1
|
Martz CD, Benner AD, Goosby BJ, Mitchell C, Gaydosh L. Structural racism in primary schools and changes in epigenetic age acceleration among Black and White youth. Soc Sci Med 2024; 347:116724. [PMID: 38458127 PMCID: PMC11134904 DOI: 10.1016/j.socscimed.2024.116724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/14/2023] [Accepted: 02/23/2024] [Indexed: 03/10/2024]
Abstract
Structural racism generates racial inequities in U.S. primary education, including segregated schools, inequitable funding and resources, racial disparities in discipline and achievement, and hostile racial climates, which are risk factors for adverse youth health and development. Black youth are disproportionately exposed to adverse school contexts that may become biologically embedded via stress-mediated epigenetic pathways. This study examined whether childhood exposure to adverse school contexts is associated with changes in epigenetic aging during adolescent development. DNA methylation-based epigenetic clocks were calculated from saliva samples at ages 9 and 15 among Black (n = 774) and White (n = 287) youth in the Future of Families and Child Wellbeing Study (2009-2015). We performed latent class analyses to identify race-specific primary school contexts using administrative data on segregation, discipline, achievement, resources, economic disadvantage, and racial harassment. We then estimated change in epigenetic age acceleration from childhood to adolescence across school typologies using GrimAge, PhenoAge, and DunedinPACE epigenetic clocks. Three distinct school contexts were identified for Black youth: segregated and highly-disadvantaged (17.0%), segregated and moderately-disadvantaged (52.1%), and integrated and moderately-disadvantaged (30.8%). Two school contexts emerged for White youth: integrated and unequal (46.5%) and predominantly White & advantaged (53.5%). At age 15, Black youth who attended segregated and highly-disadvantaged primary schools experienced increases in their speed of epigenetic aging with GrimAge and DunedinPACE. Slowed epigenetic aging with GrimAge was observed for Black youth who attended integrated and moderately-disadvantaged schools. School contexts were not associated with changes in epigenetic age acceleration for White youth. Our findings suggest that manifestations of structural racism in primary school contexts are associated with early-life epigenetic age acceleration and may forecast future health inequities.
Collapse
Affiliation(s)
- Connor D Martz
- Population Research Center, The University of Texas at Austin, United States.
| | - Aprile D Benner
- Population Research Center, The University of Texas at Austin, United States; Department of Human Development and Family Sciences, The University of Texas at Austin, United States
| | - Bridget J Goosby
- Population Research Center, The University of Texas at Austin, United States; Department of Sociology, The University of Texas at Austin, United States
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, United States
| | - Lauren Gaydosh
- Population Research Center, The University of Texas at Austin, United States; Department of Sociology, The University of Texas at Austin, United States
| |
Collapse
|
2
|
Aikins M, Willems Y, Mitchell C, Goosby B, Raffington L. Linked emergence of racial disparities in mental health and epigenetic biological aging across childhood and adolescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586786. [PMID: 38586008 PMCID: PMC10996608 DOI: 10.1101/2024.03.26.586786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Marginalization due to structural racism may confer an increased risk for aging-related diseases - in part - via effects on people's mental health. Here we leverage a prospective birth cohort study to examine whether the emergence of racial disparities in mental health and DNA-methylation measures of biological aging (i.e., DunedinPACE, GrimAge Acceleration, PhenoAge Acceleration) are linked across childhood and adolescence. We further consider to what extent racial disparities are statistically accounted for by perinatal and postnatal factors in preregistered analyses of N=4,898 participants from the Future of Families & Child Wellbeing Study, of which N=2,039 had repeated saliva DNA methylation at ages 9 and 15 years. We find that racially marginalized children had higher levels of externalizing and internalizing behaviors and diverging longitudinal internalizing slopes. Black compared to White identifying children, children living in more racially segregated neighborhoods, and racially marginalized children more affected by colorism tended to have higher age-9 levels of biological aging and more biological age acceleration over adolescence. Notably, longitudinal increases in internalizing and externalizing behavior were correlated with longitudinal increases in biological aging. While racial and ethnic disparities in mental health were largely statistically accounted for by socioeconomic variables, racial differences in biological aging were often still visible beyond covariate controls. Our findings indicate that racial disparities in mental health and biological aging are linked and emerge early in life. Programs promoting racial health equity must address the psychological and physical impacts of structural racism in children. Comprehensive measures of racism are lacking in current population cohorts.
Collapse
Affiliation(s)
- Muna Aikins
- Max Planck Research Group Biosocial – Biology, Social Disparities, and Development; Max Planck Institute for Human Development; Berlin, Germany
| | - Yayouk Willems
- Max Planck Research Group Biosocial – Biology, Social Disparities, and Development; Max Planck Institute for Human Development; Berlin, Germany
| | - Colter Mitchell
- Survey Research Center of the Institute for Social Research; University of Michigan, Ann Arbor, MI, USA
- Population Studies Center of the Institute for Social Research; University of Michigan, Ann Arbor, MI, USA
| | - Bridget Goosby
- Population Research Center; University of Texas at Austin, Austin, TX, USA
| | - Laurel Raffington
- Max Planck Research Group Biosocial – Biology, Social Disparities, and Development; Max Planck Institute for Human Development; Berlin, Germany
| |
Collapse
|
3
|
Raffington L. Utilizing epigenetics to study the shared nature of development and biological aging across the lifespan. NPJ SCIENCE OF LEARNING 2024; 9:24. [PMID: 38509146 PMCID: PMC10954727 DOI: 10.1038/s41539-024-00239-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
Recently, biological aging has been quantified in DNA-methylation samples of older adults and applied as so-called "methylation profile scores" (MPSs) in separate target samples, including samples of children. This nascent research indicates that (1) biological aging can be quantified early in the life course, decades before the onset of aging-related disease, (2) is affected by common environmental predictors of childhood development, and (3) shows overlap with "developmental processes" (e.g., puberty). Because the MPSs were computed using algorithms developed in adults, these studies indicate a molecular link between childhood environments, development, and adult biological aging. Yet, if MPSs can be used to connect development and aging, previous research has only traveled one way, deriving MPSs developed in adults and applying them to samples of children. Researchers have not yet quantified epigenetic measures that reflect the pace of child development, and tested whether resulting MPSs are associated with physical and psychological aging. In this perspective I posit that combining measures of biological aging with new quantifications of child development has the power to address fundamental questions about life span: How are development and experience in childhood related to biological aging in adulthood? And what is aging?
Collapse
Affiliation(s)
- Laurel Raffington
- Max Planck Research Group Biosocial-Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany.
| |
Collapse
|
4
|
Labaut L, Lage-Castellanos A, Rodrigo MJ, Herrero-Roldán S, Mitchell C, Fisher J, León I. Mother adversity and co-residence time impact mother-child similarity in genome-wide and gene-specific methylation profiles. Clin Epigenetics 2024; 16:44. [PMID: 38509601 PMCID: PMC10953278 DOI: 10.1186/s13148-024-01655-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND The effects of adverse life events on physical and psychological health, with DNA methylation (DNAm) as a critical underlying mechanism, have been extensively studied. However, the epigenetic resemblance between mother and child in the context of neglectful caregiving, and whether it may be shaped by the emotional impact of maternal stressful events and the duration of co-residence (indexed by child age), remains unknown. The present study examined mother-child similarity in methylation profiles, considering the potential effect of mother adversity, mother empathy, neglect-control group, child age (an index of years of mother-child co-residence), and mother age. Using Illumina Epic arrays, we quantified DNAm in 115 mother-child saliva samples. We obtained a methylation similarity index by computing correlation coefficients between methylation profiles within dyads, for the entire epigenome, and five specific genes related to stress and empathy: NR3C1, FKPB5, OXTR, SCL6A4, and BDNF. RESULTS The methylation profiles of the mother-child familial pairs significantly correlated as compared to mother-child random pairs for the entire epigenome and NR3C1, FKBP5, OXTR and BDNF genes. Next, multiple linear regression models observed associations of mother adversity, child age, and neglect-control group on mother-child methylation similarity, only significant in mother-child familial pairs, after correcting for multiple comparisons. Higher mother adversity was associated with lower mother-child methylation similarity for the epigenome-wide analysis, for the BDNF gene, and in the neglect-control group for the OXTR gene. In turn, being an older child (longer co-residence) was associated with higher mother-child methylation similarity. CONCLUSIONS Mother adversity and co-residence time are modulating factors in the intergenerational methylation process that offer a window into development-dependent adaptations that can be affected by both hereditary and environmental factors, significantly observed only in biological dyads. A twofold implication for child well-being emerges, one is positive in that children of mothers exposed to life adversity or neglect did not necessarily inherit their methylation patterns. The other is concerning due to the influence of time spent living together, which affects similarity with the mother and potentially increases the risk of inheriting an epigenetic profile associated with future dysfunctional parenting patterns. This underscores the importance of the 'the earlier, the better' recommendation by the Child Protection System, which is not always followed.
Collapse
Affiliation(s)
- Lucía Labaut
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain
| | - Agustín Lage-Castellanos
- Department of NeuroInformatics, Cuban Center for Neuroscience, Havana, Cuba
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - María José Rodrigo
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Silvia Herrero-Roldán
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain
- Facultad de Ciencias Sociales Aplicadas y de la Comunicación, UNIE Universidad, Madrid, Spain
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, Ann Abor, MI, USA
| | - Jonah Fisher
- Institute for Social Research, University of Michigan, Ann Abor, MI, USA
| | - Inmaculada León
- Instituto Universitario de Neurociencia, Campus de Guajara, Universidad de La Laguna, 38201, La Laguna, Tenerife, Spain.
