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Sullivan ADW, Merrill SM, Konwar C, Coccia M, Rivera L, MacIsaac JL, Lieberman AF, Kobor MS, Bush NR. Intervening After Trauma: Child-Parent Psychotherapy Treatment Is Associated With Lower Pediatric Epigenetic Age Acceleration. Psychol Sci 2024:9567976241260247. [PMID: 39141017 DOI: 10.1177/09567976241260247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024] Open
Abstract
Early-life adversity increases the risk of health problems. Interventions supporting protective and responsive caregiving offer a promising approach to attenuating adversity-induced changes in stress-sensitive biomarkers. This study tested whether participation in an evidence-based dyadic psychosocial intervention, child-parent psychotherapy (CPP), was related to lower epigenetic age acceleration, a trauma-sensitive biomarker of accelerated biological aging that is associated with later health impairment, in a sample of children with trauma histories. Within this quasi-experimental, repeated-measures study, we examined epigenetic age acceleration at baseline and postintervention in a low-income sample of children receiving CPP treatment (n = 45; age range = 2-6 years; 76% Latino) compared with a weighted, propensity-matched community-comparison sample (n = 110; age range = 3-6 years; 40% Latino). Baseline epigenetic age acceleration was equivalent across groups. However, posttreatment, epigenetic age acceleration in the treatment group was lower than in the matched community sample. Findings highlight the potential for a dyadic psychosocial intervention to ameliorate accelerated biological aging in trauma-exposed children.
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Affiliation(s)
- Alexandra D W Sullivan
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco
| | - Sarah M Merrill
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia
- Centre for Molecular Medicine and Therapeutics, Faculty of Medicine, University of British Columbia
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University
| | - Chaini Konwar
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia
- Centre for Molecular Medicine and Therapeutics, Faculty of Medicine, University of British Columbia
| | - Michael Coccia
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco
| | - Luisa Rivera
- Neukom Institute for Computational Science, Dartmouth College
| | - Julia L MacIsaac
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia
- Centre for Molecular Medicine and Therapeutics, Faculty of Medicine, University of British Columbia
| | - Alicia F Lieberman
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco
| | - Michael S Kobor
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia
- Centre for Molecular Medicine and Therapeutics, Faculty of Medicine, University of British Columbia
- Child and Brain Development Program, Canadian Institute for Advanced Research Institute, Toronto, Ontario, Canada
- Edwin S.H. Leong Centre for Healthy Aging, University of British Columbia
| | - Nicole R Bush
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco
- Department of Pediatrics, Division of Developmental Medicine, University of California, San Francisco
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England-Mason G, Merrill SM, Liu J, Martin JW, MacDonald AM, Kinniburgh DW, Gladish N, MacIsaac JL, Giesbrecht GF, Letourneau N, Kobor MS, Dewey D. Sex-Specific Associations between Prenatal Exposure to Bisphenols and Phthalates and Infant Epigenetic Age Acceleration. EPIGENOMES 2024; 8:31. [PMID: 39189257 PMCID: PMC11348373 DOI: 10.3390/epigenomes8030031] [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: 06/06/2024] [Revised: 07/19/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024] Open
Abstract
We examined whether prenatal exposure to two classes of endocrine-disrupting chemicals (EDCs) was associated with infant epigenetic age acceleration (EAA), a DNA methylation biomarker of aging. Participants included 224 maternal-infant pairs from a Canadian pregnancy cohort study. Two bisphenols and 12 phthalate metabolites were measured in maternal second trimester urines. Buccal epithelial cell cheek swabs were collected from 3 month old infants and DNA methylation was profiled using the Infinium MethylationEPIC BeadChip. The Pediatric-Buccal-Epigenetic tool was used to estimate EAA. Sex-stratified robust regressions examined individual chemical associations with EAA, and Bayesian kernel machine regression (BKMR) examined chemical mixture effects. Adjusted robust models showed that in female infants, prenatal exposure to total bisphenol A (BPA) was positively associated with EAA (B = 0.72, 95% CI: 0.21, 1.24), and multiple phthalate metabolites were inversely associated with EAA (Bs from -0.36 to -0.66, 95% CIs from -1.28 to -0.02). BKMR showed that prenatal BPA was the most important chemical in the mixture and was positively associated with EAA in both sexes. No overall chemical mixture effects or male-specific associations were noted. These findings indicate that prenatal EDC exposures are associated with sex-specific deviations in biological aging, which may have lasting implications for child health and development.
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Affiliation(s)
- Gillian England-Mason
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Owerko Centre, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sarah M. Merrill
- Department of Psychiatry and Human Behavior, The Warren Alpert Medical School at Brown University, Providence, RI 02903, USA
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V6H 0B3, Canada
| | - Jiaying Liu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Jonathan W. Martin
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, 114 19 Stockholm, Sweden
| | - Amy M. MacDonald
- Alberta Centre for Toxicology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - David W. Kinniburgh
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Alberta Centre for Toxicology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Nicole Gladish
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V6H 0B3, Canada
| | - Julia L. MacIsaac
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V6H 0B3, Canada
| | - Gerald F. Giesbrecht
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Owerko Centre, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Psychology, Faculty of Arts, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Nicole Letourneau
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Owerko Centre, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Faculty of Nursing, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Hotchkiss Brain Institute, Calgary, AB T2N 4N1, Canada
| | - Michael S. Kobor
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC V6H 0B3, Canada
- Program in Child and Brain Development, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
| | - Deborah Dewey
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Owerko Centre, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Hotchkiss Brain Institute, Calgary, AB T2N 4N1, Canada
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3
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Cuyvers B, Ein-Dor T, Houbrechts M, Freson K, Goossens L, Van Den Noortgate W, van Leeuwen K, Bijttebier P, Claes S, Turner J, Chubar V, Bakermans-Kranenburg MJ, Bosmans G. Exploring the role of OXTR gene methylation in attachment development: A longitudinal study. Dev Psychobiol 2024; 66:e22496. [PMID: 38689124 DOI: 10.1002/dev.22496] [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: 04/03/2023] [Revised: 03/26/2024] [Accepted: 04/07/2024] [Indexed: 05/02/2024]
Abstract
The current study explored longitudinally whether oxytocin receptor gene methylation (OXTRm) changes moderated the association between parental sensitivity changes and children's attachment changes over three waves. Six hundred six Flemish children (10-12 years, 42.8%-44.8% boys) completed attachment measures and provided salivary OXTRm data on seven CpG sites. Their parents reported their sensitive parenting. Results suggest that OXTRm changes hardly link to attachment (in)security changes after the age of 10. Some support was found for interaction effects between parental sensitivity changes and OXTRm changes on attachment changes over time. Effects suggest that for children with increased OXTRm in the promotor region and decreased methylation in the inhibitor region over time, increased parental sensitivity was associated with increased secure attachment and decreased insecure attachment over time.
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Affiliation(s)
- Bien Cuyvers
- Clinical Psychology, KU Leuven University, Leuven, Belgium
| | - Tsachi Ein-Dor
- Social Sciences, School of Psychology, Reichman University Herzliya, Herzliya, Israel
| | | | - Kathleen Freson
- Centre for Molecular and Vascular Biology, KU Leuven University, Leuven, Belgium
| | - Luc Goossens
- School Psychology and Development in Context, KU Leuven University, Leuven, Belgium
| | | | - Karla van Leeuwen
- Family and Educational Sciences, KU Leuven University, Leuven, Belgium
| | - Patricia Bijttebier
- School Psychology and Development in Context, KU Leuven University, Leuven, Belgium
| | - Stephan Claes
- Research Group Psychiatry, UZ Leuven-KU Leuven University, Leuven, Belgium
| | - Jonathan Turner
- Immune Endocrine Epigenetics Research Group, Luxembourg Institute of Health, Esch sur Alzette, Luxembourg, Luxembourg
| | - Viktoria Chubar
- Research Group Psychiatry, UZ Leuven-KU Leuven University, Leuven, Belgium
| | - Marian J Bakermans-Kranenburg
- William James Center for Research, ISPA University Institute of sychological, Social and Life Sciences, Lisbon, Portugal
- Centre for Attachment Research, the New School for Social Research, New York, USA
| | - Guy Bosmans
- Clinical Psychology, KU Leuven University, Leuven, Belgium
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Short AK, Weber R, Kamei N, Wilcox Thai C, Arora H, Mortazavi A, Stern HS, Glynn L, Baram TZ. Individual longitudinal changes in DNA-methylome identify signatures of early-life adversity and correlate with later outcome. Neurobiol Stress 2024; 31:100652. [PMID: 38962694 PMCID: PMC11219970 DOI: 10.1016/j.ynstr.2024.100652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/02/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Adverse early-life experiences (ELA) affect a majority of the world's children. Whereas the enduring impact of ELA on cognitive and emotional health is established, there are no tools to predict vulnerability to ELA consequences in an individual child. Epigenetic markers including peripheral-cell DNA-methylation profiles may encode ELA and provide predictive outcome markers, yet the interindividual variance of the human genome and rapid changes in DNA methylation in childhood pose significant challenges. Hoping to mitigate these challenges we examined the relation of several ELA dimensions to DNA methylation changes and outcome using a within-subject longitudinal design and a high methylation-change threshold. DNA methylation was analyzed in buccal swab/saliva samples collected twice (neonatally and at 12 months) in 110 infants. We identified CpGs differentially methylated across time for each child and determined whether they associated with ELA indicators and executive function at age 5. We assessed sex differences and derived a sex-dependent 'impact score' based on sites that most contributed to methylation changes. Changes in methylation between two samples of an individual child reflected age-related trends and correlated with executive function years later. Among tested ELA dimensions and life factors including income to needs ratios, maternal sensitivity, body mass index and infant sex, unpredictability of parental and household signals was the strongest predictor of executive function. In girls, high early-life unpredictability interacted with methylation changes to presage executive function. Thus, longitudinal, within-subject changes in methylation profiles may provide a signature of ELA and a potential predictive marker of individual outcome.
