Individual CpG sites that are associated with age and life expectancy become hypomethylated upon aging

Abstract

Background: There is a growing interest in simple molecular biomarkers for biological aging. Age-associated DNA methylation (DNAm) changes at specific CG dinucleotides can be combined into epigenetic age predictors to estimate chronological age-and the deviation of chronological and predicted age (∆_age) seems to be associated with all-cause mortality. In this study, we have further validated this association and analyzed whether or not individual age-associated CG-dinucleotides (CpGs) are related to life expectancy.

Findings: In the German ESTHER cohort, we used 864 DNAm profiles of blood samples as the discovery set and 1000 DNAm profiles as the validation set to predict chronological age with three previously reported age predictors-based on 99, 71, or 353 age-associated CpGs. Several of these individual CpGs were significantly associated with life expectancy, and for some of these CpGs, this was even reproducible in the independent datasets. Notably, those CpGs that revealed significant association with life expectancy were overall rather hypomethylated upon aging.

Conclusion: Individual age-associated CpGs may provide biomarkers for all-cause mortality-but confounding factors need to be critically taken into consideration, and alternative methods, which facilitate more quantitative measurements at individual CpGs, might be advantageous. Our data suggest that particularly specific CpGs that become hypomethylated upon aging are indicative of biological aging.

Keywords: Aging; DNA methylation; Epigenetic; Life expectancy; Mortality; Predictor.

Fig. 1

Correlation of predicted age with chronological age. Epigenetic age predictions based on the 99 CpGs of the Weidner predictor [17] were plotted against chronological age for a 864 DNAm profiles of the discovery set and b 1000 DNAm profiles of the validation set of the ESTHER cohort. The distribution of chronological age and predicted age with the three aging models described by Weidner et al. [17], Hannum et al. [16], and Horvath [15] is demonstrated c for the discovery set and d for the validation set. Age predictions by the Hannum predictor were overall overestimated by 5.5 and 6.5 years, respectively

Fig. 2

CpGs that correlate with all-cause mortality are hypomethylated upon aging. a For all individual CpGs of the three age predictors (Weidner et al., 99 CpGs; Hannum et al., 71 CpGs; and Horvath, 353 CpGs), the association of ∆_age with all-cause mortality was estimated. The P values in the discovery and validation sets of the ESTHER cohort demonstrate moderate reproducibility between the two independent datasets. b, c Subsequently, we analyzed the Spearman correlation of these CpGs with chronological age. CpGs with significant association with all-cause mortality were overall hypomethylated upon aging (in the discovery set (b) and in the validation set (c)). The lines indicate a FDR significance level of 0.05