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.
| |
Collapse
|
5
|
Ramsteijn AS, Ndiaye M, Kalashikam RR, Htet MK, Yadav Dm D, Augustine LF, Zahra NL, Djigal A, Yanti D, Angelin TC, Nurfadilah M, Gorre M, Subrahamanyam D, Vadakattu SS, Munikumar M, Horgan GW, Fahmida U, Faye B, Kulkarni B, Haggarty P. Epigenetic studies in children at risk of stunting and their parents in India, Indonesia and Senegal: a UKRI GCRF Action Against Stunting Hub protocol paper. BMJ Paediatr Open 2024; 8:e001770. [PMID: 38417921 PMCID: PMC10900567 DOI: 10.1136/bmjpo-2022-001770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/21/2023] [Indexed: 03/01/2024] Open
Abstract
INTRODUCTION In 2020, an estimated 150 million children under the age of 5 years were stunted. Stunting results from early-life adversity and it is associated with significant physical and cognitive deficit, lifelong socioeconomic disadvantage and reduced life expectancy. There is a need to understand the causes of stunting and its effects in order to develop strategies to avoid it and to mitigate the consequences once stunting has occurred. Epigenetics is an important mechanism through which early-life factors are thought to influence biological function, with long-term consequences. We describe a series of epigenetic studies designed to understand how early-life adversity results in stunting and to inform the development of practical tools such as predictive markers and therapeutic targets. This work is part of the UKRI GCRF Action Against Stunting Hub. METHODS AND ANALYSIS The project-in India, Indonesia and Senegal-comprises an observational study of mothers, fathers, and offspring (n=500) spanning the first 1000 days of life, and an intervention study in each country. Epigenetic status (DNA methylation) is determined in saliva from babies collected within 1 month of birth and again at 18 months of age, and from mothers and fathers around the time of birth. Epigenome-wide analysis is carried out using the Illumina EPIC array, augmented by high-definition sequencing approaches. Statistical analysis is carried out at the level of candidate genes/regions, higher dimensional epigenetic states and epigenome-wide association. Data analysis focuses on the determinants of stunting, the effectiveness of interventions, population comparisons and the link between epigenetics and other thematic areas, which include anthropometry, microbiome, gut health, parasitology, cognition, nutrition, food hygiene and water sanitation, food systems and the home environment. ETHICS AND DISSEMINATION This study has been approved by the relevant Ethics Committees in Indonesia, India and Senegal, and the UK. Research data will be published and posted in public repositories.
Collapse
Affiliation(s)
| | - Magatte Ndiaye
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | | | - Min Kyaw Htet
- South East Asian Ministers of Education Organization Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | | | | | - Nur L Zahra
- South East Asian Ministers of Education Organization Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | - Aicha Djigal
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | - Dwi Yanti
- South East Asian Ministers of Education Organization Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | - Tiffany C Angelin
- South East Asian Ministers of Education Organization Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | - Mifa Nurfadilah
- South East Asian Ministers of Education Organization Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | - Manjula Gorre
- ICMR-National Institute of Nutrition, Hyderabad, India
| | | | | | | | | | - Umi Fahmida
- South East Asian Ministers of Education Organization Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | - Babacar Faye
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Senegal
| | | | - Paul Haggarty
- Rowett Institute, University of Aberdeen, Aberdeen, UK
| |
Collapse
|
6
|
Willems YE, deSteiguer A, Tanksley PT, Vinnik L, Fraemke D, Okbay A, Richter D, Wagner GG, Hertwig R, Koellinger P, Tucker-Drob EM, Harden KP, Raffington L. Self-control is associated with health-relevant disparities in buccal DNA-methylation measures of biological aging in older adults. Clin Epigenetics 2024; 16:22. [PMID: 38331797 PMCID: PMC10854186 DOI: 10.1186/s13148-024-01637-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
Self-control is a personality dimension that is associated with better physical health and a longer lifespan. Here, we examined (1) whether self-control is associated with buccal and saliva DNA-methylation (DNAm) measures of biological aging quantified in children, adolescents, and adults, and (2) whether biological aging measured in buccal DNAm is associated with self-reported health. Following preregistered analyses, we computed two DNAm measures of advanced biological age (principal-component PhenoAge and GrimAge Acceleration) and a DNAm measure of pace of aging (DunedinPACE) in buccal samples from the German Socioeconomic Panel Study (SOEP-G[ene], n = 1058, age range 0-72, Mage = 42.65) and saliva samples from the Texas Twin Project (TTP, n = 1327, age range 8-20, Mage = 13.50). We found that lower self-control was associated with advanced biological age in older adults (PhenoAge Acceleration β = - .34, [- .51, - .17], p < .001; GrimAge Acceleration β = - .34, [- .49, - .19], p < .001), but not young adults, adolescents or children. These associations remained statistically robust even after correcting for possible confounders such as socioeconomic contexts, BMI, or genetic correlates of low self-control. Moreover, a faster pace of aging and advanced biological age measured in buccal DNAm were associated with self-reported disease (PhenoAge Acceleration: β = .13 [.06, .19], p < .001; GrimAge Acceleration: β = .19 [.12, .26], p < .001; DunedinPACE: β = .09 [.02, .17], p = .01). However, effect sizes were weaker than observations in blood, suggesting that customization of DNAm aging measures to buccal and saliva tissues may be necessary. Our findings are consistent with the hypothesis that self-control is associated with health via pathways that accelerate biological aging in older adults.
Collapse
Affiliation(s)
- Y E Willems
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany
| | - A deSteiguer
- Population Research Center, The University of Texas, Austin, USA
| | - P T Tanksley
- Population Research Center, The University of Texas, Austin, USA
| | - L Vinnik
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany
| | - D Fraemke
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany
| | - A Okbay
- School of Business and Economics, Economics Fellow, Tinbergen Institute, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - D Richter
- SHARE Berlin Institute GmbH, Berlin, Germany
- Department of Education and Psychology, Freie Universität Berlin, Berlin, Germany
| | - G G Wagner
- Max Planck Institute for Human Development, Berlin, Germany
- German Socio Economic Panel Study (SOEP), Berlin, Germany
| | - R Hertwig
- Max Planck Institute for Human Development, Berlin, Germany
| | - P Koellinger
- School of Business and Economics, Economics Fellow, Tinbergen Institute, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - E M Tucker-Drob
- Population Research Center, The University of Texas, Austin, USA
| | - K P Harden
- Population Research Center, The University of Texas, Austin, USA
| | - Laurel Raffington
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Lentzeallee 94, 14195, Berlin, Germany.
| |
Collapse
|
7
|
Bakulski KM, Blostein F, London SJ. Linking Prenatal Environmental Exposures to Lifetime Health with Epigenome-Wide Association Studies: State-of-the-Science Review and Future Recommendations. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:126001. [PMID: 38048101 PMCID: PMC10695268 DOI: 10.1289/ehp12956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND The prenatal environment influences lifetime health; epigenetic mechanisms likely predominate. In 2016, the first international consortium paper on cigarette smoking during pregnancy and offspring DNA methylation identified extensive, reproducible exposure signals. This finding raised expectations for epigenome-wide association studies (EWAS) of other exposures. OBJECTIVE We review the current state-of-the-science for DNA methylation associations across prenatal exposures in humans and provide future recommendations. METHODS We reviewed 134 prenatal environmental EWAS of DNA methylation in newborns, focusing on 51 epidemiological studies with meta-analysis or replication testing. Exposures spanned cigarette smoking, alcohol consumption, air pollution, dietary factors, psychosocial stress, metals, other chemicals, and other exogenous factors. Of the reproducible DNA methylation signatures, we examined implementation as exposure biomarkers. RESULTS Only 19 (14%) of these prenatal EWAS were conducted in cohorts of 1,000 or more individuals, reflecting the still early stage of the field. To date, the largest perinatal EWAS sample size was 6,685 participants. For comparison, the most recent genome-wide association study for birth weight included more than 300,000 individuals. Replication, at some level, was successful with exposures to cigarette smoking, folate, dietary glycemic index, particulate matter with aerodynamic diameter < 10 μ m and < 2.5 μ m , nitrogen dioxide, mercury, cadmium, arsenic, electronic waste, PFAS, and DDT. Reproducible effects of a more limited set of prenatal exposures (smoking, folate) enabled robust methylation biomarker creation. DISCUSSION Current evidence demonstrates the scientific premise for reproducible DNA methylation exposure signatures. Better powered EWAS could identify signatures across many exposures and enable comprehensive biomarker development. Whether methylation biomarkers of exposures themselves cause health effects remains unclear. We expect that larger EWAS with enhanced coverage of epigenome and exposome, along with improved single-cell technologies and evolving methods for integrative multi-omics analyses and causal inference, will expand mechanistic understanding of causal links between environmental exposures, the epigenome, and health outcomes throughout the life course. https://doi.org/10.1289/EHP12956.
Collapse
Affiliation(s)
| | - Freida Blostein
- University of Michigan, Ann Arbor, Michigan, USA
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Stephanie J. London
- National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| |
Collapse
|
8
|
Reiner A, Bakulski KM, Fisher JD, Dou JF, Schneper L, Mitchell C, Notterman DA, Zawistowski M, Ware EB. Sex-specific DNA methylation in saliva from the multi-ethnic Future of Families and Child Wellbeing Study. Epigenetics 2023; 18:2222244. [PMID: 37300819 PMCID: PMC10259311 DOI: 10.1080/15592294.2023.2222244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/11/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
The prevalence and severity of many diseases differs by sex, potentially due to sex-specific patterns in DNA methylation. Autosomal sex-specific differences in DNA methylation have been observed in cord blood and placental tissue but are not well studied in saliva or in diverse populations. We sought to characterize sex-specific DNA methylation on autosomal chromosomes in saliva samples from children in the Future of Families and Child Wellbeing Study, a multi-ethnic prospective birth cohort containing an oversampling of Black, Hispanic and low-income families. DNA methylation from saliva samples was analysed on 796 children (50.6% male) at both ages 9 and 15 with DNA methylation measured using the Illumina HumanMethylation 450k array. An epigenome-wide association analysis of the age 9 samples identified 8,430 sex-differentiated autosomal DNA methylation sites (P < 2.4 × 10-7), of which 76.2% had higher DNA methylation in female children. The strongest sex-difference was in the cg26921482 probe, in the AMDHD2 gene, with 30.6% higher DNA methylation in female compared to male children (P < 1 × 10-300). Treating the age 15 samples as an internal replication set, we observed highly consistent results between the ages 9 and 15 measurements, indicating stable and replicable sex-differentiation. Further, we directly compared our results to previously published DNA methylation sex differences in both cord blood and saliva and again found strong consistency. Our findings support widespread and robust sex-differential DNA methylation across age, human tissues, and populations. These findings help inform our understanding of potential biological processes contributing to sex differences in human physiology and disease.