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Affiliation(s)
- Annabel K. Short
- Department of Anatomy and Neurobiology, ersity of California- Irvine, Irvine, CA, 92697, USA
- Departments of Pediatrics and Neurology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Ryan Weber
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Noriko Kamei
- Department of Anatomy and Neurobiology, ersity of California- Irvine, Irvine, CA, 92697, USA
| | - Christina Wilcox Thai
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Hina Arora
- Department of Statistics, University of California-Irvine, Irvine, CA, 92697, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Hal S. Stern
- Department of Statistics, University of California-Irvine, Irvine, CA, 92697, USA
| | - Laura Glynn
- Department of Psychology, Chapman University, Orange, CA, 92866, USA
| | - Tallie Z. Baram
- Department of Anatomy and Neurobiology, ersity of California- Irvine, Irvine, CA, 92697, USA
- Departments of Pediatrics and Neurology, University of California-Irvine, Irvine, CA, 92697, USA
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Yang M, Wang M, Zhao X, Xu F, Liang S, Wang Y, Wang N, Sambou ML, Jiang Y, Dai J. DNA methylation marker identification and poly-methylation risk score in prediction of healthspan termination. Epigenomics 2024; 16:461-472. [PMID: 38482663 DOI: 10.2217/epi-2023-0343] [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] [Indexed: 03/23/2024] Open
Abstract
Aim: To elucidate the epigenetic consequences of DNA methylation in healthspan termination (HST), considering the current limited understanding. Materials & methods: Genetically predicted DNA methylation models were established (n = 2478). These models were applied to genome-wide association study data on HST. Then, a poly-methylation risk score (PMRS) was established in 241,008 individuals from the UK Biobank. Results: Of the 63,046 CpGs from the prediction models, 13 novel CpGs were associated with HST. Furthermore, people with high PMRSs showed higher HST risk (hazard ratio: 1.18; 95% CI: 1.13-1.25). Conclusion: The study indicates that DNA methylation may influence HST by regulating the expression of genes (e.g., PRMT6, CTSK). PMRSs have a promising application in discriminating subpopulations to facilitate early prevention.
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Affiliation(s)
- Meiqi Yang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Mei Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xiaoyu Zhao
- Department of Statistics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Feifei Xu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Shuang Liang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yifan Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Nanxi Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Muhammed Lamin Sambou
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yue Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Collaborative Innovation Center for Cancer Personalized Medicine & China International Cooperation Center for Environment & Human Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Collaborative Innovation Center for Cancer Personalized Medicine & China International Cooperation Center for Environment & Human Health, Gusu School, Nanjing Medical University, Nanjing, 211166, China
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Zhang Z, Reynolds SR, Stolrow HG, Chen J, Christensen BC, Salas LA. Deciphering the role of immune cell composition in epigenetic age acceleration: Insights from cell-type deconvolution applied to human blood epigenetic clocks. Aging Cell 2024; 23:e14071. [PMID: 38146185 PMCID: PMC10928575 DOI: 10.1111/acel.14071] [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: 08/17/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/27/2023] Open
Abstract
Aging is a significant risk factor for various human disorders, and DNA methylation clocks have emerged as powerful tools for estimating biological age and predicting health-related outcomes. Methylation data from blood DNA has been a focus of more recently developed DNA methylation clocks. However, the impact of immune cell composition on epigenetic age acceleration (EAA) remains unclear as only some clocks incorporate partial cell type composition information when analyzing EAA. We investigated associations of 12 immune cell types measured by cell-type deconvolution with EAA predicted by six widely-used DNA methylation clocks in data from >10,000 blood samples. We observed significant associations of immune cell composition with EAA for all six clocks tested. Across the clocks, nine or more of the 12 cell types tested exhibited significant associations with EAA. Higher memory lymphocyte subtype proportions were associated with increased EAA, and naïve lymphocyte subtypes were associated with decreased EAA. To demonstrate the potential confounding of EAA by immune cell composition, we applied EAA in rheumatoid arthritis. Our research maps immune cell type contributions to EAA in human blood and offers opportunities to adjust for immune cell composition in EAA studies to a significantly more granular level. Understanding associations of EAA with immune profiles has implications for the interpretation of epigenetic age and its relevance in aging and disease research. Our detailed map of immune cell type contributions serves as a resource for studies utilizing epigenetic clocks across diverse research fields, including aging-related diseases, precision medicine, and therapeutic interventions.
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Affiliation(s)
- Ze Zhang
- Department of EpidemiologyGeisel School of Medicine at DartmouthLebanonNew HampshireUSA
- Dartmouth Cancer CenterDartmouth‐Hitchcock Medical CenterLebanonNew HampshireUSA
- Quantitative Biomedical Sciences ProgramGuarini School of Graduate and Advanced StudiesHanoverNew HampshireUSA
| | - Samuel R. Reynolds
- Department of EpidemiologyGeisel School of Medicine at DartmouthLebanonNew HampshireUSA
| | - Hannah G. Stolrow
- Department of EpidemiologyGeisel School of Medicine at DartmouthLebanonNew HampshireUSA
- Dartmouth Cancer CenterDartmouth‐Hitchcock Medical CenterLebanonNew HampshireUSA
| | - Ji‐Qing Chen
- Department of EpidemiologyGeisel School of Medicine at DartmouthLebanonNew HampshireUSA
- Molecular and Cellular Biology ProgramGuarini School of Graduate and Advanced StudiesHanoverNew HampshireUSA
| | - Brock C. Christensen
- Department of EpidemiologyGeisel School of Medicine at DartmouthLebanonNew HampshireUSA
- Dartmouth Cancer CenterDartmouth‐Hitchcock Medical CenterLebanonNew HampshireUSA
- Quantitative Biomedical Sciences ProgramGuarini School of Graduate and Advanced StudiesHanoverNew HampshireUSA
- Molecular and Cellular Biology ProgramGuarini School of Graduate and Advanced StudiesHanoverNew HampshireUSA
| | - Lucas A. Salas
- Department of EpidemiologyGeisel School of Medicine at DartmouthLebanonNew HampshireUSA
- Dartmouth Cancer CenterDartmouth‐Hitchcock Medical CenterLebanonNew HampshireUSA
- Quantitative Biomedical Sciences ProgramGuarini School of Graduate and Advanced StudiesHanoverNew HampshireUSA
- Molecular and Cellular Biology ProgramGuarini School of Graduate and Advanced StudiesHanoverNew HampshireUSA
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Rallis D, Papathanasiou AE, Christou H. Maternal Obesity Modulates Cord Blood Concentrations of Proprotein Convertase Subtilisin/Kexin-type 9 Levels. J Endocr Soc 2024; 8:bvae031. [PMID: 38440108 PMCID: PMC10910593 DOI: 10.1210/jendso/bvae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Indexed: 03/06/2024] Open
Abstract
Context In utero exposure to maternal obesity or diabetes is considered a pro-inflammatory state. Objective To evaluate whether cord blood proprotein convertase subtilisin/kexin-type 9 (PCSK9), which is regulated by inflammation and metabolic derangements, is elevated in neonates born to overweight, obese, or diabetic mothers. Methods A retrospective study in full-term neonates born between 2010 and 2023, at Brigham and Women's Hospital. There were 116 neonates included in our study, of which 74 (64%) were born to overweight/obese mothers and 42 (36%) were born to nonoverweight/nonobese mothers. Results Neonates born to overweight/obese mothers had significantly higher cord blood concentrations of PCSK9 compared with neonates born to nonoverweight/nonobese group (323 [253-442] ng/mL compared with 270 [244-382] ng/mL, P = .041). We found no significant difference in cord blood concentrations of PCSK9 between neonates of diabetic mothers compared with neonates of nondiabetic mothers. In multivariate linear regression analysis, higher cord plasma PCSK9 concentration was significantly associated with maternal overweight/obesity status (b = 50.12; 95% CI, 4.02-96.22; P = .033), after adjusting for gestational age, birth weight, male sex, and intrauterine growth restriction. Conclusion Neonates born to mothers with overweight/obesity have higher cord blood PCSK9 concentrations compared with the nonoverweight/nonobese group, and higher cord blood PCSK9 concentrations were significantly associated with maternal overweight/obesity status, after adjusting for perinatal factors. Larger longitudinal studies are needed to examine the role of PCSK9 in the development of metabolic syndrome in high-risk neonates born to overweight, obese, or diabetic mothers.
