The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells

• Type of Material: Article
• Authors: Lisa M. McEwen, University of British Columbia; Kieran J. O'Donnell, McGill University; Megan G. McGill, McGill University; Rachel D. Edgar, University of British Columbia; Meaghan J. Jones, University of British Columbia; Julia L. MacIsaac, University of British Columbia; Kerry Ressler, Emory University; Bekh Bradley-Davino, Emory University; Tanja Jovanovic, Emory University; Elisabeth Binder, Emory University
• Language: English
• Date: 2020-09-22
• Publisher: NATL ACAD SCIENCES
• Publication Version: Final Published Version
• Copyright Statement: Published under the PNAS license
• Final Published Version (URL): http://dx.doi.org/10.1073/pnas.1820843116
• Title of Journal or Parent Work: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• Volume: 117
• Issue: 38
• Start Page: 23329
• End Page: 23335
• Grant/Funding Information: L.M.M. is supported by a Frederick Banting and Charles Best Canadian Institutes of Health Research Doctoral Research Award (F15-04283). S.H. acknowledges support by NIH/National Institute on Aging (U34AG051425-01).
• Keywords: CHILDREN; development; age; epigenetic clock; Science & Technology; adolescence; Science & Technology - Other Topics; DNA methylation; Multidisciplinary Sciences
• Research Categories: Health Sciences, Human Development; Biology, Genetics

Abstract

The development of biological markers of aging has primarily focused on adult samples. Epigenetic clocks are a promising tool for measuring biological age that show impressive accuracy across most tissues and age ranges. In adults, deviations from the DNA methylation (DNAm) age prediction are correlated with several agerelated phenotypes, such as mortality and frailty. In children, however, fewer such associations have been made, possibly because DNAm changes are more dynamic in pediatric populations as compared to adults. To address this gap, we aimed to develop a highly accurate, noninvasive, biological measure of age specific to pediatric samples using buccal epithelial cell DNAm. We gathered 1,721 genome-wide DNAm profiles from 11 different cohorts of typically developing individuals aged 0 to 20 y old. Elastic net penalized regression was used to select 94 CpG sites from a training dataset (n = 1,032), with performance assessed in a separate test dataset (n = 689). DNAm at these 94 CpG sites was highly predictive of age in the test cohort (median absolute error = 0.35 y). The Pediatric-Buccal-Epigenetic (PedBE) clock was characterized in additional cohorts, showcasing the accuracy in longitudinal data, the performance in nonbuccal tissues and adult age ranges, and the association with obstetric outcomes. The PedBE tool for measuring biological age in children might help in understanding the environmental and contextual factors that shape the DNA methylome during child development, and how it, in turn, might relate to child health and disease.