Collapse
Affiliation(s)
- Allison Reiner
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonah D Fisher
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Colter Mitchell
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel A Notterman
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Erin B Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
9
|
deSteiguer AJ, Raffington L, Sabhlok A, Tanksley P, Tucker-Drob EM, Harden KP. Stability of DNA-Methylation Profiles of Biological Aging in Children and Adolescents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564766. [PMID: 37961459 PMCID: PMC10635005 DOI: 10.1101/2023.10.30.564766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background and Objectives Methylation profile scores (MPSs) index biological aging and aging-related disease in adults and are cross-sectionally associated with social determinants of health in childhood. MPSs thus provide an opportunity to trace how aging-related biology responds to environmental changes in early life. Information regarding the stability of MPSs in early life is currently lacking. Method We use longitudinal data from children and adolescents ages 8-18 (N = 428, M age = 12.15 years) from the Texas Twin Project. Participants contributed two waves of salivary DNA-methylation data (mean lag = 3.94 years), which were used to construct four MPSs reflecting multi-system physiological decline and mortality risk (PhenoAgeAccel and GrimAgeAccel), pace of biological aging (DunedinPACE), and cognitive function (Epigenetic-g). Furthermore, we exploit variation among participants in whether they were exposed to the COVID-19 pandemic during the course of study participation, in order to test how a historical period characterized by environmental disruption might affect children's aging-related MPSs. Results All MPSs showed moderate longitudinal stability (test-retest rs = 0.42, 0.44, 0.46, 0.51 for PhenoAgeAccel, GrimAgeAccel, and Epigenetic-g, and DunedinPACE, respectively). No differences in the stability of MPSs were apparent between those whose second assessment took place after the onset of the COVID-19 pandemic vs. those for whom both assessments took place prior to the pandemic. Conclusions Aging-related DNA-methylation patterns are less stable in childhood than has been previously observed in adulthood. Further developmental research on the methylome is necessary to understand which environmental perturbations in childhood impact trajectories of biological aging and when children are most sensitive to those impacts.
Collapse
Affiliation(s)
- Abby J. deSteiguer
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
| | - Laurel Raffington
- Max Planck Research Group Biosocial – Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin, Germany
| | - Aditi Sabhlok
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
| | - Peter Tanksley
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
| | - Elliot M. Tucker-Drob
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
| | - K. Paige Harden
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
10
|
Raffington L, Schneper L, Mallard T, Fisher J, Vinnik L, Hollis-Hansen K, Notterman DA, Tucker-Drob EM, Mitchell C, Harden KP. Salivary Epigenetic Measures of Body Mass Index and Social Determinants of Health Across Childhood and Adolescence. JAMA Pediatr 2023; 177:1047-1054. [PMID: 37669030 PMCID: PMC10481322 DOI: 10.1001/jamapediatrics.2023.3017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/07/2023] [Indexed: 09/06/2023]
Abstract
Importance Children who are socioeconomically disadvantaged are at increased risk for high body mass index (BMI) and multiple diseases in adulthood. The developmental origins of health and disease hypothesis proposes that early life conditions affect later-life health in a manner that is only partially modifiable by later-life experiences. Objective To examine whether epigenetic measures of BMI developed in adults are valid biomarkers of childhood BMI and if they are sensitive to early life social determinants of health. Design, Setting, and Participants This population-based study of over 3200 children and adolescents aged 8 to 18 years included data from 2 demographically diverse US pediatric cohort studies that combine longitudinal and twin study designs. Analyses were conducted from 2021 to 2022. Exposures Socioeconomic status, marginalized groups. Main Outcome and Measure Salivary epigenetic BMI, BMI. Analyses were conducted to validate the use of saliva epigenetic BMI as a potential biomarker of child BMI and to examine associations between epigenetic BMI and social determinants of health. Results Salivary epigenetic BMI was calculated from 2 cohorts: (1) 1183 individuals aged 8 to 18 years (609 female [51%]; mean age, 13.4 years) from the Texas Twin Project and (2) 2020 children (1011 female [50%]) measured at 9 years of age and 15 years of age from the Future of Families and Child Well-Being Study. Salivary epigenetic BMI was associated with children's BMI (r = 0.36; 95% CI, 0.31-0.40 to r = 0.50; 95% CI, 0.42-0.59). Longitudinal analysis found that epigenetic BMI was highly stable across adolescence but remained both a leading and lagging indicator of BMI change. Twin analyses showed that epigenetic BMI captured differences in BMI between monozygotic twins. Moreover, children from more disadvantaged socioeconomic status (b = -0.13 to -0.15 across samples) and marginalized racial and ethnic groups (b = 0.08-0.34 across samples) had higher epigenetic BMI, even when controlling for concurrent BMI, pubertal development, and tobacco exposure. Socioeconomic status at birth relative to concurrent socioeconomic status best predicted epigenetic BMI in childhood and adolescence (b = -0.15; 95% CI, -0.20 to -0.09). Conclusion and Relevance This study demonstrated that epigenetic measures of BMI calculated from pediatric saliva samples were valid biomarkers of childhood BMI and may be associated with early-life social inequalities. The findings are in line with the hypothesis that early-life conditions are especially important factors in epigenetic regulation of later-life health. Research showing that health later in life is linked to early-life conditions has important implications for the development of early-life interventions that could significantly extend healthy life span.
Collapse
Affiliation(s)
- Laurel Raffington
- Max Planck Research Group Biosocial – Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin, Germany
- Population Research Center, The University of Texas at Austin, Austin
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Travis Mallard
- Population Research Center, The University of Texas at Austin, Austin
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Jonah Fisher
- Survey Research Center, University of Michigan, Ann Arbor
| | - Liza Vinnik
- Population Research Center, The University of Texas at Austin, Austin
| | | | - Daniel A. Notterman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | | | - Colter Mitchell
- Survey Research Center, University of Michigan, Ann Arbor
- Population Studies Center, University of Michigan, Ann Arbor
| | - K. Paige Harden
- Population Research Center, The University of Texas at Austin, Austin
| |
Collapse
|
11
|
Maharaj A, Jefferies JL, Mulrooney DA, Armstrong GT, Brinkman TM, O'Neil ST, Terrell S, Partin RE, Srivastava DK, Hudson MM, Wang Z, Ness KK. Design and methods of a randomized telehealth-based intervention to improve fitness in survivors of childhood cancer with exercise intolerance. Contemp Clin Trials 2023; 133:107339. [PMID: 37730199 PMCID: PMC10591872 DOI: 10.1016/j.cct.2023.107339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND Exercise intolerance among childhood cancer survivors substantially increases risk for early mortality, reduced cognitive function, poor quality of life, emotional distress, and sub-optimal participation in social roles. Fortunately, exercise intolerance is modifiable, even among individuals with impaired cardiopulmonary and neuromuscular health. This study aims to evaluate the impact of tailored exercise intervention remotely supervised by fitness professionals in survivors with exercise intolerance. Telehealth-based delivery of the intervention aims to enhance uptake by removing the burden of travel and allowing participants to gain confidence with exercise and physical activity at home. METHODS This is an ongoing single-blind, two-arm, prospective, clinical trial that will randomize 160 participants 1:1 to intervention (n = 80) and attention control (n = 80) groups. The intervention group receives an individually tailored exercise prescription based on results from baseline assessments performed remotely via a Health Insurance Portability and Accountability Act-compliant virtual platform and personal preferences for aerobic exercise. Each prescription includes aerobic and strengthening components designed to progress gradually to 150-300-min of moderate aerobic activity and twice weekly strengthening exercises over 20-weeks. The first two weeks are supervised for 6 sessions, tapering to twice/week for weeks 3-4, once/week for weeks 5-8, every other week for weeks 9-16 and once midway between weeks 17-20. The schedule is modifiable depending on participant need, adherence, and response to exercise. Each session is approximately one hour. CONCLUSION This study tests the efficacy of an individually prescribed, virtually supervised exercise intervention on exercise intolerant childhood cancer survivors. CLINICALTRIALS gov registration: NCT04714840.
Collapse
Affiliation(s)
- Arun Maharaj
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS-735, Memphis, TN 38105, USA.
| | - John L Jefferies
- Department of Medicine, University of Tennessee Health Science Center, 920 Madison Avenue, Memphis, TN 38163, USA.
| | - Daniel A Mulrooney
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS-260, Memphis, TN 38105, USA.
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS-735, Memphis, TN 38105, USA.
| | - Tara M Brinkman
- Department of Psychology and Biobehavioral Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS-740, Memphis, TN 38105, USA.
| | - Sean T O'Neil
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS-735, Memphis, TN 38105, USA.
| | - Sarah Terrell
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS-735, Memphis, TN 38105, USA.
| | - Robyn E Partin
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS-735, Memphis, TN 38105, USA.
| | - Deo Kumar Srivastava
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS-768, Memphis, TN 38105, USA.
| | - Melissa M Hudson
- Departments of Oncology and Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS-735, Memphis, TN 38105, USA.
| | - Zhaoming Wang
- Departments of Epidemiology and Cancer Control and Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS-735, Memphis, TN 38105, USA.
| | - Kirsten K Ness
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS-735, Memphis, TN 38105, USA.
| |
Collapse
|
12
|
Sullivan ADW, Bozack AK, Cardenas A, Comer JS, Bagner DM, Forehand R, Parent J. Parenting Practices May Buffer the Impact of Adversity on Epigenetic Age Acceleration Among Young Children With Developmental Delays. Psychol Sci 2023; 34:1173-1185. [PMID: 37733001 PMCID: PMC10626625 DOI: 10.1177/09567976231194221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/26/2023] [Indexed: 09/22/2023] Open
Abstract
This study examined whether children exposed to adversity would exhibit lower epigenetic age acceleration in the context of improved parenting. Children with developmental delays and externalizing behavior problems (N = 62; Mage = 36.26 months; 70.97% boys, 29.03% girls; 71% Latinx, 22.6% Black) were drawn from a larger randomized controlled trial (RCT), which randomized them to receive Internet-delivered parent-child interaction therapy (iPCIT; n = 30) or community referrals as usual (RAU; n = 32). Epigenetic age acceleration was estimated with the pediatric buccal epigenetic clock, using saliva. Adversity was assessed using parent, family, and neighborhood-level cumulative-risk indicators. Adversity interacted with Time 2 (T2) observations of positive and negative-parenting practices to predict epigenetic age acceleration 1.5 years later, regardless of treatment assignment. Children exposed to more adversity displayed lower epigenetic age acceleration when parents evidenced increased positive (b = -0.15, p = .001) and decreased negative (b = -0.12, p = .01) parenting practices.
