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Short AK, Weber R, Kamei N, Wilcox Thai C, Arora H, Mortazavi A, Stern HS, Glynn L, Baram TZ. Individual longitudinal changes in DNA-methylome identify signatures of early-life adversity and correlate with later outcome. Neurobiol Stress 2024; 31:100652. [PMID: 38962694 PMCID: PMC11219970 DOI: 10.1016/j.ynstr.2024.100652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/02/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
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.
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Affiliation(s)
- Annabel K. Short
- Department of Anatomy and Neurobiology, ersity of California- Irvine, Irvine, CA, 92697, USA
- Departments of Pediatrics and Neurology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Ryan Weber
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Noriko Kamei
- Department of Anatomy and Neurobiology, ersity of California- Irvine, Irvine, CA, 92697, USA
| | - Christina Wilcox Thai
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Hina Arora
- Department of Statistics, University of California-Irvine, Irvine, CA, 92697, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Hal S. Stern
- Department of Statistics, University of California-Irvine, Irvine, CA, 92697, USA
| | - Laura Glynn
- Department of Psychology, Chapman University, Orange, CA, 92866, USA
| | - Tallie Z. Baram
- Department of Anatomy and Neurobiology, ersity of California- Irvine, Irvine, CA, 92697, USA
- Departments of Pediatrics and Neurology, University of California-Irvine, Irvine, CA, 92697, USA
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Short AK, Weber R, Kamei N, Thai CW, Arora H, Mortazavi A, Stern HS, Glynn L, Baram TZ. Within-subject changes in methylome profile identify individual signatures of early-life adversity, with a potential to predict neuropsychiatric outcome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.16.571594. [PMID: 38187766 PMCID: PMC10769190 DOI: 10.1101/2023.12.16.571594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Background Adverse early-life experiences (ELA), including poverty, trauma and neglect, affect a majority of the world's children. Whereas the impact of ELA on cognitive and emotional health throughout the lifespan is well-established, it is not clear how distinct types of ELA influence child development, and there are no tools to predict for an individual child their vulnerability or resilience to the consequences of ELAs. Epigenetic markers including DNA-methylation profiles of peripheral cells may encode ELA and provide a predictive outcome marker. However, the rapid dynamic changes in DNA methylation in childhood and the inter-individual variance of the human genome pose barriers to identifying profiles predicting outcomes of ELA exposure. Here, we examined the relation of several dimensions of ELA to changes of DNA methylation, using a longitudinal within-subject design and a high threshold for methylation changes in the hope of mitigating the above challenges. Methods We analyzed DNA methylation in buccal swab samples collected twice for each of 110 infants: neonatally and at 12 months. We identified CpGs differentially methylated across time, calculated methylation changes for each child, and determined whether several indicators of ELA associated with changes of DNA methylation for individual infants. We then correlated select dimensions of ELA with methylation changes as well as with measures of executive function at age 5 years. We examined for sex differences, and derived a sex-dependent 'impact score' based on sites that most contributed to the methylation changes. Findings Setting a high threshold for methylation changes, we discovered that changes in methylation between two samples of an individual child reflected age-related trends towards augmented methylation, and also correlated with executive function years later. Among the tested factors and ELA dimensions, including income to needs ratios, maternal sensitivity, body mass index and sex, unpredictability of parental and household signals was the strongest predictor of executive function. In girls, an interaction was observed between a measure of high early-life unpredictability and methylation changes, in presaging executive function. Interpretation These findings establish longitudinal, within-subject changes in methylation profiles as a signature of some types of ELA in an individual child. Notably, such changes are detectable beyond the age-associated DNA methylation dynamics. Future studies are required to determine if the methylation profile changes identified here provide a predictive marker of vulnerabilities to poorer cognitive and emotional outcomes.
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Affiliation(s)
- Annabel K. Short
- Department of Anatomy and Neurobiology, University of California- Irvine, Irvine, CA 92697
- Departments of Pediatrics and Neurology, University of California-Irvine, Irvine, CA, 92697
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia, 6009 (current)
- Division of Paediatrics/Centre for Child Health Research, Medical School, University of Western Australia, Crawley, WA, Australia, 6009 (current)
| | - Ryan Weber
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA 92697
| | - Noriko Kamei
- Department of Anatomy and Neurobiology, University of California- Irvine, Irvine, CA 92697
| | - Christina Wilcox Thai
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA 92697
| | - Hina Arora
- Department of Statistics, University of California-Irvine, Irvine, CA, 92697
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA 92697
| | - Hal S. Stern
- Department of Statistics, University of California-Irvine, Irvine, CA, 92697
| | - Laura Glynn
- Department of Psychology, Chapman University, Orange, CA, 92866
| | - Tallie Z. Baram
- Department of Anatomy and Neurobiology, University of California- Irvine, Irvine, CA 92697
- Departments of Pediatrics and Neurology, University of California-Irvine, Irvine, CA, 92697
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