Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment

Abstract

Background: Global but predictable changes impact the DNA methylome as we age, acting as a type of molecular clock. This clock can be hastened by conditions that decrease lifespan, raising the question of whether it can also be slowed, for example, by conditions that increase lifespan. Mice are particularly appealing organisms for studies of mammalian aging; however, epigenetic clocks have thus far been formulated only in humans.

Results: We first examined whether mice and humans experience similar patterns of change in the methylome with age. We found moderate conservation of CpG sites for which methylation is altered with age, with both species showing an increase in methylome disorder during aging. Based on this analysis, we formulated an epigenetic-aging model in mice using the liver methylomes of 107 mice from 0.2 to 26.0 months old. To examine whether epigenetic aging signatures are slowed by longevity-promoting interventions, we analyzed 28 additional methylomes from mice subjected to lifespan-extending conditions, including Prop1^df/df dwarfism, calorie restriction or dietary rapamycin. We found that mice treated with these lifespan-extending interventions were significantly younger in epigenetic age than their untreated, wild-type age-matched controls.

Conclusions: This study shows that lifespan-extending conditions can slow molecular changes associated with an epigenetic clock in mice livers.

Keywords: Aging; DNA methylation; Epigenetic aging; Epigenomics.

Fig. 1

Comparison of methylation aging in mice and human livers. a Mapping from mouse CpG sites profiled by reduced representation bisulfite sequencing (RRBS) to orthologous CpG sites profiled by Illumina 450 K human methylation array. Detailed procedures can be found in “Methods.” The Venn diagram describes the age-associated sites in the orthologous–profiled space. b, c Entropy across all age-associated sites in mouse (b) and in humans (c) is plotted over age. Pearson’s correlation (r) is displayed (mouse p < 10⁻¹¹, human p < 10⁻¹¹). FDR false discovery rate

Fig. 2

Validation of an epigenetic-aging model in mice livers. a Four-fold cross validation of the age predictions (y-axis, “Epigenetic age”) versus chronological age (x-axis) in log₂ scale. Each dot represents a prediction made for a single mouse. Overall, each fold has a high Pearson’s correlation (r) between epigenetic and chronological age, and the average among all folds is depicted. b Epigenetic ages versus chronological ages for 50 wild-type mice. Different symbols/colors are used to indicate the mouse genetic background. The dashed line represents the diagonal in both plots

Fig. 3

Effects of lifespan extension on a mouse epigenetic clock. a, b The 148 CpG sites used in the mouse epigenetic-aging model (used for a mouse epigenetic clock) were subjected to principal component analysis. Principal component 1 is plotted for wild-type mice according to age and lifespan extension status, for wild-type Ames or dwarf mice (a) or wild-type UM-HET3, rapamycin-treated or calorie-restricted mice (b). c The mouse epigenetic-aging model applied to long-lived mice, with colors and shapes representing the different lifespan-enhancing conditions. The gray markers are the wild-type mice (identical to Fig. 2b), and the black line represents the linear fit of the epigenetic age versus chronological age of the wild-type mice. The green line represents the linear fit of the epigenetic age versus chronological age for long-lived mice. The gray dashed line represents the diagonal. d The residual (epigenetic age minus chronological age) is plotted for all mice according to their strain and treatment, and colors represent 2 or 22 months of age. p-values were calculated by comparing ages of long-lived mice to age-matched controls of the same genetic background using a t-test. *p < 0.05; **p < 0.01. e Hierarchical clustering of the top 20 most variable sites used by this epigenetic clock using average linkage with Euclidean distance. Treatment is depicted under the dendrogram, CpG sites are to the right of the heatmap (chromosome:start, 0-based) and rows are blocked according to clusters of sites that increase or decrease methylation with age. m Months, R Rapamycin treatment, C, CR Calorie restriction, D Ames Dwarf, W wild-type Ames or untreated, wild-type UM-HET3