Collapse
Affiliation(s)
- Alexandra D. W. Sullivan
- Department of Psychological Science, University of Vermont
- Department of Psychiatry, Center for Health and Community, University of California, San Francisco
| | - Anne K. Bozack
- Department of Epidemiology and Population Health, School of Medicine, Stanford University
| | - Andres Cardenas
- Department of Epidemiology and Population Health, School of Medicine, Stanford University
- Department of Pediatrics, School of Medicine, Stanford University
| | - Jonathan S. Comer
- Department of Psychology and Center for Children and Families, Florida International University
| | - Daniel M. Bagner
- Department of Psychology and Center for Children and Families, Florida International University
| | - Rex Forehand
- Department of Psychological Science, University of Vermont
| | - Justin Parent
- Bradley-Hasbro Children’s Research Center, E. P. Bradley Hospital, Providence, RI
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University
| |
Collapse
|
13
|
Willems YE, deSteiguer A, Tanksley PT, Vinnik L, Främke D, Okbay A, Richter D, Wagner GG, Hertwig R, Koellinger P, Tucker-Drob EM, Harden KP, Raffington L. Self-control is associated with health-relevant disparities in buccal DNA-methylation measures of biological aging in older adults. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.30.23294816. [PMID: 37693450 PMCID: PMC10491374 DOI: 10.1101/2023.08.30.23294816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Self-control is a personality dimension that is associated with better physical health and a longer lifespan. Here we examined (1) whether self-control is associated with buccal and saliva DNA-methylation (DNAm) measures of biological aging quantified in children, adolescents, and adults, and (2) whether biological aging measured in buccal DNAm is associated with self-reported health. Following preregistered analyses, we computed two DNAm measures of advanced biological age (PhenoAge and GrimAge Acceleration) and a DNAm measure of pace of aging (DunedinPACE) in buccal samples from the German Socioeconomic Panel Study (SOEP-G[ene], n = 1058, age range 0-72, Mage = 42.65) and saliva samples from the Texas Twin Project (TTP, n = 1327, age range 8-20, Mage = 13.50). We found that lower self-control was associated with advanced biological age in older adults (β =-.34), but not young adults, adolescents or children. This association was not accounted for by statistical correction for socioeconomic contexts, BMI, or genetic correlates of low self-control. Moreover, a faster pace of aging and advanced biological age measured in buccal DNAm were associated with worse self-reported health (β =.13 to β = .19). But, effect sizes were weaker than observations in blood, thus customization of DNAm aging measures to buccal and saliva tissues may be necessary. Our findings are consistent with the hypothesis that self-control is associated with health via pathways that accelerate biological aging in older adults.
Collapse
Affiliation(s)
- Y E Willems
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin
| | - A deSteiguer
- Population Research Center, The University of Texas, Austin
| | - P T Tanksley
- Population Research Center, The University of Texas, Austin
| | - L Vinnik
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin
| | - D Främke
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin
| | - A Okbay
- School of Business and Economics, Economics Fellow, Tinbergen Institute, Amsterdam
- Amsterdam Neuroscience, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam
| | - D Richter
- Department of Education and Psychology, Freie Universität Berlin
- SHARE Berlin, Berlin
| | - G G Wagner
- Max Planck Institute for Human Development, Berlin
- German Socio Economic Panel Study (SOEP), Berlin
| | - R Hertwig
- Max Planck Institute for Human Development, Berlin
| | - P Koellinger
- School of Business and Economics, Economics Fellow, Tinbergen Institute, Amsterdam
- Amsterdam Neuroscience, Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam
| | | | - K P Harden
- Population Research Center, The University of Texas, Austin
| | - L Raffington
- Max Planck Research Group Biosocial - Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin
| |
Collapse
|
14
|
Liu W, Yang X, Mao Z, Du Y, Lassiter C, AlAkwaa FM, Benny PA, Garmire LX. Severe preeclampsia is not associated with significant DNA methylation changes but cell proportion changes in the cord blood - caution on the importance of confounding adjustment. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.31.23294898. [PMID: 37693517 PMCID: PMC10491383 DOI: 10.1101/2023.08.31.23294898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Epigenome-wide DNA methylation analysis (EWAS) is an important approach to identify biomarkers for early disease detection and prognosis prediction, yet its results could be confounded by other factors such as cell-type heterogeneity and patient characteristics. In this study, we address the importance of confounding adjustment by examining DNA methylation patterns in cord blood exposed to severe preeclampsia (PE), a prevalent and potentially fatal pregnancy complication. Without such adjustment, a misleading global hypomethylation pattern is obtained. However, after adjusting cell type proportions and patient clinical characteristics, most of the so-called significant CpG methylation changes associated with severe PE disappear. Rather, the major effect of PE on cord blood is through the proportion changes in different cell types. These results are validated using a previously published cord blood DNA methylation dataset, where global hypomethylation pattern was also wrongfully obtained without confounding adjustment. Additionally, several cell types significantly change as gestation progress (eg. granulocyte, nRBC, CD4T, and B cells), further confirming the importance of cell type adjustment in EWAS study of cord blood tissues. Our study urges the community to perform confounding adjustments in EWAS studies, based on cell type heterogeneity and other patient characteristics.
Collapse
Affiliation(s)
- Wenting Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Xiaotong Yang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Zhixin Mao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Yuheng Du
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | | | - Fadhl M AlAkwaa
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Paula A Benny
- University of Hawaii Cancer Center, Epidemiology, Honolulu, HI
| | - Lana X Garmire
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| |
Collapse
|
15
|
Lussier AA, Zhu Y, Smith BJ, Cerutti J, Fisher J, Melton PE, Wood NM, Cohen-Woods S, Huang RC, Mitchell C, Schneper L, Notterman DA, Simpkin AJ, Smith ADAC, Suderman MJ, Walton E, Relton CL, Ressler KJ, Dunn EC. Association between the timing of childhood adversity and epigenetic patterns across childhood and adolescence: findings from the Avon Longitudinal Study of Parents and Children (ALSPAC) prospective cohort. THE LANCET. CHILD & ADOLESCENT HEALTH 2023; 7:532-543. [PMID: 37327798 PMCID: PMC10527482 DOI: 10.1016/s2352-4642(23)00127-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/14/2023] [Accepted: 04/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Childhood adversity is a potent determinant of health across development and is associated with altered DNA methylation signatures, which might be more common in children exposed during sensitive periods in development. However, it remains unclear whether adversity has persistent epigenetic associations across childhood and adolescence. We aimed to examine the relationship between time-varying adversity (defined through sensitive period, accumulation of risk, and recency life course hypotheses) and genome-wide DNA methylation, measured three times from birth to adolescence, using data from a prospective, longitudinal cohort study. METHODS We first investigated the relationship between the timing of exposure to childhood adversity between birth and 11 years and blood DNA methylation at age 15 years in the Avon Longitudinal Study of Parents and Children (ALSPAC) prospective cohort study. Our analytic sample included ALSPAC participants with DNA methylation data and complete childhood adversity data between birth and 11 years. We analysed seven types of adversity (caregiver physical or emotional abuse, sexual or physical abuse [by anyone], maternal psychopathology, one-adult households, family instability, financial hardship, and neighbourhood disadvantage) reported by mothers five to eight times between birth and 11 years. We used the structured life course modelling approach (SLCMA) to identify time-varying associations between childhood adversity and adolescent DNA methylation. Top loci were identified using an R2 threshold of 0·035 (ie, ≥3·5% of DNA methylation variance explained by adversity). We attempted to replicate these associations using data from the Raine Study and Future of Families and Child Wellbeing Study (FFCWS). We also assessed the persistence of adversity-DNA methylation associations we previously identified from age 7 blood DNA methylation into adolescence and the influence of adversity on DNA methylation trajectories from ages 0-15 years. FINDINGS Of 13 988 children in the ALSPAC cohort, 609-665 children (311-337 [50-51%] boys and 298-332 [49-50%] girls) had complete data available for at least one of the seven childhood adversities and DNA methylation at 15 years. Exposure to adversity was associated with differences in DNA methylation at 15 years for 41 loci (R2 ≥0·035). Sensitive periods were the most often selected life course hypothesis by the SLCMA. 20 (49%) of 41 loci were associated with adversities occurring between age 3 and 5 years. Exposure to one-adult households was associated with differences in DNA methylation at 20 [49%] of 41 loci, exposure to financial hardship was associated with changes at nine (22%) loci, and physical or sexual abuse was associated with changes at four (10%) loci. We replicated the direction of associations for 18 (90%) of 20 loci associated with exposure to one-adult household using adolescent blood DNA methylation from the Raine Study and 18 (64%) of 28 loci using saliva DNA methylation from the FFCWS. The directions of effects for 11 one-adult household loci were replicated in both cohorts. Differences in DNA methylation at 15 years were not present at 7 years and differences identified at 7 years were no longer apparent by 15 years. We also identified six distinct DNA methylation trajectories from these patterns of stability and persistence. INTERPRETATION These findings highlight the time-varying effect of childhood adversity on DNA methylation profiles across development, which might link exposure to adversity to potential adverse health outcomes in children and adolescents. If replicated, these epigenetic signatures could ultimately serve as biological indicators or early warning signs of initiated disease processes, helping identify people at greater risk for the adverse health consequences of childhood adversity. FUNDING Canadian Institutes of Health Research, Cohort and Longitudinal Studies Enhancement Resources, EU's Horizon 2020, US National Institute of Mental Health.
