DunedinPACE, a DNA methylation biomarker of the pace of aging

Abstract

Background: Measures to quantify changes in the pace of biological aging in response to intervention are needed to evaluate geroprotective interventions for humans. Previously, we showed that quantification of the pace of biological aging from a DNA-methylation blood test was possible (Belsky et al., 2020). Here, we report a next-generation DNA-methylation biomarker of Pace of Aging, DunedinPACE (for Pace of Aging Calculated from the Epigenome).

Methods: We used data from the Dunedin Study 1972-1973 birth cohort tracking within-individual decline in 19 indicators of organ-system integrity across four time points spanning two decades to model Pace of Aging. We distilled this two-decade Pace of Aging into a single-time-point DNA-methylation blood-test using elastic-net regression and a DNA-methylation dataset restricted to exclude probes with low test-retest reliability. We evaluated the resulting measure, named DunedinPACE, in five additional datasets.

Results: DunedinPACE showed high test-retest reliability, was associated with morbidity, disability, and mortality, and indicated faster aging in young adults with childhood adversity. DunedinPACE effect-sizes were similar to GrimAge Clock effect-sizes. In analysis of incident morbidity, disability, and mortality, DunedinPACE and added incremental prediction beyond GrimAge.

Conclusions: DunedinPACE is a novel blood biomarker of the pace of aging for gerontology and geroscience.

Funding: This research was supported by US-National Institute on Aging grants AG032282, AG061378, AG066887, and UK Medical Research Council grant MR/P005918/1.

Keywords: DNA methylation; aging; biological aging; biomarker; epidemiology; epigenetic; epigenetics; genetics; genomics; gerontology; geroscience; global health; healthspan; methylation.

Figure 1.. DunedinPACE correlation with 20-year Pace of Aging and association with decline in physical and cognitive functions and subjective signs of aging.

Panel A shows the association of DunedinPACE with the 20-year Pace of Aging in the Dunedin Study cohort (r = 0.78). Panel B shows effect-sizes for associations of DunedinPACE with measures of physical and cognitive functioning and subjective signs of aging in Dunedin Study members at age 45 years. Colors indicate groupings of measures (physical functions in shades of orange, cognitive functions in shades of yellow, subjective signs of aging in shades of green). Stars next to labels for Physical Limitations and Facial Aging indicate that these meaures were reverse-coded for this analysis. Panel C shows binned scatterplots of associations of DunedinPACE with declines in physical and cognitive function and subjective signs of aging. Plotted points show average values for ‘bins’ of approximately 20 Study members. Regression slopes are estimated from the raw, un-binned data. In Panel C, y-axis scales are denominated in units of standard deviations computed from the baseline measurement for all outcomes except self-rated health, for which the y-axis shows probability of incident fair/poor self-rated health. Changes were calculated over the interval between age-38 and age-45 assessments for all measures except cognition, for which change was calculated over the interval between the age-13 and age-45 assessments. DunedinPACE and DunedinPoAm were developed from analysis of Pace of Aging in the Dunedin cohort; effect-sizes for these measures may be over-estimated.

Figure 1—figure supplement 1.. Correlations among the 12-year and 20-year Pace of Aging measures and the DunedinPoAm and DunedinPACE DNA methylation measures.

Figure 1—figure supplement 2.. Effect-sizes for associations of DunedinPACE and the 20-year Pace of Aging with measures of physical and cognitive functioning and subjective signs of aging measured when Dunedin Study participants were aged 45 years.

The * indicates measures reverse-coded for analysis.

Figure 1—figure supplement 3.. Effect-sizes for associations of DunedinPACE, DunedinPoAm, and the DNA methylation clocks proposed by Horvath, 2013, Hannum et al., 2013, Levine et al., 2018 (PhenoAge), and Lu et al., 2019 (GrimAge) with measures of physical and cognitive functioning and subjective signs of aging measured when Dunedin Study participants were aged 45 years.

The * indicates measures reverse-coded for analysis. DunedinPACE and DunedinPoAm were developed from analysis of Pace of Aging in the Dunedin cohort; effect-sizes for these measures may be over-estimated.

Figure 1—figure supplement 4.. Effect-sizes for associations of aging measures with measures of change in physical functioning and subjective signs of aging over ages 38–45 years and with cognitive functioning from adolescent baseline to age-45 follow-up.

The * indicates measures reverse-coded for analysis. DunedinPACE and DunedinPoAm were developed from analysis of Pace of Aging in the Dunedin cohort; effect-sizes for these measures may be over-estimated.

Figure 2.. Test-retest reliability of DunedinPACE.

The figure graphs DunedinPACE values for replicate Illumnina450k datasets for n = 36 individuals in the dataset published by Lehne and colleagues (Lehne et al., 2015) (GEO Accession GSE55763). The ICC for DunedinPACE in the Lehne dataset is 0.96 95% CI [0.92–0.98].

Figure 2—figure supplement 1.. Reliability of DunedinPACE, DunedinPoAm, and DNA methylation clocks.

The figure plots intraclass correlation coefficients (ICCs) estimated from replicate DNA methylation datasets for DunedinPACE, original DunedinPoAm, and the DNA methylation clocks proposed by Horvath, Hannum et al., Levine et al. (PhenoAge), and Lu et al. (GrimAge). Error bars show 95% confidence intervals. Data are graphed from three datasets, 36 Illumina 450 k technical replicates from GSE55763 (Lehne et al., 2015), and 28 Illumina EPIC array technical replicates and 350 Illumina 450k-EPIC replicates from Sugden et al., 2020. The Sugden et al. EPIC technical replicate dataset (Sugden A) included arrays analyzed as part of the Dunedin Study dataset. The Sugden et al. 450k-EPIC dataset (Sugden B) was used to identify probes for inclusion in the machine learning analysis from which DunedinPACE was derived.