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Affiliation(s)
- Dimitrios Rallis
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Neonatal Intensive Care Unit, University of Ioannina, Faculty of Medicine, Ioannina 45110, Greece
| | | | - Helen Christou
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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8
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Refn MR, Andersen MM, Kampmann ML, Tfelt-Hansen J, Sørensen E, Larsen MH, Morling N, Børsting C, Pereira V. Longitudinal changes and variation in human DNA methylation analysed with the Illumina MethylationEPIC BeadChip assay and their implications on forensic age prediction. Sci Rep 2023; 13:21658. [PMID: 38066081 PMCID: PMC10709620 DOI: 10.1038/s41598-023-49064-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
DNA methylation, a pivotal epigenetic modification, plays a crucial role in regulating gene expression and is known to undergo dynamic changes with age. The present study investigated epigenome-wide methylation profiles in 64 individuals over two time points, 15 years apart, using the Illumina EPIC850k arrays. A mixed-effects model identified 2821 age-associated differentially methylated CpG positions (aDMPs) with a median rate of change of 0.18% per year, consistent with a 10-15% change during a human lifespan. Significant variation in the baseline DNA methylation levels between individuals of similar ages as well as inconsistent direction of change with time across individuals were observed for all the aDMPs. Twenty-three of the 2821 aDMPs were previously incorporated into forensic age prediction models. These markers displayed larger changes in DNA methylation with age compared to all the aDMPs and less variation among individuals. Nevertheless, the forensic aDMPs also showed inter-individual variations in the direction of DNA methylation changes. Only cg16867657 in ELOVL2 exhibited a uniform direction of the age-related change among the investigated individuals, which supports the current knowledge that CpG sites in ELOVL2 are the best markers for age prediction.
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Affiliation(s)
- Mie Rath Refn
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Mikkel Meyer Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- The Department of Mathematical Sciences, Aalborg University, 9220, Aalborg, Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Margit Hørup Larsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
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9
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Gorzkiewicz M, Łoś-Rycharska E, Gawryjołek J, Gołębiewski M, Krogulska A, Grzybowski T. The methylation profile of IL4, IL5, IL10, IFNG and FOXP3 associated with environmental exposures differed between Polish infants with the food allergy and/or atopic dermatitis and without the disease. Front Immunol 2023; 14:1209190. [PMID: 37520545 PMCID: PMC10373304 DOI: 10.3389/fimmu.2023.1209190] [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: 04/20/2023] [Accepted: 06/29/2023] [Indexed: 08/01/2023] Open
Abstract
Objectives Epigenetic dynamics has been indicated to play a role in allergy development. The environmental stimuli have been shown to influence the methylation processes. This study investigated the differences in CpGs methylation rate of immune-attached genes between healthy and allergic infants. The research was aimed at finding evidence for the impact of environmental factors on methylation-based regulation of immunological processes in early childhood. Methods The analysis of methylation level of CpGs in the IL4, IL5, IL10, IFNG and FOXP3 genes was performed using high resolution melt real time PCR technology. DNA was isolated from whole blood of Polish healthy and allergic infants, with food allergy and/or atopic dermatitis, aged under six months. Results The significantly lower methylation level of FOXP3 among allergic infants compared to healthy ones was reported. Additional differences in methylation rates were found, when combining with environmental factors. In different studied groups, negative correlations between age and the IL10 and FOXP3 methylation were detected, and positive - in the case of IL4. Among infants with different allergy symptoms, the decrease in methylation level of IFNG, IL10, IL4 and FOXP3 associated with passive smoke exposure was observed. Complications during pregnancy were linked to different pattern of the IFNG, IL5, IL4 and IL10 methylation depending on allergy status. The IFNG and IL5 methylation rates were higher among exclusively breastfed infants with atopic dermatitis compared to the non-breastfed. A decrease in the IFNG methylation was noted among allergic patients fed exclusively with milk formula. In different study groups, a negative correlation between IFNG, IL5 methylation and maternal BMI or IL5 methylation and weight was noted. Some positive correlations between methylation rate of IL10 and child's weight were found. A higher methylation of IL4 was positively correlated with the number of family members with allergy. Conclusion The FOXP3 methylation in allergic infants was lower than in the healthy ones. The methylation profile of IL4, IL5, IL10, IFNG and FOXP3 associated with environmental exposures differed between the studied groups. The results offer insights into epigenetic regulation of immunological response in early childhood.
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Affiliation(s)
- Marta Gorzkiewicz
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Ewa Łoś-Rycharska
- Department of Pediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Julia Gawryjołek
- Department of Pediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Marcin Gołębiewski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Aneta Krogulska
- Department of Pediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
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10
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Gao C, Amador C, Walker RM, Campbell A, Madden RA, Adams MJ, Bai X, Liu Y, Li M, Hayward C, Porteous DJ, Shen X, Evans KL, Haley CS, McIntosh AM, Navarro P, Zeng Y. Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans. Genome Biol 2023; 24:117. [PMID: 37189164 PMCID: PMC10184337 DOI: 10.1186/s13059-023-02953-6] [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: 10/05/2022] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND The variation in the rate at which humans age may be rooted in early events acting through the genomic regions that are influenced by such events and subsequently are related to health phenotypes in later life. The parent-of-origin-effect (POE)-regulated methylome includes regions enriched for genetically controlled imprinting effects (the typical type of POE) and regions influenced by environmental effects associated with parents (the atypical POE). This part of the methylome is heavily influenced by early events, making it a potential route connecting early exposures, the epigenome, and aging. We aim to test the association of POE-CpGs with early and later exposures and subsequently with health-related phenotypes and adult aging. RESULTS We perform a phenome-wide association analysis for the POE-influenced methylome using GS:SFHS (Ndiscovery = 5087, Nreplication = 4450). We identify and replicate 92 POE-CpG-phenotype associations. Most of the associations are contributed by the POE-CpGs belonging to the atypical class where the most strongly enriched associations are with aging (DNAmTL acceleration), intelligence, and parental (maternal) smoking exposure phenotypes. A proportion of the atypical POE-CpGs form co-methylation networks (modules) which are associated with these phenotypes, with one of the aging-associated modules displaying increased within-module methylation connectivity with age. The atypical POE-CpGs also display high levels of methylation heterogeneity, fast information loss with age, and a strong correlation with CpGs contained within epigenetic clocks. CONCLUSIONS These results identify the association between the atypical POE-influenced methylome and aging and provide new evidence for the "early development of origin" hypothesis for aging in humans.