Collapse
Affiliation(s)
- Alexandre A Lussier
- Psychiatric and Neurodevelopmental Genetics Unit, Centre for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Harvard University, Boston, MA, USA; Stanley Center for Psychiatric Research, The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Yiwen Zhu
- Psychiatric and Neurodevelopmental Genetics Unit, Centre for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Epidemiology, Harvard T H Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Brooke J Smith
- Psychiatric and Neurodevelopmental Genetics Unit, Centre for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Janine Cerutti
- Psychiatric and Neurodevelopmental Genetics Unit, Centre for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jonah Fisher
- Institute for Social Research, University of Michigan, Ann Abor, MI, USA
| | - Phillip E Melton
- School of Population and Global Health, University of Western Australia, Crawley, WA, Australia; Menzies Research Institute, University of Tasmania, Hobart, TAS, Australia
| | - Natasha M Wood
- College of Education, Psychology, and Social Work, Flinders University, Adelaide, SA, Australia
| | - Sarah Cohen-Woods
- College of Education, Psychology, and Social Work, Flinders University, Adelaide, SA, Australia; Flinders Institute for Mental Health and Wellbeing, Flinders University, Adelaide, SA, Australia; Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Rae-Chi Huang
- Nutrition Health Innovation Research Institute, Edith Cowan University, Perth, WA, Australia
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, Ann Abor, MI, USA
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Daniel A Notterman
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Andrew J Simpkin
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland
| | - Andrew D A C Smith
- Mathematics and Statistics Research Group, University of the West of England, Bristol, UK
| | - Matthew J Suderman
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Esther Walton
- Department of Psychology, University of Bath, Bath, UK
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School, Harvard University, Boston, MA, USA; Department of Psychiatry, McLean Hospital, Belmont, MA, USA
| | - Erin C Dunn
- Psychiatric and Neurodevelopmental Genetics Unit, Centre for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Harvard University, Boston, MA, USA; Center on the Developing Child, Harvard University, Boston, MA, USA; Stanley Center for Psychiatric Research, The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
16
|
Hernández HG, Aranzazu-Moya GC, Pinzón-Reyes EH. Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers. Biomedicines 2023; 11:1797. [PMID: 37509437 PMCID: PMC10376800 DOI: 10.3390/biomedicines11071797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 07/30/2023] Open
Abstract
OBJECTIVE To identify DNA methylation patterns of heavy smokers in oral rinse samples. METHODS Genome-wide DNA methylation data was imported from Gene Expression Omnibus GSE70977 using the GEOquery package. Two independent sets were analyzed: (a) 71 epigenomes of cancer-free subjects (heavy smokers n = 37 vs. non-smokers n = 31); for concordance assessment (b) 139 oral-cancer patients' epigenomes (heavy smokers n = 92 vs. non-smokers n = 47). Differential DNA methylation for CpG positions and at the regional level was determined using Limma and DMRcate Bioconductor packages. The linear model included sex, age, and alcohol consumption. The statistical threshold was set to p < 0.05. Functional gene prioritization analysis was performed for gene-targeted analysis. RESULTS In individuals without cancer and heavy smokers, the FAM184B gene was found with two CpG positions differentially hypermethylated (p = 0.012 after FDR adjustment), in a region of 48 bp with an absolute methylation difference >10% between groups (p = 1.76 × 10-8). In the analysis corresponding to oral-cancer patients, we found AHRR differentially hypomethylated cancer patients, but also in subjects without oral cancer in the targeted analyses. Remarkably, ADAMTS2 was found differentially hypermethylated in heavy smokers without a diagnosis of cancer in two consecutive probes cg05575921 (p = 3.13 × 10-7) and cg10208897 (p = 1.36 × 10-5). CONCLUSIONS Differentially methylated AHRR, ADAMTS2, and FAM184B genes are biomarker candidates in oral rinse samples.
Collapse
Affiliation(s)
- Hernán Guillermo Hernández
- School of Dentistry, Universidad Santo Tomás, Bucaramanga 680001, Colombia
- PhD Program in Dentistry, Universidad Santo Tomás, Bucaramanga 680001, Colombia
| | | | - Efraín Hernando Pinzón-Reyes
- Facultad de Ciencias Médicas y de la Salud, Instituto de Investigación Masira, Universidad de Santander, Bucaramanga 680003, Colombia
| |
Collapse
|
17
|
Protsenko E, Wolkowitz OM, Yaffe K. Associations of stress and stress-related psychiatric disorders with GrimAge acceleration: review and suggestions for future work. Transl Psychiatry 2023; 13:142. [PMID: 37130894 PMCID: PMC10154294 DOI: 10.1038/s41398-023-02360-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 05/04/2023] Open
Abstract
The notion of "biological aging" as distinct from chronological aging has been of increasing interest in psychiatry, and many studies have explored associations of stress and psychiatric illness with accelerated biological aging. The "epigenetic clocks" are one avenue of this research, wherein "biological age" is estimated using DNA methylation data from specific CpG dinucleotide sites within the human genome. Many iterations of the epigenetic clocks have been developed, but the GrimAge clock continues to stand out for its ability to predict morbidity and mortality. Several studies have now explored associations of stress, PTSD, and MDD with GrimAge acceleration (GrimAA). While stress, PTSD, and MDD are distinct psychiatric entities, they may share common mechanisms underlying accelerated biological aging. Yet, no one has offered a review of the evidence on associations of stress and stress-related psychopathology with GrimAA. In this review, we identify nine publications on associations of stress, PTSD, and MDD with GrimAA. We find that results are mixed both within and across each of these exposures. However, we also find that analytic methods - and specifically, the choice of covariates - vary widely between studies. To address this, we draw upon popular methods from the field of clinical epidemiology to offer (1) a systematic framework for covariate selection, and (2) an approach to results reporting that facilitates analytic consensus. Although covariate selection will differ by the research question, we encourage researchers to consider adjustment for tobacco, alcohol use, physical activity, race, sex, adult socioeconomic status, medical comorbidity, and blood cell composition.
Collapse
Affiliation(s)
- Ekaterina Protsenko
- Department of Psychiatry, Stanford University School of Medicine, Palo Alto, CA, USA.
- Department Epidemiology & Biostatistics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA.
| | - Owen M Wolkowitz
- Weill Institute for Neurosciences and Department of Psychiatry and Behavioral Sciences, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Kristine Yaffe
- Department Epidemiology & Biostatistics, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
- Weill Institute for Neurosciences and Department of Psychiatry and Behavioral Sciences, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| |
Collapse
|
18
|
Watanabe K, Yamagishi T, Toyomane K, Akutsu T. Validation of a novel fluorescent probe-based real-time PCR assay to detect saliva-specific unmethylated CpG sites for saliva identification. Leg Med (Tokyo) 2023; 63:102260. [PMID: 37094513 DOI: 10.1016/j.legalmed.2023.102260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/27/2023] [Accepted: 04/13/2023] [Indexed: 04/26/2023]
Abstract
The identification of saliva from forensic samples is often important to establish what happened at a crime scene, especially in sexual assault cases. Recently, CpG sites that are specifically methylated or unmethylated in saliva have been reported as markers for saliva identification. In this study, we designed a fluorescent probe-based real-time polymerase chain reaction (PCR) assay for analyzing the methylation status of two neighboring CpG sites, which we previously found were saliva-specifically unmethylated. Specificity analysis using various types of body fluid/tissue samples demonstrated a probe detecting the unmethylation of the two CpG sites reacted only to saliva DNA, indicating this probe as an all-or-nothing marker for the presence of saliva DNA. Sensitivity analysis demonstrated that the detection limit was 0.5 ng saliva DNA as input for bisulfite conversion, while we confirmed a negative effect of larger amounts of non-saliva DNA on sensitivity in the analysis of saliva-vaginal DNA mixtures. We finally validated the applicability of this test to swabs from licked skin and bottles after drinking as mock forensic samples in comparison with other saliva-specific markers. We confirmed the potential usefulness of this test for skin samples, from which a saliva-specific mRNA was not detected reliably, while the ingredients in several beverages might affect methylation analysis. Given the simplicity of real-time PCR as well as the high specificity and sensitivity of the test, we believe the developed method is suitable for routine forensic analysis and can play an important role in saliva identification.
Collapse
Affiliation(s)
- Ken Watanabe
- National Research Institute of Police Science, Chiba 277-0882, Japan.
| | | | - Kochi Toyomane
- National Research Institute of Police Science, Chiba 277-0882, Japan
| | - Tomoko Akutsu
- National Research Institute of Police Science, Chiba 277-0882, Japan
| |
Collapse
|
19
|
Raffington L, Tanksley PT, Sabhlok A, Vinnik L, Mallard T, King LS, Goosby B, Harden KP, Tucker-Drob EM. Socially Stratified Epigenetic Profiles Are Associated With Cognitive Functioning in Children and Adolescents. Psychol Sci 2023; 34:170-185. [PMID: 36459657 PMCID: PMC10068508 DOI: 10.1177/09567976221122760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 08/09/2022] [Indexed: 12/04/2022] Open
Abstract
Children's cognitive functioning and educational performance are socially stratified. Social inequality, including classism and racism, may operate partly via epigenetic mechanisms that modulate neurocognitive development. Following preregistered analyses of data from 1,183 participants, ages 8 to 19 years, from the Texas Twin Project, we found that children growing up in more socioeconomically disadvantaged families and neighborhoods and children from marginalized racial/ethnic groups exhibit DNA methylation profiles that, in previous studies of adults, were indicative of higher chronic inflammation, lower cognitive functioning, and a faster pace of biological aging. Furthermore, children's salivary DNA methylation profiles were associated with their performance on in-laboratory tests of cognitive and academic skills, including processing speed, general executive function, perceptual reasoning, verbal comprehension, reading, and math. Given that the DNA methylation measures that we examined were originally developed in adults, our results suggest that children show molecular signatures that reflect the early life social determinants of lifelong disparities in health and cognition.