Figure 3.. Associations of DunedinPACE with chronological age, epigenetic clocks, Physiology-based measures of biological age, and self-rated health in Understanding Society.

Panel A shows a scatterplot and fitted slopes illustrating the association between chronological age (x-axis) and DunedinPACE (y-axis) in women and men in the Understanding Society sample. Data for women are plotted with yellow dots (orange slope) and for men with blue crosses (navy slope). The figure illustrates a positive association between chronological age and DunedinPACE (Pearson r = 0.32). Panel B shows a matrix of correlations and association plots among DunedinPACE and age-acceleration residuals of Horvath, Hannum, Levine-PhenoAge and Lu-GrimAge epigenetic clocks. The diagonal cells of the matrix list the DNA methylation measures. The half of the matrix below the diagonal shows scatter plots of associations. For each scatter-plot cell, the y-axis corresponds to the variable named along the matrix diagonal to the right of the plot and the x-axis corresponds to the variable named along the matrix diagonal above the plot. The half of the matrix above the diagonal lists Pearson correlations between the DNA methylation measures. For each correlation cell, the value reflects the correlation of the variables named along the matrix diagonal to the left of the cell and below the cell. Panel C graphs scatterplots of associations of DunedinPACE with three physiology-based measures of biological age (KDM Biological Age Advancement, r = 0.30 [0.24–0.36]; Phenotypic Age Advancement, r = 0.32 95% CI [0.26–0.38]; and Homeostatic Dysregulation r = 0.09 [0.03–0.16]) and a plot of DunedinPACE means and 95% confidence intervals by self-rated health category (r = 0.20 [0.15–0.26]).

Figure 3—figure supplement 1.. Effect-sizes for associations of DunedinPACE, DunedinPoAm, and DNA methylation clocks with physiology-based measures of biological age and self-rated health.

Figure shows effect-sizes estimated from the Understanding Society data (n=1,175). Effect-sizes are reported as standardized regression coefficients interpretable as Pearson r values. Error bars show 95% confidence intervals. DNA methylation clocks were residualized for chronological age prior to analysis. Models included covariates for chronological age and sex. Physiology-based measures of biological age were computed from Understanding Society biomarker data (albumin, alkaline phosphatase, creatinine, C-reactive protein, blood urea nitrogen, glycated hemoglobin, systolic blood pressure, and forced expiratory volume in 1second) based on algorithms derived in data from the US NHANES according to the methods developed by Levine et al., 2018, (Klemera and Doubal, 2006), and (Cohen et al., 2013).

Figure 4.. Association of DunedinPACE with mortality.

Panel A shows mortality in the Normative Aging Study (NAS). Panel B shows mortality in the Framingham Heart Study Offspring Cohort. The figure plots Kaplan-Meier curves for three groups of participants in each of the two cohorts: those with DunedinPACE 1 SD or more below the mean (‘slow’ DunedinPACE, blue line); those with DunedinPACE within 1 SD of the mean (‘average’ DunedinPACE, purple line); and those with DunedinPACE 1 SD or more above the mean (‘fast’ DunedinPACE, red line). Censoring of participants prior to death is indicated with a gold hash marks. The table below the figure details the number of participants at risk per 3-year interval and, in parentheses, the number who died during the interval.

Figure 4—figure supplement 1.. Effect-sizes for analysis of mortality in the Normative Aging Study and the Framingham Heart Study Offspring cohort.

Effect-sizes are reported as hazard ratios (HR) per standard deviation increment of the aging measures estimated from Cox proportional hazard regression. All models included covariates for chronological age and sex.

Figure 4—figure supplement 2.. Effect-sizes for analysis of incident and prevalent chronic disease morbidity in the Normative Aging Study.

Effect-sizes are reported as relative risks (RR) per standard deviation increment of the aging measures estimated from Poisson regression. All models included covariates for chronological age and sex.

Figure 4—figure supplement 3.. Effect-sizes for analysis of time-to-diagnosis with cardiovascular disease (CVD) and time to stroke or transient ischemic attack (TIA) in the Framingham Heart Study Offspring Cohort.

Effect-sizes are reported as hazard ratios (HR) per standard deviation increment of the aging measures estimated from Cox proportional hazard regression. All models included covariates for chronological age and sex.

Figure 4—figure supplement 4.. Effect-sizes for analysis of incident disability from repeated-measures of limitations to activities of daily living (ADLs).

For all panels, error bars show 95% confidence intervals. DNA methylation clocks were residualized for chronological age prior to analysis. All models included covariates for chronological age and sex.

Figure 5.. DunedinPACE levels by strata of childhood socioeconomic status (SES) and victimization in the E-Risk Study.

Panel A (left side) plots means and 95% CIs for DunedinPACE measured at age 18 among E-Risk participants who grew up low, middle, and high socioeconomic status households. Panel B (right side) plots means and 95% CIs for DunedinPACE measured at age 18 among E-Risk participants who experienced 0, 1, 2, or 3 or more types of victimization through age 12 years.

Figure 5—figure supplement 1.. Effect-sizes for associations of childhood socioeconomic conditions and childhood victimization history with DunedinPACE, DunedinPoAm, and DNA methylation clocks at age 18.

Panel A plots effect-sizes for low socioeconomic status (SES) in childhood (vs. high SES in childhood). Panel B plots effect-sizes for childhood polyvictimization (vs. no childhood victimization). Effect-sizes are reported as Cohen’s d. For both panels, error bars show 95% confidence intervals. DNA methylation clocks were residualized for chronological age prior to analysis. All models included sex as a covariate. (All E-Risk participants are the same chronological age; no age covariate is needed.).