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Epigenetics. 2019 Jun 12:1-16. doi: 10.1080/15592294.2019.1626651. [Epub ahead of print]

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

Author information

1
a Department of Psychiatry, Division of Behavioral Medicine , Columbia University Irving Medical Center , New York , NY , USA.
2
b Division of Environmental Health Sciences , University of California, Berkeley, School of Public Health , Berkeley , CA , USA.
3
c Department of Statistics , Harvard University , Cambridge , MA , USA.
4
d Human Genetics, David Geffen School of Medicine , University of California Los Angeles , Los Angeles , CA , USA.
5
e Department of Biostatistics , Mailman School of Public Health, Columbia University Medical Center , New York , NY , USA.
6
f Department of Medical Epidemiology and Biostatistics , Karolinska Institutet , Stockholm , Sweden.
7
g Department of Neurology , H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center , New York , NY , USA.
8
h Columbia Aging Center , Columbia University Mailman School of Public Health , New York , NY , USA.

Abstract

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.

KEYWORDS:

Aging; DNA methylation; accelerated aging; epigenetic age; lifespan; primary culture

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