Collapse
Affiliation(s)
- Laurel Raffington
- Department of Psychology, The
University of Texas at Austin
- Population Research Center, The
University of Texas at Austin
- Max Planck Research Group Biosocial –
Biology, Social Disparities, and Development; Max Planck Institute for Human
Development, Berlin, Germany
| | - Peter T. Tanksley
- Department of Psychology, The
University of Texas at Austin
- Population Research Center, The
University of Texas at Austin
| | - Aditi Sabhlok
- Department of Psychology, The
University of Texas at Austin
| | - Liza Vinnik
- Department of Psychology, The
University of Texas at Austin
| | - Travis Mallard
- Department of Psychology, The
University of Texas at Austin
| | - Lucy S. King
- Department of Psychology, The
University of Texas at Austin
- Department of Psychiatry and Behavioral
Sciences, Tulane University School of Medicine
| | - Bridget Goosby
- Population Research Center, The
University of Texas at Austin
- Department of Sociology, The University
of Texas at Austin
| | - K. Paige Harden
- Department of Psychology, The
University of Texas at Austin
- Population Research Center, The
University of Texas at Austin
| | - Elliot M. Tucker-Drob
- Department of Psychology, The
University of Texas at Austin
- Population Research Center, The
University of Texas at Austin
| |
Collapse
|
20
|
Raffington L, Schneper L, Mallard T, Fisher J, Vinnik L, Hollis-Hansen K, Notterman DA, Tucker-Drob EM, Mitchell C, Harden KP. Measuring the long arm of childhood in real-time: Epigenetic predictors of BMI and social determinants of health across childhood and adolescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524709. [PMID: 36712110 PMCID: PMC9882281 DOI: 10.1101/2023.01.20.524709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Children who are socioeconomically disadvantaged are at increased risk for high body mass index (BMI) and multiple diseases in adulthood. The developmental origins of health and disease hypothesis proposes that early life conditions affect later-life health in a manner that is only partially modifiable by later-life experiences. Epigenetic mechanisms may regulate the influence of early life conditions on later life health. Recent epigenetic studies of adult blood samples have identified DNA-methylation sites associated with higher BMI and worse health (epigenetic-BMI). Here, we used longitudinal and twin study designs to examine whether epigenetic predictors of BMI developed in adults are valid biomarkers of child BMI and are sensitive to early life social determinants of health. Salivary epigenetic-BMI was calculated from two samples: (1) N=1,183 8-to-19-year-olds (609 female, mean age=13.4) from the Texas Twin Project (TTP), and (2) N=2,020 children (1,011 female) measured at 9 and 15 years from the Future of Families and Child Well-Being Study (FFCWS). We found that salivary epigenetic-BMI is robustly associated with children's BMI (r=0.36 to r=0.50). Longitudinal analysis suggested that epigenetic-BMI is highly stable across adolescence, but remains both a leading and lagging indicator of BMI change. Twin analyses showed that epigenetic-BMI captures differences in BMI between monozygotic twins. Moreover, children from more disadvantaged socioeconomic status (SES) and marginalized race/ethnic groups had higher epigenetic-BMI, even when controlling for concurrent BMI, pubertal development, and tobacco exposure. SES at birth relative to concurrent SES best predicted epigenetic-BMI in childhood and adolescence. We show for the first time that epigenetic predictors of BMI calculated from pediatric saliva samples are valid biomarkers of childhood BMI that are sensitive to social inequalities. Our findings are in line with the hypothesis that early life conditions are especially important factors in epigenetic regulation of later life health. Research showing that health later in life is linked to early life conditions have important implications for the development of early-life interventions that could significantly extend healthy life span.
Collapse
Affiliation(s)
- Laurel Raffington
- Max Planck Institute for Human Development, Max Planck Research Group Biosocial – Biology, Social Disparities, and Development, Lentzeallee 94, 14195 Berlin, Germany
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, NJ
| | - Travis Mallard
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Jonah Fisher
- Survey Research Center, University of Michigan, Ann Arbor, MI
| | - Liza Vinnik
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
| | | | | | | | - Colter Mitchell
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Population Studies Center, University of Michigan, Ann Arbor, MI
| | - Kathryn P. Harden
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
21
|
Perret LC, Geoffroy MC, Barr E, Parnet F, Provencal N, Boivin M, O’Donnell KJ, Suderman M, Power C, Turecki G, Ouellet-Morin I. Associations between epigenetic aging and childhood peer victimization, depression, and suicidal ideation in adolescence and adulthood: A study of two population-based samples. Front Cell Dev Biol 2023; 10:1051556. [PMID: 36712964 PMCID: PMC9879289 DOI: 10.3389/fcell.2022.1051556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Background: Prior studies indicate that peer victimization (including bullying) is associated with higher risk for depression and suicidal ideation across the life course. However, molecular mechanisms underlying these associations remain unclear. This two-cohort study proposes to test whether epigenetic aging and pace of aging, as well as a DNA methylation marker of responsive to glucocorticoids, are associated to childhood peer victimization and later depressive symptoms, or suicidal ideation. Methods: Cohort 1: Epigenome-wide DNA methylation (EPIC array) was measured in saliva collected when participants were 10.47 years (standard deviation = 0.35) in a subsample of the Quebec Longitudinal Study of Child Development (QLSCD, n = 149 participants), with self-reported peer victimization at 6-8 years, depressive symptoms (mean symptoms, and dichotomized top 30% symptoms) and suicidal ideation at 15-17 years. Cohort 2: Epigenome-wide DNA methylation (EPIC array) was measured in blood collected from participants aged 45.13 years (standard deviation = 0.37) in a subsample of the 1958 British Birth cohort (1958BBC, n = 238 participants) with information on mother-reported peer victimization at 7-11 years, self-reported depressive symptoms at 50 years, and suicidal ideation at 45 years. Five epigenetic indices were derived: three indicators of epigenetic aging [Horvath's pan-tissue (Horvath1), Horvath's Skin-and-Blood (Horvath2), Pediatric-Buccal-Epigenetic age (PedBE)], pace of aging (DunedinPACE), and stress response reactivity (Epistress). Results: Peer victimization was not associated with the epigenetic indices in either cohort. In the QLSCD, higher PedBE epigenetic aging and a slower pace of aging as measured by DunedinPACE predicted higher depressive symptoms scores. In contrast, neither the Horvath1, or Horvath2 epigenetic age estimates, nor the Epistress score were associated with depressive symptoms in either cohort, and none of the epigenetic indices predicted suicidal ideation. Conclusion: The findings are consistent with epigenome-wide and candidate gene studies suggesting that these epigenetic indices did not relate to peer victimization, challenging the hypothesis that cumulative epigenetic aging indices could translate vulnerability to depressive symptoms and suicidal ideation following peer victimization. Since some indices of epigenetic aging and pace of aging signaled higher risk for depressive symptoms, future studies should pursue this investigation to further evaluate the robustness and generalization of these preliminary findings.
Collapse
Affiliation(s)
- L. C. Perret
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - M-C. Geoffroy
- Department of Psychiatry, McGill University, Montreal, QC, Canada,Department of Educational and Counselling Psychology, McGill University, Montreal, QC, Canada
| | - E. Barr
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - F. Parnet
- School of Criminology, Research Center of the Montreal Mental Health University Institute, Université de Montréal, Montreal, QC, Canada
| | - N. Provencal
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - M. Boivin
- School of Psychology, Université Laval, Québec City, QC, Canada
| | - K. J. O’Donnell
- Department of Psychiatry, McGill University, Montreal, QC, Canada,Yale Child Study Center, Yale School of Medicine, New Haven, CT, United States,Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, United States,Child and Brain Development Program, CIFAR, Toronto, ON, Canada
| | - M. Suderman
- MRC Integrative Epidemiology Unit, Bristol Medical School, Bristol Population Health Science Institute, Bristol, United Kingdom
| | - C. Power
- UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - G. Turecki
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - I. Ouellet-Morin
- School of Criminology, Research Center of the Montreal Mental Health University Institute, Université de Montréal, Montreal, QC, Canada,*Correspondence: I. Ouellet-Morin,
| |
Collapse
|
22
|
Song M, Bai H, Zhang P, Zhou X, Ying B. Promising applications of human-derived saliva biomarker testing in clinical diagnostics. Int J Oral Sci 2023; 15:2. [PMID: 36596771 PMCID: PMC9810734 DOI: 10.1038/s41368-022-00209-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/23/2022] [Accepted: 11/03/2022] [Indexed: 01/05/2023] Open
Abstract
Saliva testing is a vital method for clinical applications, for its noninvasive features, richness in substances, and the huge amount. Due to its direct anatomical connection with oral, digestive, and endocrine systems, clinical usage of saliva testing for these diseases is promising. Furthermore, for other diseases that seeming to have no correlations with saliva, such as neurodegenerative diseases and psychological diseases, researchers also reckon saliva informative. Tremendous papers are being produced in this field. Updated summaries of recent literature give newcomers a shortcut to have a grasp of this topic. Here, we focused on recent research about saliva biomarkers that are derived from humans, not from other organisms. The review mostly addresses the proceedings from 2016 to 2022, to shed light on the promising usage of saliva testing in clinical diagnostics. We recap the recent advances following the category of different types of biomarkers, such as intracellular DNA, RNA, proteins and intercellular exosomes, cell-free DNA, to give a comprehensive impression of saliva biomarker testing.
