human aging DNA methylation signatures are conserved but accelerated in cultured fibroblasts

Version 2 2019-06-12, 10:27
Version 1 2019-06-03, 10:02
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posted on 2019-06-12, 10:27 authored by Gabriel Sturm, Andres Cardenas, Marie-Abèle Bind, Steve Horvath, Shuang Wang, Yunzhang Wang, Sara Hägg, Michio Hirano, Martin Picard

Aging is associated with progressive and site-specific changes in DNA methylation (DNAm). These global changes are captured by DNAm clocks that accurately predict chronological age in humans but relatively little is known about how clocks perform in vitro. Here we culture primary human fibroblasts across the cellular lifespan (~6 months) and use four different DNAm clocks to show that age-related DNAm signatures are conserved and accelerated in vitro. The Skin & Blood clock shows the best linear correlation with chronological time (r = 0.90), including during replicative senescence. Although similar in nature, the rate of epigenetic aging is approximately 62x times faster in cultured cells than in the human body. Consistent with in vivo data, cells aged under hyperglycemic conditions exhibit an approximately three years elevation in baseline DNAm age. Moreover, candidate gene-based analyses further corroborate the conserved but accelerated biological aging process in cultured fibroblasts. Fibroblasts mirror the established DNAm topology of the age-related ELOVL2 gene in human blood and the rapid hypermethylation of its promoter cg16867657, which correlates with a linear decrease in ELOVL2 mRNA levels across the lifespan. Using generalized additive modeling on twelve timepoints across the lifespan, we also show how single CpGs exhibit loci-specific, linear and nonlinear trajectories that reach rates up to −47% (hypomethylation) to +23% (hypermethylation) per month. Together, these high-temporal resolution global, gene-specific, and single CpG data highlight the conserved and accelerated nature of epigenetic aging in cultured fibroblasts, which may constitute a system to evaluate age-modifying interventions across the lifespan.

Funding

This work was supported by the National Institute of Child Health and Human Development [HD32062];National Institute of Mental Health [MH113011];National Institute of Neurological Disorders and Stroke [NS078059];National Institute on Aging (US) [AG060908];Swedish Research Council [825-2007-7460, 825-2009-6141, 521-2013-8689, 2015-03255, 2015-06796];U.S. National Library of Medicine (US) [LM013061];National Institute on Aging (US) [AG04563, AG10175, AG028555];Forskningsrådet om Hälsa, Arbetsliv och Välfärd (SE) 97:0147:1B, 2009-0795, 2013-2292];NIH Office of the Director (US) [DP5OD021412];National Institute of Mental Health (US) [MH119336];National Institute of General Medical Sciences (US) [GM119793];National Cancer Institute (US) [CA226672]

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