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Affiliation(s)
- Chenhao Gao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Centre for Clinical Brain Sciences, Chancellor's Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- School of Psychology, University of Exeter, Perry Road, Exeter, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Xiaomeng Bai
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Ying Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xueyi Shen
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Chris S Haley
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - Yanni Zeng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
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11
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Levin G, Ein-Dor T. A unified model of the biology of peripartum depression. Transl Psychiatry 2023; 13:138. [PMID: 37117197 PMCID: PMC10147643 DOI: 10.1038/s41398-023-02439-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 04/30/2023] Open
Abstract
Peripartum depression (PPD) is a prevalent and debilitating disorder that adversely affects the development of mothers and infants. Recently, there has been a plea for increased mental health screening during the peripartum period; however, currently, there is no accurate screening tool to identify women at risk of PPD. In addition, some women do not respond to current treatment schemes and develop treatment-resistant depression. The current perspective aims to propose a unified understanding of the biological underpinnings of PPD (UmPPD) that considers the heterogeneity in the onset, symptoms cluster, and severity of PPD. Such a model could promote basic and applied research on PPD and suggest new treatment avenues. The central hub of the model is the kynurenine pathway (KP) and the KP-serotonin ratio. The forces and specific processes at play that cause an imbalance within the KP and between KP and serotonin are inflammation, stress, reproductive hormones (especially estradiol and progesterone), and oxytocin. UmPPD predicts that the most severe PPD would comprise prolonged inflammation, ongoing or multiple stressors, excessive estrogen, progesterone resistance, and avoidance of breastfeeding, skin-to-skin contact, and social proximity. These factors would be associated with a higher likelihood of developing PPD, early onset, and more significant symptom severity. In addition, subtypes of PPD would consist of different compositions and expressions of these components, with one central common factor. UmPPD could aid in directing future research and possibly detecting critical processes that could help discover, develop, and utilize novel treatments for PPD.
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Affiliation(s)
- Gal Levin
- Reichman University. Please address all correspondence to: Tsachi Ein-Dor, Baruch Ivcher School of Psychology, Reichman University, University St. 8, Herzliya, 4610101, Israel
| | - Tsachi Ein-Dor
- Reichman University. Please address all correspondence to: Tsachi Ein-Dor, Baruch Ivcher School of Psychology, Reichman University, University St. 8, Herzliya, 4610101, Israel.
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12
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Zhang Z, Stolrow HG, Christensen BC, Salas LA. Down Syndrome Altered Cell Composition in Blood, Brain, and Buccal Swab Samples Profiled by DNA-Methylation-Based Cell-Type Deconvolution. Cells 2023; 12:cells12081168. [PMID: 37190077 DOI: 10.3390/cells12081168] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Down syndrome (DS) is a genetic disorder caused by an extra copy of chromosome 21 that presents developmental dysfunction and intellectual disability. To better understand the cellular changes associated with DS, we investigated the cell composition in blood, brain, and buccal swab samples from DS patients and controls using DNA methylation-based cell-type deconvolution. We used genome-scale DNA methylation data from Illumina HumanMethylation450k and HumanMethylationEPIC arrays to profile cell composition and trace fetal lineage cells in blood samples (DS N = 46; control N = 1469), brain samples from various regions (DS N = 71; control N = 101), and buccal swab samples (DS N = 10; control N = 10). In early development, the number of cells from the fetal lineage in the blood is drastically lower in DS patients (Δ = 17.5%), indicating an epigenetically dysregulated maturation process for DS patients. Across sample types, we observed significant alterations in relative cell-type proportions for DS subjects compared with the controls. Cell-type proportion alterations were present in samples from early development and adulthood. Our findings provide insight into DS cellular biology and suggest potential cellular interventional targets for DS.
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Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Hannah G Stolrow
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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13
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Alba-Linares JJ, Pérez RF, Tejedor JR, Bastante-Rodríguez D, Ponce F, Carbonell NG, Zafra RG, Fernández AF, Fraga MF, Lurbe E. Maternal obesity and gestational diabetes reprogram the methylome of offspring beyond birth by inducing epigenetic signatures in metabolic and developmental pathways. Cardiovasc Diabetol 2023; 22:44. [PMID: 36870961 PMCID: PMC9985842 DOI: 10.1186/s12933-023-01774-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Obesity is a negative chronic metabolic health condition that represents an additional risk for the development of multiple pathologies. Epidemiological studies have shown how maternal obesity or gestational diabetes mellitus during pregnancy constitute serious risk factors in relation to the appearance of cardiometabolic diseases in the offspring. Furthermore, epigenetic remodelling may help explain the molecular mechanisms that underlie these epidemiological findings. Thus, in this study we explored the DNA methylation landscape of children born to mothers with obesity and gestational diabetes during their first year of life. METHODS We used Illumina Infinium MethylationEPIC BeadChip arrays to profile more than 770,000 genome-wide CpG sites in blood samples from a paediatric longitudinal cohort consisting of 26 children born to mothers who suffered from obesity or obesity with gestational diabetes mellitus during pregnancy and 13 healthy controls (measurements taken at 0, 6 and 12 month; total N = 90). We carried out cross-sectional and longitudinal analyses to derive DNA methylation alterations associated with developmental and pathology-related epigenomics. RESULTS We identified abundant DNA methylation changes during child development from birth to 6 months and, to a lesser extent, up to 12 months of age. Using cross-sectional analyses, we discovered DNA methylation biomarkers maintained across the first year of life that could discriminate children born to mothers who suffered from obesity or obesity with gestational diabetes. Importantly, enrichment analyses suggested that these alterations constitute epigenetic signatures that affect genes and pathways involved in the metabolism of fatty acids, postnatal developmental processes and mitochondrial bioenergetics, such as CPT1B, SLC38A4, SLC35F3 and FN3K. Finally, we observed evidence of an interaction between developmental DNA methylation changes and maternal metabolic condition alterations. CONCLUSIONS Our observations highlight the first six months of development as being the most crucial for epigenetic remodelling. Furthermore, our results support the existence of systemic intrauterine foetal programming linked to obesity and gestational diabetes that affects the childhood methylome beyond birth, which involves alterations related to metabolic pathways, and which may interact with ordinary postnatal development programmes.
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Affiliation(s)
- Juan José Alba-Linares
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Raúl F Pérez
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - David Bastante-Rodríguez
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Francisco Ponce
- Health Research Institute INCLIVA, Valencia, Spain
- Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Nuria García Carbonell
- Health Research Institute INCLIVA, Valencia, Spain
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Rafael Gómez Zafra
- Health Research Institute INCLIVA, Valencia, Spain
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Agustín F Fernández
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Mario F Fraga
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), University of Oviedo, Oviedo, Spain.
- Health Research Institute of Asturias (ISPA-FINBA), University of Oviedo, Oviedo, Spain.
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain.
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain.
| | - Empar Lurbe
- Health Research Institute INCLIVA, Valencia, Spain.
- Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III (ISCIII), Madrid, Spain.
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, Valencia, Spain.
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14
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Choi YJ, Cho J, Hong YC, Lee DW, Moon S, Park SJ, Lee KS, Shin CH, Lee YA, Kim BN, Kaminsky Z, Kim JI, Lim YH. DNA methylation is associated with prenatal exposure to sulfur dioxide and childhood attention-deficit hyperactivity disorder symptoms. Sci Rep 2023; 13:3501. [PMID: 36859453 PMCID: PMC9977725 DOI: 10.1038/s41598-023-29843-y] [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: 06/18/2022] [Accepted: 02/10/2023] [Indexed: 03/03/2023] Open
Abstract
Epigenetic influence plays a role in the association between exposure to air pollution and attention deficit hyperactivity disorder (ADHD); however, research regarding sulfur dioxide (SO2) is scarce. Herein, we investigate the associations between prenatal SO2 exposure and ADHD rating scale (ARS) at ages 4, 6 and 8 years repeatedly in a mother-child cohort (n = 329). Whole blood samples were obtained at ages 2 and 6 years, and genome-wide DNA methylation (DNAm) was analyzed for 51 children using the Illumina Infinium HumanMethylation BeadChip. We analyzed the associations between prenatal SO2 exposure and DNAm levels at ages 2 and 6, and further investigated the association between the DNAm and ARS at ages 4, 6 and 8. Prenatal SO2 exposure was associated with ADHD symptoms. From candidate gene analysis, DNAm levels at the 6 CpGs at age 2 were associated with prenatal SO2 exposure levels. Of the 6 CpGs, cg07583420 (INS-IGF2) was persistently linked with ARS at ages 4, 6 and 8. Epigenome-wide analysis showed that DNAm at 6733 CpG sites were associated with prenatal SO2 exposure, of which 58 CpGs involved in Notch signalling pathway were further associated with ARS at age 4, 6 and 8 years, persistently. DNAm at age 6 was not associated with prenatal SO2 exposure. Changes in DNAm levels associated with prenatal SO2 exposure during early childhood are associated with increases in ARS in later childhood.