Collapse
Affiliation(s)
- Mengyuan Song
- grid.13291.380000 0001 0807 1581Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Bai
- grid.13291.380000 0001 0807 1581Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ping Zhang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases & Human Saliva Laboratory & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases & Human Saliva Laboratory & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.
| |
Collapse
|
23
|
Blostein FA, Fisher J, Dou J, Schneper L, Ware EB, Notterman DA, Mitchell C, Bakulski KM. Polymethylation scores for prenatal maternal smoke exposure persist until age 15 and are detected in saliva in the Fragile Families and Child Wellbeing cohort. Epigenetics 2022; 17:2223-2240. [PMID: 35980258 PMCID: PMC9665138 DOI: 10.1080/15592294.2022.2112815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/05/2022] [Indexed: 01/18/2023] Open
Abstract
Prenatal maternal smoking is associated with low birthweight, neurological disorders, and asthma in exposed children. DNA methylation signatures can function as biomarkers of prenatal smoke exposure. However, the robustness of DNA methylation signatures across child ages, genetic ancestry groups, or tissues is not clear. Using coefficients from a meta-analysis of prenatal smoke exposure and DNA methylation in newborn cord blood, we created polymethylation scores of saliva DNA methylation from children at ages 9 and 15 in the Fragile Families and Child Wellbeing study. In the full sample at age 9 (n = 753), prenatal smoke exposure was associated with a 0.51 (95%CI: 0.35, 0.66) standard deviation higher polymethylation score. The direction and magnitude of the association was consistent in European and African genetic ancestry samples. In the full sample at age 15 (n = 747), prenatal smoke exposure was associated with a 0.48 (95%CI: 0.32, 0.63) standard deviation higher polymethylation score, and the association was attenuated among the European and Admixed-Latin genetic ancestry samples. The polymethylation score classified prenatal smoke exposure accurately (AUC age 9 = 0.77, age 15 = 0.76). Including the polymethylation score increased the AUC of base model covariates by 5 (95% CI: (2.1, 7.2)) percentage points, while including a single candidate site in the AHRR gene did not (P-value = 0.19). Polymethylation scores for prenatal smoking were portable across genetic ancestries and more accurate than an individual DNA methylation site. Polymethylation scores from saliva samples could serve as robust and practical biomarkers of prenatal smoke exposure.
Collapse
Affiliation(s)
- Freida A. Blostein
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Jonah Fisher
- Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - John Dou
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Erin B. Ware
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel A. Notterman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Kelly M. Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| |
Collapse
|
24
|
Koeck RM, Busato F, Tost J, Zandstra H, Remy S, Langie S, Gielen M, van Golde R, Dumoulin JCM, Brunner H, Zamani Esteki M, van Montfoort APA. At age 9, the methylome of assisted reproductive technology children that underwent embryo culture in different media is not significantly different on a genome-wide scale. Hum Reprod 2022; 37:2709-2721. [PMID: 36206092 DOI: 10.1093/humrep/deac213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 09/05/2022] [Indexed: 11/12/2022] Open
Abstract
STUDY QUESTION Can we detect DNA methylation differences between ART children that underwent embryo culture in different media? SUMMARY ANSWER We identified no significant differences in site-specific or regional DNA methylation between the different culture medium groups. WHAT IS KNOWN ALREADY Embryo culture in G3 or K-SICM medium leads to differences in embryonic, neonatal and childhood outcomes, including growth and weight. The methylome may mediate this association as the period of in vitro culture of ART treatments coincides with epigenetic reprogramming. STUDY DESIGN, SIZE, DURATION This study was conducted as a follow-up to a previous culture medium comparison study in which couples were pseudo-randomized to embryo culture in G3 or K-SICM medium. Of the resultant singletons, 120 (n = 65 G3, n = 55 K-SICM), were recruited at age 9. PARTICIPANTS/MATERIALS, SETTING, METHODS The ART children provided a saliva sample from which the methylome was analysed using the Infinium MethylationEPIC array. After quality and context filtering, 106 (n = 57 G3, n = 49 K-SICM) samples and 659 708 sites were retained for the analyses. Differential methylation analyses were conducted using mixed effects linear models corrected for age, sex, sample plate and cell composition. These were applied to all cytosine-guanine dinucleotide (CpG) sites, various genomic regions (genes, promoters, CpG Islands (CGIs)) and as a targeted analysis of imprinted genes and birth weight-associated CpG sites. Differential variance was assessed using the improved epigenetic variable outliers for risk prediction analysis (iEVORA) algorithm and methylation outliers were identified using a previously defined threshold (upper or lower quartile plus or minus three times the interquartile range, respectively). MAIN RESULTS AND THE ROLE OF CHANCE After correcting for multiple testing, we did not identify any significantly differentially methylated CpG sites, genes, promoters or CGIs between G3 and K-SICM children despite a lenient corrected P-value threshold of 0.1. Targeted analyses of (sites within) imprinted genes and birth weight-associated sites also did not identify any significant differences. The number of DNA methylation outliers per sample was comparable between the culture medium groups. iEVORA identified 101 differentially variable CpG sites of which 94 were more variable in the G3 group. LARGE SCALE DATA Gene Expression Omnibus (GEO) GSE196432. LIMITATIONS, REASONS FOR CAUTION To detect significant methylation differences with a magnitude of <10% between the groups many more participants would be necessary; however, the clinical relevance of such small differences is unclear. WIDER IMPLICATIONS OF THE FINDINGS The results of this study are reassuring, suggesting that if there is an effect of the culture medium on DNA methylation (and methylation-mediated diseases risk), it does not differ between the two media investigated here. The findings concur with other methylome studies of ART neonates and children that underwent embryo culture in different media, which also found no significant methylome differences. STUDY FUNDING/COMPETING INTEREST(S) Study funded by March of Dimes (6-FY13-153), EVA (Erfelijkheid Voortplanting & Aanleg) specialty programme (grant no. KP111513) of Maastricht University Medical Centre (MUMC+) and the Horizon 2020 innovation (ERIN) (grant no. EU952516) of the European Commission. The authors do not report any conflicts of interest relevant to this study. TRIAL REGISTRATION NUMBER Dutch Trial register-NL4083.
Collapse
Affiliation(s)
- Rebekka M Koeck
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Florence Busato
- Laboratory for Epigenetics & Environment, CEA-Centre National de Recherche en Genomique Humaine, Evry, France
| | - Jorg Tost
- Laboratory for Epigenetics & Environment, CEA-Centre National de Recherche en Genomique Humaine, Evry, France
| | - Heleen Zandstra
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Sylvie Remy
- Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Sabine Langie
- Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium.,Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, The Netherlands
| | - Marij Gielen
- Department of Epidemiology and Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Ron van Golde
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - John C M Dumoulin
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Han Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Aafke P A van Montfoort
- Department of Obstetrics and Gynaecology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, The Netherlands
| |
Collapse
|
25
|
León I, Herrero Roldán S, Rodrigo MJ, López Rodríguez M, Fisher J, Mitchell C, Lage-Castellanos A. The shared mother-child epigenetic signature of neglect is related to maternal adverse events. Front Physiol 2022; 13:966740. [PMID: 36091392 PMCID: PMC9448913 DOI: 10.3389/fphys.2022.966740] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Studies of DNA methylation have revealed the biological mechanisms by which life adversity confers risk for later physical and mental health problems. What remains unknown is the “biologically embedding” of maternal adverse experiences resulting in maladaptive parenting and whether these epigenetic effects are transmitted to the next generation. This study focuses on neglectful mothering indexed by a severe disregard for the basic and psychological needs of the child. Using the Illumina Human Methylation EPIC BeadChip in saliva samples, we identified genes with differentially methylated regions (DMRs) in those mothers with (n = 51), versus those without (n = 87), neglectful behavior that present similar DMRs patterns in their children being neglected versus non-neglected (n = 40 vs. 75). Mothers reported the emotional intensity of adverse life events. After covariate adjustment and multiple testing corrections, we identified 69 DMRs in the mother epigenome and 42 DMRs in the child epigenome that were simultaneously above the α = 0.01 threshold. The common set of nine DMRs contained genes related to childhood adversity, neonatal and infant diabetes, child neurobehavioral development and other health problems such as obesity, hypertension, cancer, posttraumatic stress, and the Alzheimer’s disease; four of the genes were associated with maternal life adversity. Identifying a shared epigenetic signature of neglect linked to maternal life adversity is an essential step in breaking the intergenerational transmission of one of the most common forms of childhood maltreatment.
Collapse
Affiliation(s)
- Inmaculada León
- Instituto Universitario de Neurociencia, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
| | - Silvia Herrero Roldán
- Instituto Universitario de Neurociencia, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- *Correspondence: Silvia Herrero Roldán,
| | - María José Rodrigo
- Instituto Universitario de Neurociencia, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
| | - Maykel López Rodríguez
- Department of Pathology and Experimental Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, United States
| | - Jonah Fisher
- Institute for Social Research, University of Michigan, Ann Abor, MI, United States
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, Ann Abor, MI, United States
| | - Agustín Lage-Castellanos
- Department of NeuroInformatics, Cuban Center for Neuroscience, Havana, Cuba
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
| |
Collapse
|
26
|
Cosin-Tomas M, Cilleros-Portet A, Aguilar-Lacasaña S, Fernandez-Jimenez N, Bustamante M. Prenatal Maternal Smoke, DNA Methylation, and Multi-omics of Tissues and Child Health. Curr Environ Health Rep 2022; 9:502-512. [PMID: 35670920 PMCID: PMC9363403 DOI: 10.1007/s40572-022-00361-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW Maternal tobacco smoking during pregnancy is of public health concern, and understanding the biological mechanisms can help to promote smoking cessation campaigns. This non-systematic review focuses on the effects of maternal smoking during pregnancy on offspring's epigenome, consistent in chemical modifications of the genome that regulate gene expression. RECENT FINDINGS Recent meta-analyses of epigenome-wide association studies have shown that maternal smoking during pregnancy is consistently associated with offspring's DNA methylation changes, both in the placenta and blood. These studies indicate that effects on blood DNA methylation can persist for years, and that the longer the duration of the exposure and the higher the dose, the larger the effects. Hence, DNA methylation scores have been developed to estimate past exposure to maternal smoking during pregnancy as biomarkers. There is robust evidence for DNA methylation alterations associated with maternal smoking during pregnancy; however, the role of sex, ethnicity, and genetic background needs further exploration. Moreover, there are no conclusive studies about exposure to low doses or during the preconception period. Similarly, studies on tissues other than the placenta and blood are scarce, and cell-type specificity within tissues needs further investigation. In addition, biological interpretation of DNA methylation findings requires multi-omics data, poorly available in epidemiological settings. Finally, although several mediation analyses link DNA methylation changes with health outcomes, they do not allow causal inference. For this, a combination of data from multiple study designs will be essential in the future to better address this topic.
