DNA Methylation Clocks in Aging: Categories, Causes, and Consequences

Abstract

Age-associated changes to the mammalian DNA methylome are well documented and thought to promote diseases of aging, such as cancer. Recent studies have identified collections of individual methylation sites whose aggregate methylation status measures chronological age, referred to as the DNA methylation clock. DNA methylation may also have value as a biomarker of healthy versus unhealthy aging and disease risk; in other words, a biological clock. Here we consider the relationship between the chronological and biological clocks, their underlying mechanisms, potential consequences, and their utility as biomarkers and as targets for intervention to promote healthy aging and longevity.

Keywords: DNA methylation; aging; biological age; chronological age; clock; epigenetics.

Figure 1. The DNA Methylation Clock: How It Works

(A) The trajectory of change with age of methylation of eight CpGs, four with negative coefficients (left) and four with positive coefficients (right), colored by the rate of change with age. Darker colors indicate faster rates of change and, thus, stronger weights (numerically larger coefficients) in the epigenetic clock. (B) Eight clock CpGs (columns) in three individuals of different chronological ages (rows) whose methylation values at each CpG are indicated by shading of the filled circle (fractional methylation, 0.0–1.0). The box color represents the coefficient of change over age (slope of line, top). In each colored box, the numerical product of the methylation value and the associated coefficient are shown. Summing across all boxes together with the intercept learned during clock building results in an epigenetic age that approximates chronological age.

Figure 2. Distribution of Mouse Clock CpGs across the Genome

The mouse clock CpGs described by Petkovich et al. (2017), Stubbs et al. (20 7), and Wang etal. (2017) were assigned to the indicated genome features. Some CpGs map to more than one feature. Hence, the sum of percentages for any one mouse clock is greater than 100.

Figure 3. Chronological versus Biological Age and Their Assessment by Methylation Clocks

(A) Two people, blue and red, born at the same time, will always share the same chronological age (gray arrow timeline measured in years). However, because of genetic, epigenetic, and environmental factors and lifestyle choices, they may progress through the functional decline that characterizes biological aging at different rates. Shown here, red ages biologically more quickly than blue, likely associated with earlier onset of lethal disease. As illustrated, in early life, red and blue are assumed to have the same biological age. (B) By definition, a perfect chronological clock deft), whether based on DNA methylation or any other molecular parameter, measures time elapsed since birth. Therefore, it cannot distinguish between individuals that biologically age fast (red) or slow (blue). In contrast, a biological clock (center) can distinguish between unhealthy (red) versus healthy (green) aging but is a less accurate chronological clock. A hybrid clock (right) tracks closely with chronological age, but deviation from the position of the 45° perfect chronological clock is a reflection of biological age. However, the hybrid clock is likely a less accurate predictor of age and disease than a bona fide biological clock. The human clocks calibrated against chronological age are likely hybrid clocks (Hannum et al., 2013; Horvath, 2013; Weidner et al., 2014). The colors of the filled circles indicate the donor, red or blue, from (A).

Figure 4. Chromostasis, a Presumptive Process that Prevents Age-Associated Epigenetic and Phenotypic Change, Promotes Healthy Aging and Longevity

Healthy aging and longevity depend upon maintenance of cell phenotype. Because chromatin, in part, determines cell phenotype, this preservation of phenotype depends on a level of chromatin stability. Because chromatin is a dynamic structure, this, in turn, depends on chromatin homeostasis (chromostasis). Presumptive, but largely unknown, mechanisms of chromostasis may retard the ticking of DNAmethylation and epigenetic clocks and, perhaps, be a target for interventions to promote healthy aging and longevity.

Figure 5. Some Outstanding Questions

(A) In the mouse liver, hypomethylation of enhancers is linked to chronological age and contributes to the clock, but the rate of hypomethylation is decreased by interventions thought to slow biological aging (calorie restriction (CR), rapamycin (rapa), and Ames dwarfism [not shown]), suggesting that enhancers are a hybrid chronological and biological clock (but potentially separable) (Cole et al„ 2017; Wang et al., 2017). (B-F) Many questions remain, although the answers to these questions likely differ for different clock CpGs (e.g., at enhancers versus promoters). (B) To date, methylation clocks have been generated from data obtained from populations of cells, is there cell-to-cell variation in ticking of the clock? (C) Does enhancer hypomethylation result from downregulation of DNMTs or their methyl donor substrate (SAM), increased TET demethylase activity, increased TET cofactor α-KG, increased passive demethylation, or another mechanism? (D) At enhancers, does hypomethylation affect gene expression, expression of cryptic transcripts that are normally silenced by DNA methylation, enhancer-gene interactions, or all or none of these? (E) Can a biological clock, probably tissue-specific, predict disease with sufficient sensitivity and specificity to be clinically useful? (F) How do pro-longevity interventions slow ticking of the clock, and does this contribute to their pro-longevity and/or pro-health aging benefits?