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Affiliation(s)
- Yoon-Jung Choi
- National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jinwoo Cho
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea.,Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Dong-Wook Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea.,Public Healthcare Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sungji Moon
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soo Jin Park
- Department of Surgery, Wonkwang University Sanbon Hospital, Gunpo, Republic of Korea
| | - Kyung-Shin Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea.,Public Health Research Institute, National Medical Center, Seoul, Republic of Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Young Ah Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Bung-Nyun Kim
- Division of Children and Adolescent Psychiatry, Department of Psychiatry, Seoul National University Hospital, Seoul, Republic of Korea
| | - Zachary Kaminsky
- Institute of Mental Health Research, University of Ottawa, Ottawa, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Johanna Inhyang Kim
- Department of Psychiatry, Hanyang University Medical Center, 222-1 Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea.
| | - Youn-Hee Lim
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Section of Environmental Epidemiology, Department of Public Health, University of Copenhagen, Østerster Farimagsgade 5, 1014, København K, Copenhagen, Denmark.
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15
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Merrill SM, Gladish N, Fu MP, Moore SR, Konwar C, Giesbrecht GF, MacIssac JL, Kobor MS, Letourneau NL. Associations of peripheral blood DNA methylation and estimated monocyte proportion differences during infancy with toddler attachment style. Attach Hum Dev 2023; 25:132-161. [PMID: 34196256 DOI: 10.1080/14616734.2021.1938872] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Attachment is a motivational system promoting felt security to a caregiver resulting in a persistent internal working model of interpersonal behavior. Attachment styles are developed in early social environments and predict future health and development outcomes with potential biological signatures, such as epigenetic modifications like DNA methylation (DNAm). Thus, we hypothesized infant DNAm would associate with toddler attachment styles. An epigenome-wide association study (EWAS) of blood DNAm from 3-month-old infants was regressed onto children's attachment style from the Strange Situation Procedure at 22-months at multiple DNAm Cytosine-phosphate-Guanine (CpG) sites. The 26 identified CpGs associated with proinflammatory immune phenotypes and cognitive development. In post-hoc analyses, only maternal cognitive-growth fostering, encouraging intellectual exploration, contributed. For disorganized children, DNAm-derived cell-type proportions estimated higher monocytes -cells in immune responses hypothesized to increase with early adversity. Collectively, these findings suggested the potential biological embedding of both adverse and advantageous social environments as early as 3-months-old.
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Affiliation(s)
- Sarah M Merrill
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Nicole Gladish
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Maggie P Fu
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Sarah R Moore
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Chaini Konwar
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Gerald F Giesbrecht
- Department of Pediatrics, University of Calgary, Calgary, Canada.,Owerko Centre at the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Julia L MacIssac
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Michael S Kobor
- BC Children's Hospital Research Institute Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, Canada.,Program in Child and Brain Development, CIFAR, Toronto, Canada
| | - Nicole L Letourneau
- Department of Pediatrics, University of Calgary, Calgary, Canada.,Owerko Centre at the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada.,Department of Psychiatry, University of Calgary, Calgary, Canada.,Faculty of Nursing, University of Calgary, Calgary, Canada
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16
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Gao C, Amador C, Walker RM, Campbell A, Madden RA, Adams MJ, Bai X, Liu Y, Li M, Hayward C, Porteous DJ, Shen X, Evans KL, Haley CS, McIntosh AM, Navarro P, Zeng Y. Phenome-wide analysis identifies parent-of-origin effects on the human methylome associated with changes in the rate of aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524653. [PMID: 36711749 PMCID: PMC9882261 DOI: 10.1101/2023.01.18.524653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Variation in the rate at which humans age may be rooted in early life events acting through genomic regions that are influenced by such events and subsequently are related to health phenotypes in later life. The parent-of-origin-effect (POE)-regulated methylome includes regions either enriched for genetically controlled imprinting effects (the typical type of POE) or atypical POE introduced by environmental effects associated with parents. This part of the methylome is heavily influenced by early life events, making it a potential route connecting early environmental exposures, the epigenome and the rate of aging. Here, we aim to test the association of POE-influenced methylation of CpG dinucleotides (POE-CpG sites) with early and later environmental exposures and subsequently with health-related phenotypes and adult aging phenotypes. We do this by performing phenome-wide association analyses of the POE-influenced methylome using a large family-based population cohort (GS:SFHS, Ndiscovery=5,087, Nreplication=4,450). At the single CpG level, 92 associations of POE-CpGs with phenotypic variation were identified and replicated. Most of the associations were contributed by POE-CpGs belonging to the atypical class and the most strongly enriched associations were with aging (DNAmTL acceleration), intelligence and parental (maternal) smoking exposure phenotypes. We further found that a proportion of the atypical-POE-CpGs formed co-methylation networks (modules) which are associated with these phenotypes, with one of the aging-associated modules displaying increased internal module connectivity (strength of methylation correlation across constituent CpGs) with age. Atypical POE-CpGs also displayed high levels of methylation heterogeneity and epigenetic drift (i.e. information loss with age) and a strong correlation with CpGs contained within epigenetic clocks. These results identified associations between the atypical-POE-influenced methylome and aging and provided new evidence for the "early development of origin" hypothesis for aging in humans.
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Affiliation(s)
- Chenhao Gao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rosie M. Walker
- Centre for Clinical Brain Sciences, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- School of Psychology, University of Exeter, Perry Road, Exeter, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rebecca A Madden
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Mark J. Adams
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Xiaomeng Bai
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Ying Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xueyi Shen
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Chris S. Haley
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Andrew M. McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Yanni Zeng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
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Long-term impact of paediatric critical illness on the difference between epigenetic and chronological age in relation to physical growth. Clin Epigenetics 2023; 15:8. [PMID: 36639798 PMCID: PMC9840263 DOI: 10.1186/s13148-023-01424-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/07/2023] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Altered DNA-methylation affects biological ageing in adults and developmental processes in children. DNA-methylation is altered by environmental factors, trauma and illnesses. We hypothesised that paediatric critical illness, and the nutritional management in the paediatric intensive care unit (PICU), affects DNA-methylation changes that underly the developmental processes of childhood ageing. RESULTS We studied the impact of critical illness, and of the early use of parenteral nutrition (early-PN) versus late-PN, on "epigenetic age-deviation" in buccal mucosa of 818 former PICU-patients (406 early-PN, 412 late-PN) who participated in the 2-year follow-up of the multicentre PEPaNIC-RCT (ClinicalTrials.gov-NCT01536275), as compared with 392 matched healthy children, and assessed whether this relates to their impaired growth. The epigenetic age-deviation (difference between PedBE clock-estimated epigenetic age and chronological age) was calculated. Using bootstrapped multivariable linear regression models, we assessed the impact hereon of critical illness, and of early-PN versus late-PN. As compared with healthy children, epigenetic age of patients assessed 2 years after PICU-admission deviated negatively from chronological age (p < 0.05 in 51% of bootstrapped replicates), similarly in early-PN and late-PN groups. Next, we identified vulnerable subgroups for epigenetic age-deviation using interaction analysis. We revealed that DNA-methylation age-deceleration in former PICU-patients was dependent on age at time of illness (p < 0.05 for 83% of bootstrapped replicates), with vulnerability starting from 6 years onwards. Finally, we assessed whether vulnerability to epigenetic age-deviation could be related to impaired growth from PICU-admission to follow-up at 2 and 4 years. Multivariable repeated measures ANOVA showed that former PICU-patients, as compared with healthy children, grew less in height (p = 0.0002) and transiently gained weight (p = 0.0003) over the 4-year time course. Growth in height was more stunted in former PICU-patients aged ≥ 6-years at time of critical illness (p = 0.002) than in the younger patients. CONCLUSIONS As compared with healthy children, former PICU-patients, in particular those aged ≥ 6-years at time of illness, revealed epigenetic age-deceleration, with a physical correlate revealing stunted growth in height. Whether this vulnerability around the age of 6 years for epigenetic age-deceleration and stunted growth years later relates to altered endocrine pathways activated at the time of adrenarche requires further investigation.