Collapse
Affiliation(s)
- Marta Cosin-Tomas
- ISGlobal, Institute for Global Health, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,CIBER Epidemiología Y Salud Pública, Madrid, Spain.
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Basque Country, Spain
| | - Sofía Aguilar-Lacasaña
- ISGlobal, Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología Y Salud Pública, Madrid, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Basque Country, Spain
| | - Mariona Bustamante
- ISGlobal, Institute for Global Health, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología Y Salud Pública, Madrid, Spain
| |
Collapse
|
27
|
Mehta D, Bruenig D, Pierce J, Sathyanarayanan A, Stringfellow R, Miller O, Mullens AB, Shakespeare-Finch J. Recalibrating the epigenetic clock after exposure to trauma: The role of risk and protective psychosocial factors. J Psychiatr Res 2022; 149:374-381. [PMID: 34823878 DOI: 10.1016/j.jpsychires.2021.11.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Epigenetic aging is associated with a plethora of negative health outcomes and increased mortality. Yet, the dynamicity of epigenetic age after exposure to trauma and the factors that influence epigenetic age are not fully understood. This research evaluated longitudinal changes in epigenetic age before and after exposure to work-related trauma among paramedicine students. We further investigated psychological and social risk (psychological distress, posttraumatic stress disorder/PTSD symptom severity, professional quality of life) and protective factors (social support and organisational membership) that drive epigenetic aging at both time points. METHODS The study comprised of 80 samples of University paramedicine students including 40 individuals at two time points - t0 (baseline) and t1 (post-trauma exposure). Epigenome-wide analysis was performed from t0 and t1 saliva using the Illumina EPIC arrays that cover >860k probes. Data analysis was performed using R via generalized regression models. The epigenetic age was calculated based on the Horvath algorithm, GrimAge and SkinBloodAge were calculated using the Horvath online calculator, and p-value for significance was corrected using the FDR method for multiple testing corrections. RESULTS The epigenetic age at t0 and t1 were highly correlated with chronological age and with each other (r = 0.84-0.94). Baseline epigenetic age and follow-up epigenetic age were significantly associated with risk factors of psychological distress and PTSD symptom severity. Among the protective factors, a sense of psychological organisational membership at the start of the paramedicine course as measured at baseline significantly reduced epigenetic age at baseline and post-trauma exposure. On the other hand, receiving social support acted as a protective factor only after exposure to trauma (follow-up), decreasing epigenetic aging at follow-up. GrimAge acceleration at follow-up was significantly associated with increased PTSD symptom severity at baseline and follow-up. Moreover, increased social support at baseline and follow-up was associated with reduced follow-up GrimAge acceleration. CONCLUSION These results demonstrate that epigenetic aging is dynamic and changes after exposure to trauma. Additionally, results demonstrate that different risk and protective factors influence epigenetic aging at different times. In conclusion, the research identified risk and protective factors associated with epigenetic aging pre- and post-trauma exposure, with implications for health and well-being among individuals exposed to trauma.
Collapse
Affiliation(s)
- Divya Mehta
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Faculty of Health, Kelvin Grove, Queensland, 4059, Australia; Queensland University of Technology (QUT), School of Biomedical Sciences, Faculty of Health, Kelvin Grove, Queensland, 4059, Australia.
| | - Dagmar Bruenig
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Faculty of Health, Kelvin Grove, Queensland, 4059, Australia; Queensland University of Technology (QUT), School of Psychology and Counselling, Faculty of Health, Kelvin Grove, Queensland, 4059, Australia
| | - John Pierce
- Queensland University of Technology (QUT), School of Psychology and Counselling, Faculty of Health, Kelvin Grove, Queensland, 4059, Australia
| | - Anita Sathyanarayanan
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Faculty of Health, Kelvin Grove, Queensland, 4059, Australia; Queensland University of Technology (QUT), School of Biomedical Sciences, Faculty of Health, Kelvin Grove, Queensland, 4059, Australia
| | - Rachel Stringfellow
- Queensland University of Technology (QUT), School of Psychology and Counselling, Faculty of Health, Kelvin Grove, Queensland, 4059, Australia
| | - Olivia Miller
- Queensland University of Technology (QUT), School of Psychology and Counselling, Faculty of Health, Kelvin Grove, Queensland, 4059, Australia
| | - Amy B Mullens
- School of Psychology and Counselling, Centre for Health Research, Institute for Resilient Regions, University of Southern Queensland (USQ), 11 Salisbury Rd, Ipswich, QLD, 4305, Australia
| | - Jane Shakespeare-Finch
- Queensland University of Technology (QUT), School of Psychology and Counselling, Faculty of Health, Kelvin Grove, Queensland, 4059, Australia
| |
Collapse
|
28
|
Skyberg AM, Beeler-Duden S, Goldstein AM, Gancayco CA, Lillard AS, Connelly JJ, Morris JP. Neuroepigenetic impact on mentalizing in childhood. Dev Cogn Neurosci 2022; 54:101080. [PMID: 35158164 PMCID: PMC8844842 DOI: 10.1016/j.dcn.2022.101080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 01/20/2022] [Accepted: 01/31/2022] [Indexed: 12/02/2022] Open
Abstract
Mentalizing, or the ability to understand the mental states and intentions of others, is an essential social cognitive function that children learn and continue to cultivate into adolescence. While most typically developing children acquire sufficient mentalizing skills, individual differences in mentalizing persist throughout childhood and are likely influenced by a combination of cognitive functioning, the social environment, and biological factors. DNA methylation of the oxytocin receptor gene (OXTRm) impacts gene expression and is associated with increased brain activity in mentalizing regions during displays of animacy in healthy young adults. The establishment, fine-tuning, and implications of such associations in the context of broader social functioning remain unclear. Using a developmental neuroimaging epigenetic approach, we investigated the contributions of OXTRm to individual variability in brain function during animate motion perception in middle childhood. We find that higher levels of OXTRm are associated with increased neural responses in the left temporo-parietal junction and inferior frontal gyrus. We also find a positive association between neural activity in LTPJ and social skills. These findings provide evidence of epigenetic influence on the developing child brain and demonstrate that variability in neural social perception in childhood is multifaceted with contributions from individual social experience and the endogenous oxytocin system. Variation in oxytocin receptor (OXTR) DNA methylation is associated with neural function during the perception of animacy. OXTR DNA methylation and social skills are positively associated with BOLD response in the left temporo-parietal junction. The variance explained by OXTR DNA methylation and social skills are unique. OXTR DNA methylation is positively associated with BOLD response in the left inferior frontal gyrus.
Collapse
|
29
|
Prenatal Particulate Matter Exposure Is Associated with Saliva DNA Methylation at Age 15: Applying Cumulative DNA Methylation Scores as an Exposure Biomarker. TOXICS 2021; 9:toxics9100262. [PMID: 34678958 PMCID: PMC8538839 DOI: 10.3390/toxics9100262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022]
Abstract
Exposure in utero to particulate matter (PM2.5 and PM10) is associated with maladaptive health outcomes. Although exposure to prenatal PM2.5 and PM10 has cord blood DNA methylation signatures at birth, signature persistence into childhood and saliva cross-tissue applicability has not been tested. In the Fragile Families and Child Wellbeing Study, a United States 20-city birth cohort, average residential PM2.5 and PM10 during the three months prior to birth was estimated using air quality monitors with inverse distance weighting. Saliva DNA methylation at ages 9 (n = 749) and 15 (n = 793) was measured using the Illumina HumanMethylation 450 k BeadArray. Cumulative DNA methylation scores for particulate matter were estimated by weighting participant DNA methylation at each site by independent meta-analysis effect estimates and standardizing the sums. Using a mixed-effects regression analysis, we tested the associations between cumulative DNA methylation scores at ages 9 and 15 and PM exposure during pregnancy, adjusted for child sex, age, race/ethnicity, maternal income-to-needs ratio, nonmartial birth status, and saliva cell-type proportions. Our study sample was 50.5% male, 56.3% non-Hispanic Black, and 19.8% Hispanic, with a median income-to-needs ratio of 1.4. Mean exposure levels for PM2.5 were 27.9 μg/m3/day (standard deviation: 7.0; 23.7% of observations exceeded safety standards) and for PM10 were 15.0 μg/m3/day (standard deviation: 3.1). An interquartile range increase in PM2.5 exposure (10.73 μg/m3/day) was associated with a −0.0287 standard deviation lower cumulative DNA methylation score for PM2.5 (95% CI: −0.0732, 0.0158, p = 0.20) across all participants. An interquartile range increase in PM10 exposure (3.20 μg/m3/day) was associated with a −0.1472 standard deviation lower cumulative DNA methylation score for PM10 (95% CI: −0.3038, 0.0095, p = 0.06) across all participants. The PM10 findings were driven by the age 15 subset where an interquartile range increase in PM10 exposure was associated with a −0.024 standard deviation lower cumulative DNA methylation score for PM10 (95% CI: −0.043, −0.005, p = 0.012). Findings were robust to adjustment for PM exposure at ages 1 and 3. In utero PM10-associated DNA methylation differences were identified at age 15 in saliva. Benchmarking the timing and cell-type generalizability is critical for epigenetic exposure biomarker assessment.
Collapse
|