Date Published: April 17, 2018
Publisher: Impact Journals
Author(s): Morgan E. Levine, Ake T. Lu, Austin Quach, Brian H. Chen, Themistocles L. Assimes, Stefania Bandinelli, Lifang Hou, Andrea A. Baccarelli, James D. Stewart, Yun Li, Eric A. Whitsel, James G Wilson, Alex P Reiner, Abraham Aviv, Kurt Lohman, Yongmei Liu, Luigi Ferrucci, Steve Horvath.
Identifying reliable biomarkers of aging is a major goal in geroscience. While the first generation of epigenetic biomarkers of aging were developed using chronological age as a surrogate for biological age, we hypothesized that incorporation of composite clinical measures of phenotypic age that capture differences in lifespan and healthspan may identify novel CpGs and facilitate the development of a more powerful epigenetic biomarker of aging. Using an innovative two-step process, we develop a new epigenetic biomarker of aging, DNAm PhenoAge, that strongly outperforms previous measures in regards to predictions for a variety of aging outcomes, including all-cause mortality, cancers, healthspan, physical functioning, and Alzheimer’s disease. While this biomarker was developed using data from whole blood, it correlates strongly with age in every tissue and cell tested. Based on an in-depth transcriptional analysis in sorted cells, we find that increased epigenetic, relative to chronological age, is associated with increased activation of pro-inflammatory and interferon pathways, and decreased activation of transcriptional/translational machinery, DNA damage response, and mitochondrial signatures. Overall, this single epigenetic biomarker of aging is able to capture risks for an array of diverse outcomes across multiple tissues and cells, and provide insight into important pathways in aging.
One of the major goals of geroscience research is to define ‘biomarkers of aging’ [1,2], which can be thought of as individual-level measures of aging that capture inter-individual differences in the timing of disease onset, functional decline, and death over the life course. While chronological age is arguably the strongest risk factor for aging-related death and disease, it is important to distinguish chronological time from biological aging. Individuals of the same chronological age may exhibit greatly different susceptibilities to age-related diseases and death, which is likely reflective of differences in their underlying biological aging processes. Such biomarkers of aging will be crucial to enable evaluation of interventions aimed at promoting healthier aging, by providing a measurable outcome, which unlike incidence of death and/or disease, does not require extremely long follow-up observation.
Using a novel two-step method, we were successful in developing a DNAm based biomarker of aging that is highly predictive of nearly every morbidity and mortality outcome we tested. Training an epigenetic predictor of phenotypic age instead of chronological age led to substantial improvement in mortality/healthspan predictions over the first generation of DNAm based biomarkers of chronological age from Hannum , Horvath  and other published DNAm biomarkers. In doing so, this is the first study to conclusively demonstrate that DNAm biomarkers of aging are highly predictive of cardiovascular disease and coronary heart disease. DNAm PhenoAge also tracks chronological age and relates to disease risk in samples other than whole blood. Finally, we find that an individual’s DNAm PhenoAge, relative to his/her chronological age, is moderately heritable and is associated with activation of pro-inflammatory, interferon, DNAm damage repair, transcriptional/translational signaling, and various markers of immunosenescenc: a decline of naïve T cells and shortened leukocyte telomere length (Supplementary Information).
Using the NHANES training data, we applied a Cox penalized regression model—where the hazard of aging-related mortality (mortality from diseases of the heart, malignant neoplasms, chronic lower respiratory disease, cerebrovascular disease, Alzheimer’s disease, Diabetes mellitus, nephritis, nephrotic syndrome, and nephrosis) was regressed on forty-two clinical markers and chronological age to select variables for inclusion in our phenotypic age score. Ten-fold cross-validation was employed to select the parameter value, lambda, for the penalized regression. In order to develop a sparse parsimonious age estimator (fewer biomarker variables preferred to produce robust results) we selected a lambda of 0.0192, which represented a one standard deviation increase over the lambda with minimum mean-squared error during cross-validation (Supplement 1: Fig. S13). Of the forty-two biomarkers included in the penalized Cox regression model, this resulted in ten variables (including chronological age) that were selected for the phenotypic age predictor.