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Caro JC, Holuka C, Menta G, Turner JD, Vögele C, D'Ambrosio C. Children's internalizing behavior development is heterogeneously associated with the pace of epigenetic aging. Biol Psychol 2023; 176:108463. [PMID: 36436681 DOI: 10.1016/j.biopsycho.2022.108463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Internalizing behaviors are an indicator of children's psychological and emotional development, predicting future mental disorders. Recent studies have identified associations between DNA methylation (DNAm) and internalizing behaviors. This prospective study aimed at exploring the associations between pace of biological aging and the developmental trajectories of internalizing behaviors. METHODS Participants were children from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort (N = 974). Measures of DNA methylation were collected at birth, age 7 and ages 15-17. The pace of aging was estimated using the DunedinPoAm algorithm (PoAm). Internalizing behaviors reported by caregivers between ages 4 and 16 using the Strengths and Difficulties Questionnaire. To explore heterogeneity in the association between PoAm and internalizing behaviors we use Poisson quantile regression in cross-section heterogeneity and longitudinal latent class analysis over the childhood and adolescence. RESULTS Internalizing behavior trajectories were identified: low-risk, childhood limited, late onset and early onset (persistent). Accelerated aging at birth was negatively associated with internalizing behaviors in early childhood but positively correlated during adolescence. Higher PoAm at birth increased chance of low-risk profile, while decreasing likelihood of childhood limited trajectory. PoAm at age 15 was negatively associated with childhood limited profile and positively linked to late onset trajectories. Associations were larger at higher values of internalizing symptoms. CONCLUSIONS The heterogeneity in the association between biological age acceleration and internalizing behaviors suggests a complex dynamic relationship, particularly in children with high or increased risk of adverse mental health outcomes.
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Affiliation(s)
- Juan Carlos Caro
- Department of Behavioral and Cognitive Sciences, University of Luxembourg, Luxembourg.
| | - Cyrielle Holuka
- Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg; Faculty of Sciences, University of Luxembourg, Luxembourg
| | - Giorgia Menta
- Luxembourg Institute of Socio-Economic Research (LISER), Luxembourg
| | - Jonathan D Turner
- Department of Infection and Immunity, Luxembourg Institute of Health, Luxembourg
| | - Claus Vögele
- Department of Behavioral and Cognitive Sciences, University of Luxembourg, Luxembourg
| | - Conchita D'Ambrosio
- Department of Behavioral and Cognitive Sciences, University of Luxembourg, Luxembourg
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Joustra V, Li Yim AYF, Hageman I, Levin E, Adams A, Satsangi J, de Jonge WJ, Henneman P, D'Haens G. Long-term Temporal Stability of Peripheral Blood DNA Methylation Profiles in Patients With Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol 2023; 15:869-885. [PMID: 36581079 PMCID: PMC9972576 DOI: 10.1016/j.jcmgh.2022.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS There is great current interest in the potential application of DNA methylation alterations in peripheral blood leukocytes (PBLs) as biomarkers of susceptibility, progression, and treatment response in inflammatory bowel disease (IBD). However, the intra-individual stability of PBL methylation in IBD has not been characterized. Here, we studied the long-term stability of all probes located on the Illumina HumanMethylation EPIC BeadChip array. METHODS We followed a cohort of 46 adult patients with IBD (36 Crohn's disease [CD], 10 ulcerative colitis [UC]; median age, 44 years; interquartile range [IQR] 27-56 years; 50% female) that received standard care follow-up at the Amsterdam University Medical Centers. Paired PBL samples were collected at 2 time points with a median of 7 years (range, 2-9 years) in between. Differential methylation and intra-class correlation (ICC) analyses were used to identify time-associated differences and temporally stable CpGs, respectively. RESULTS Around 60% of all EPIC array loci presented poor intra-individual stability (ICC <0.50); 78.114 (≈9%) showed good (ICC, 0.75-0.89), and 41.274 (≈5%) showed excellent (ICC ≥0.90) stability, between both measured time points. Focusing on previously identified consistently differentially methylated positions indicated that 22 CD-, 11 UC-, and 24 IBD-associated loci demonstrated high stability (ICC ≥0.75) over time; of these, we observed a marked stability of CpG loci associated to the HLA genes. CONCLUSIONS Our data provide insight into the long-term stability of the PBL DNA methylome within an IBD context, facilitating the selection of biologically relevant and robust IBD-associated epigenetic biomarkers with increased potential for independent validation. These data also have potential implications in understanding disease pathogenesis.
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Affiliation(s)
- Vincent Joustra
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Andrew Y F Li Yim
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Ishtu Hageman
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Evgeni Levin
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Horaizon BV, Delft, the Netherlands
| | - Alex Adams
- Oxford University- Hospitals NHS Foundation Trust- John Radcliffe Hospital, Translational Gastroenterology Unit- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Jack Satsangi
- Oxford University- Hospitals NHS Foundation Trust- John Radcliffe Hospital, Translational Gastroenterology Unit- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter Henneman
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Geert D'Haens
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
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20
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Childhood Trauma and Epigenetics: State of the Science and Future. Curr Environ Health Rep 2022; 9:661-672. [PMID: 36242743 DOI: 10.1007/s40572-022-00381-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW There is a great deal of interest regarding the biological embedding of childhood trauma and social exposures through epigenetic mechanisms, including DNA methylation (DNAm), but a comprehensive understanding has been hindered by issues of limited reproducibility between studies. This review presents a summary of the literature on childhood trauma and DNAm, highlights issues in the field, and proposes some potential solutions. RECENT FINDINGS Investigations of the associations between DNAm and childhood trauma are commonly performed using candidate gene approaches, specifically involving genes related to neurological and stress pathways. Childhood trauma is defined in a wide range of ways in several societal contexts. However, although variations in DNAm are frequently found in stress-related genes, unsupervised epigenome-wide association studies (EWAS) have shown limited reproducibility both between studies and in relating these changes to exposures. The reproducibility of childhood trauma DNAm studies, and the field of social epigenetics in general, may be improved by increasing sample sizes, standardizing variables, making use of effect size thresholds, collecting longitudinal and intervention samples, appropriately accounting for known confounding factors, and applying causal analysis wherever possible, such as "two-step epigenetic Mendelian randomization."
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21
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An evaluation of aging measures: from biomarkers to clocks. Biogerontology 2022; 24:303-328. [PMID: 36418661 DOI: 10.1007/s10522-022-09997-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2022]
Abstract
With the increasing number of aged population and growing burden of healthy aging demands, a rational standard for evaluation aging is in urgent need. The advancement of medical testing technology and the prospering of artificial intelligence make it possible to evaluate the biological status of aging from a more comprehensive view. In this review, we introduced common aging biomarkers and concluded several famous aging clocks. Aging biomarkers reflect changes in the organism at a molecular or cellular level over time while aging clocks tend to be more of a generalization of the overall state of the organism. We expect to construct a framework for aging evaluation measurement from both micro and macro perspectives. Especially, population-specific aging clocks and multi-omics aging clocks may better fit the demands to evaluate aging in a comprehensive and multidimensional manner and make a detailed classification to represent different aging rates at tissue/organ levels. This framework will promisingly provide a crucial basis for disease diagnosis and intervention assessment in geroscience.
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22
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England-Mason G, Merrill SM, Gladish N, Moore SR, Giesbrecht GF, Letourneau N, MacIsaac JL, MacDonald AM, Kinniburgh DW, Ponsonby AL, Saffery R, Martin JW, Kobor MS, Dewey D. Prenatal exposure to phthalates and peripheral blood and buccal epithelial DNA methylation in infants: An epigenome-wide association study. ENVIRONMENT INTERNATIONAL 2022; 163:107183. [PMID: 35325772 DOI: 10.1016/j.envint.2022.107183] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Prenatal exposure to phthalates has been associated with adverse health and neurodevelopmental outcomes. DNA methylation (DNAm) alterations may be a mechanism underlying these effects, but prior investigations of prenatal exposure to phthalates and neonatal DNAm profiles are limited to placental tissue and umbilical cord blood. OBJECTIVE Conduct an epigenome-wide association study (EWAS) of the associations between prenatal exposure to phthalates and DNAm in two accessible infant tissues, venous buffy coat blood and buccal epithelial cells (BECs). METHODS Participants included 152 maternal-infant pairs from the Alberta Pregnancy Outcomes and Nutrition (APrON) study. Maternal second trimester urine samples were analyzed for nine phthalate metabolites. Blood (n = 74) or BECs (n = 78) were collected from 3-month-old infants and profiled for DNAm using the Infinium HumanMethylation450 (450K) BeadChip. Robust linear regressions were used to investigate the associations between high (HMWPs) and low molecular weight phthalates (LMWPs) and change in methylation levels at variable Cytosine-phosphate-Guanine (CpG) sites in infant tissues, as well as the sensitivity of associations to potential confounders. RESULTS One candidate CpG in gene RNF39 reported by a previous study examining prenatal exposure to phthalates and cord blood DNAm was replicated. The EWAS identified 12 high-confidence CpGs in blood and another 12 in BECs associated with HMWPs and/or LMWPs. Prenatal exposure to bisphenol A (BPA) associated with two of the CpGs associated with HMWPs in BECs. DISCUSSION Prenatal exposure to phthalates was associated with DNAm variation at CpGs annotated to genes associated with endocrine hormone activity (i.e., SLCO4A1, TPO), immune pathways and DNA damage (i.e., RASGEF1B, KAZN, HLA-A, MYO18A, DIP2C, C1or109), and neurodevelopment (i.e., AMPH, NOTCH3, DNAJC5). Future studies that characterize the stability of these associations in larger samples, multiple cohorts, across tissues, and investigate the potential associations between these biomarkers and relevant health and neurodevelopmental outcomes are needed.
