Individual Longitudinal Changes in DNA-methylome Identify Signatures of Early-life Adversity and Correlate with Later Outcome

Authors

Annabel K. Short, University of California, Irvine
Ryan Weber, University of California, Irvine
Noriko Kamei, University of California, Irvine
Christina Wilcox Thai, University of California, Irvine
Hina Arora, University of California, Irvine
Ali Mortazavi, University of California, Irvine
Hal S. Stern, University of California, Irvine
Laura M. Glynn, Chapman UniversityFollow
Tallie Z. Baram, University of California, Irvine

Document Type

Article

Publication Date

5-31-2024

Abstract

Adverse early-life experiences (ELA) affect a majority of the world's children. Whereas the enduring impact of ELA on cognitive and emotional health is established, there are no tools to predict vulnerability to ELA consequences in an individual child. Epigenetic markers including peripheral-cell DNA-methylation profiles may encode ELA and provide predictive outcome markers, yet the interindividual variance of the human genome and rapid changes in DNA methylation in childhood pose significant challenges. Hoping to mitigate these challenges we examined the relation of several ELA dimensions to DNA methylation changes and outcome using a within-subject longitudinal design and a high methylation-change threshold.

DNA methylation was analyzed in buccal swab/saliva samples collected twice (neonatally and at 12 months) in 110 infants. We identified CpGs differentially methylated across time for each child and determined whether they associated with ELA indicators and executive function at age 5. We assessed sex differences and derived a sex-dependent ‘impact score’ based on sites that most contributed to methylation changes.

Changes in methylation between two samples of an individual child reflected age-related trends and correlated with executive function years later. Among tested ELA dimensions and life factors including income to needs ratios, maternal sensitivity, body mass index and infant sex, unpredictability of parental and household signals was the strongest predictor of executive function. In girls, high early-life unpredictability interacted with methylation changes to presage executive function. Thus, longitudinal, within-subject changes in methylation profiles may provide a signature of ELA and a potential predictive marker of individual outcome.

Comments

This article was originally published in Neurobiology of Stress, volume 31, in 2024. https://doi.org/10.1016/j.ynstr.2024.100652

Recommended Citation

Short, A. K., Weber, R., Kamei, N., Thai, C. W., Arora, H., Mortazavi, A., Stern, H. S., Glynn, L., & Baram, T. Z. (2024). Individual longitudinal changes in DNA-methylome identify signatures of early-life adversity and correlate with later outcome. Neurobiology of Stress, 31, 100652. https://doi.org/10.1016/j.ynstr.2024.100652

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The authors

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