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Affiliation(s)
- Gillian England-Mason
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Sarah M Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Nicole Gladish
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Sarah R Moore
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Gerald F Giesbrecht
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Psychology, Faculty of Arts, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nicole Letourneau
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Faculty of Nursing, University of Calgary, Calgary, Alberta, Canada; Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Hotchkiss Brain Institute, Calgary, Alberta, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Amy M MacDonald
- Alberta Centre for Toxicology, University of Calgary, Calgary, Alberta, Canada
| | - David W Kinniburgh
- Alberta Centre for Toxicology, University of Calgary, Calgary, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Anne-Louise Ponsonby
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan W Martin
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Södermanland, Sweden
| | - Michael S Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; Program in Child and Brain Development, CIFAR, Toronto, Ontario, Canada
| | - Deborah Dewey
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Hotchkiss Brain Institute, Calgary, Alberta, Canada.
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Campagna MP, Xavier A, Lechner-Scott J, Maltby V, Scott RJ, Butzkueven H, Jokubaitis VG, Lea RA. Epigenome-wide association studies: current knowledge, strategies and recommendations. Clin Epigenetics 2021; 13:214. [PMID: 34863305 PMCID: PMC8645110 DOI: 10.1186/s13148-021-01200-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023] Open
Abstract
The aetiology and pathophysiology of complex diseases are driven by the interaction between genetic and environmental factors. The variability in risk and outcomes in these diseases are incompletely explained by genetics or environmental risk factors individually. Therefore, researchers are now exploring the epigenome, a biological interface at which genetics and the environment can interact. There is a growing body of evidence supporting the role of epigenetic mechanisms in complex disease pathophysiology. Epigenome-wide association studies (EWASes) investigate the association between a phenotype and epigenetic variants, most commonly DNA methylation. The decreasing cost of measuring epigenome-wide methylation and the increasing accessibility of bioinformatic pipelines have contributed to the rise in EWASes published in recent years. Here, we review the current literature on these EWASes and provide further recommendations and strategies for successfully conducting them. We have constrained our review to studies using methylation data as this is the most studied epigenetic mechanism; microarray-based data as whole-genome bisulphite sequencing remains prohibitively expensive for most laboratories; and blood-based studies due to the non-invasiveness of peripheral blood collection and availability of archived DNA, as well as the accessibility of publicly available blood-cell-based methylation data. Further, we address multiple novel areas of EWAS analysis that have not been covered in previous reviews: (1) longitudinal study designs, (2) the chip analysis methylation pipeline (ChAMP), (3) differentially methylated region (DMR) identification paradigms, (4) methylation quantitative trait loci (methQTL) analysis, (5) methylation age analysis and (6) identifying cell-specific differential methylation from mixed cell data using statistical deconvolution.
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Affiliation(s)
- Maria Pia Campagna
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Alexandre Xavier
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Jeannette Lechner-Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Department of Neurology, Division of Medicine, John Hunter Hospital, Newcastle, Australia
| | - Vicky Maltby
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Rodney J Scott
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Division of Molecular Medicine, New South Wales Health Pathology North, Newcastle, Australia
| | - Helmut Butzkueven
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Vilija G Jokubaitis
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Rodney A Lea
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia.
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
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Kim JI, Lee J, Lee KS, Lee YA, Shin CH, Hong YC, Kim BN, Lim YH. Association of phthalate exposure with autistic traits in children. ENVIRONMENT INTERNATIONAL 2021; 157:106775. [PMID: 34314979 DOI: 10.1016/j.envint.2021.106775] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Phthalates are synthetic chemicals with endocrine-disrupting properties. They are reportedly associated with various neurotoxic outcomes. Studies on exposure to phthalates and children's autistic traits have shown inconsistent results with respect to sex and susceptible time periods. We investigated the association of phthalate exposure during the prenatal period and childhood with autistic traits over time using a birth cohort in South Korea. METHODS Five phthalate metabolites were measured during mid-term pregnancy and children's follow-up at ages of 4, 6, and 8 years among a total of 547 mother-child pairs. The social communication questionnaire (SCQ) was used to assess autistic traits of children at each time point. The relationship between phthalate metabolites and SCQ scores were analyzed by exposure windows and sex. RESULTS A 2.7 fold increase in di-(2-ethylhexyl) phthalate metabolite levels, mono-(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP) and mono-(2-ethyl-5-oxohexyl) phthalate (MEOHP) during pregnancy was associated with increased SCQ scores at 4 years by 8.5% (95% confidence intervals [CI]: 1.9%, 15.5%) and 7.4% (95% CI: 0.3%, 15.0%), respectively, but not at the age of 6 or 8 years. Moreover, MEHHP levels at ages of 4 and 8 years were associated with increased SCQ scores at 8 years by 9.9% (95% CI: 1.8%, 18.6%) and 9.6% (95% CI: 1.3%, 18.6%), respectively. Boys showed stronger associations between phthalate exposure and SCQ scores than girls. CONCLUSION The study suggested different susceptible time windows of phthalate exposure: exposure during pregnancy is associated with autistic traits in young children, whereas exposure during early childhood years leads to autistic traits in school-aged children, particularly boys.
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Affiliation(s)
- Johanna Inhyang Kim
- Department of Psychiatry, Hanyang University Medical Center, Seoul, Republic of Korea
| | - Jung Lee
- Integrative Care Hub, Children's Hospital, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kyung-Shin Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Ah Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea; Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, South Korea
| | - Bung-Nyun Kim
- Division of Children and Adolescent Psychiatry, Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Youn-Hee Lim
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Section of Environmental Health, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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The effect of season of birth on brain epigenome-wide DNA methylation of older adults. J Dev Orig Health Dis 2021; 13:367-377. [PMID: 34308828 DOI: 10.1017/s2040174421000453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Perinatal light exposure predisposes towards health and behaviour in adulthood. Season of birth is associated with psychiatric, allergic, cardiovascular and metabolic problems. It has been proposed that early-life environmental light disrupts the development of biological rhythms which, in turn, influence later-life health. However, the mechanisms linking perinatal seasonal light to later-life biological rhythm and health in humans are unknown. In this study, we investigated the association between season of birth and epigenome-wide DNA methylation of two postmortem human brain regions (16 hypothalamus, 14 temporal cortex). We did not find statistically significant differences at the whole epigenome level, either because we lacked statistical power or that no association exists. However, when we examined 24 CpG sites that had the highest significance or differential methylation, we identified regions which may be associated with circadian rhythm entrainment, cholinergic neurotransmission and neural development. Amongst methylation of the core clock genes, we identified that hypothalamus Neuronal PAS Domain Protein 2 (NPAS2) gene has hypermethylated regions in long photoperiod-born individuals. In addition, we found nominal associations between season of birth and genes linked to chronotype and narcolepsy. Season of birth-related brain DNA methylation profile was different than a previously reported blood methylation profile, suggesting a tissue-specific mechanism of perinatal light programming. Overall, we are the first to analyse the relationship between season of birth and human brain DNA methylation. Further studies with larger sample sizes are required to confirm an imprinting effect of perinatal light on the circadian clock.
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McKennan C, Naughton K, Stanhope C, Kattan M, O’Connor GT, Sandel MT, Visness CM, Wood RA, Bacharier LB, Beigelman A, Lovinsky-Desir S, Togias A, Gern JE, Nicolae D, Ober C. Longitudinal data reveal strong genetic and weak non-genetic components of ethnicity-dependent blood DNA methylation levels. Epigenetics 2021; 16:662-676. [PMID: 32997571 PMCID: PMC8143220 DOI: 10.1080/15592294.2020.1817290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/06/2020] [Accepted: 07/24/2020] [Indexed: 11/18/2022] Open
Abstract
Epigenetic architecture is influenced by genetic and environmental factors, but little is known about their relative contributions or longitudinal dynamics. Here, we studied DNA methylation (DNAm) at over 750,000 CpG sites in mononuclear blood cells collected at birth and age 7 from 196 children of primarily self-reported Black and Hispanic ethnicities to study race-associated DNAm patterns. We developed a novel Bayesian method for high-dimensional longitudinal data and showed that race-associated DNAm patterns at birth and age 7 are nearly identical. Additionally, we estimated that up to 51% of all self-reported race-associated CpGs had race-dependent DNAm levels that were mediated through local genotype and, quite surprisingly, found that genetic factors explained an overwhelming majority of the variation in DNAm levels at other, previously identified, environmentally-associated CpGs. These results indicate that race-associated blood DNAm patterns in particular, and blood DNAm levels in general, are primarily driven by genetic factors, and are not as sensitive to environmental exposures as previously suggested, at least during the first 7 years of life.
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Affiliation(s)
- Chris McKennan
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Meyer Kattan
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - George T. O’Connor
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Megan T. Sandel
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Robert A. Wood
- Department of Pediatrics, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Leonard B. Bacharier
- Department of Pediatrics, Washington University School of Medicine and St Louis Children’s Hospital, St. Louis, MO, USA
| | - Avraham Beigelman
- Department of Pediatrics, Washington University School of Medicine and St Louis Children’s Hospital, St. Louis, MO, USA
| | | | - Alkis Togias
- National Institute of Allergy and Infectious Disease, Bethesda, MD, USA
| | - James E. Gern
- Departments of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Dan Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Department of Statistics, University of Chicago, Chicago, IL, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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28
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The regulation mechanisms and the Lamarckian inheritance property of DNA methylation in animals. Mamm Genome 2021; 32:135-152. [PMID: 33860357 DOI: 10.1007/s00335-021-09870-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/05/2021] [Indexed: 12/19/2022]
Abstract
DNA methylation is a stable and heritable epigenetic mechanism, of which the main functions are stabilizing the transcription of genes and promoting genetic conservation. In animals, the direct molecular inducers of DNA methylation mainly include histone covalent modification and non-coding RNA, whereas the fundamental regulators of DNA methylation are genetic and environmental factors. As is well known, competition is present everywhere in life systems, and will finally strike a balance that is optimal for the animal's survival and reproduction. The same goes for the regulation of DNA methylation. Genetic and environmental factors, respectively, are responsible for the programmed and plasticity changes of DNA methylation, and keen competition exists between genetically influenced procedural remodeling and environmentally influenced plastic alteration. In this process, genetic and environmental factors collaboratively decide the methylation patterns of corresponding loci. DNA methylation alterations induced by environmental factors can be transgenerationally inherited, and exhibit the characteristic of Lamarckian inheritance. Further research on regulatory mechanisms and the environmental plasticity of DNA methylation will provide strong support for understanding the biological function and evolutionary effects of DNA methylation.
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Planterose Jiménez B, Liu F, Caliebe A, Montiel González D, Bell JT, Kayser M, Vidaki A. Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarity. Genome Biol 2021; 22:18. [PMID: 33402197 PMCID: PMC7786996 DOI: 10.1186/s13059-020-02223-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/07/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Although the genomes of monozygotic twins are practically identical, their methylomes may evolve divergently throughout their lifetime as a consequence of factors such as the environment or aging. Particularly for young and healthy monozygotic twins, DNA methylation divergence, if any, may be restricted to stochastic processes occurring post-twinning during embryonic development and early life. However, to what extent such stochastic mechanisms can systematically provide a stable source of inter-individual epigenetic variation remains uncertain until now. RESULTS We enriched for inter-individual stochastic variation by using an equivalence testing-based statistical approach on whole blood methylation microarray data from healthy adolescent monozygotic twins. As a result, we identified 333 CpGs displaying similarly large methylation variation between monozygotic co-twins and unrelated individuals. Although their methylation variation surpasses measurement error and is stable in a short timescale, susceptibility to aging is apparent in the long term. Additionally, 46% of these CpGs were replicated in adipose tissue. The identified sites are significantly enriched at the clustered protocadherin loci, known for stochastic methylation in developing neurons. We also confirmed an enrichment in monozygotic twin DNA methylation discordance at these loci in whole genome bisulfite sequencing data from blood and adipose tissue. CONCLUSIONS We have isolated a component of stochastic methylation variation, distinct from genetic influence, measurement error, and epigenetic drift. Biomarkers enriched in this component may serve in the future as the basis for universal epigenetic fingerprinting, relevant for instance in the discrimination of monozygotic twin individuals in forensic applications, currently impossible with standard DNA profiling.
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Affiliation(s)
- Benjamin Planterose Jiménez
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
- University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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F C Lopes A. Mitochondrial metabolism and DNA methylation: a review of the interaction between two genomes. Clin Epigenetics 2020; 12:182. [PMID: 33228792 PMCID: PMC7684747 DOI: 10.1186/s13148-020-00976-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are controlled by the coordination of two genomes: the mitochondrial and the nuclear DNA. As such, variations in nuclear gene expression as a consequence of mutations and epigenetic modifications can affect mitochondrial functionality. Conversely, the opposite could also be true. However, the relationship between mitochondrial dysfunction and epigenetics, such as nuclear DNA methylation, remains largely unexplored.
Mitochondria function as central metabolic hubs controlling some of the main substrates involved in nuclear DNA methylation, via the one carbon metabolism, the tricarboxylic acid cycle and the methionine pathway. Here, we review key findings and highlight new areas of focus, with the ultimate goal of getting one step closer to understanding the genomic effects of mitochondrial dysfunction on nuclear epigenetic landscapes.
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Affiliation(s)
- Amanda F C Lopes
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK. .,Medical Research Council - Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
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31
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Kling T, Wenger A, Carén H. DNA methylation-based age estimation in pediatric healthy tissues and brain tumors. Aging (Albany NY) 2020; 12:21037-21056. [PMID: 33168783 PMCID: PMC7695434 DOI: 10.18632/aging.202145] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/03/2020] [Indexed: 12/20/2022]
Abstract
Several DNA methylation clocks have been developed to reflect chronological age of human tissues, but most clocks have been trained on adult samples. The rapid methylome changes in children and the role of epigenetics in pediatric tumors calls for tools accurately estimating methylation age in children. We aimed to evaluate seven methylation clocks in multiple tissues from healthy children to inform future studies on the optimal clock for pediatric cohorts, and analyzed the methylation age in brain tumors. We found that clocks trained on pediatric samples were the best in all tested tissues, highlighting the need for dedicated clocks. For blood samples, the Skin and blood clock had the best correlation with chronological age, while PedBE was the most accurate for saliva and buccal samples, and Horvath for brain tissue. Horvath methylation age was accelerated in pediatric brain tumors and the acceleration was subtype-specific for atypical teratoid rhabdoid tumor (ATRT), ependymoma, medulloblastoma and glioma. The subtypes with the highest acceleration corresponded to the worst prognostic categories in ATRT, ependymoma and glioma, whereas the relationship was reversed in medulloblastoma. This suggests that methylation age has potential as a prognostic biomarker in pediatric brain tumors and should be further explored.
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Affiliation(s)
- Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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32
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Kraan CM, Baker EK, Arpone M, Bui M, Ling L, Gamage D, Bretherton L, Rogers C, Field MJ, Wotton TL, Francis D, Hunter MF, Cohen J, Amor DJ, Godler DE. DNA Methylation at Birth Predicts Intellectual Functioning and Autism Features in Children with Fragile X Syndrome. Int J Mol Sci 2020; 21:ijms21207735. [PMID: 33086711 PMCID: PMC7589848 DOI: 10.3390/ijms21207735] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Fragile X syndrome (FXS) is a leading single-gene cause of intellectual disability (ID) with autism features. This study analysed diagnostic and prognostic utility of the Fragile X-Related Epigenetic Element 2 DNA methylation (FREE2m) assessed by Methylation Specific-Quantitative Melt Analysis and the EpiTYPER system, in retrospectively retrieved newborn blood spots (NBS) and newly created dried blood spots (DBS) from 65 children with FXS (~2–17 years). A further 168 NBS from infants from the general population were used to establish control reference ranges, in both sexes. FREE2m analysis showed sensitivity and specificity approaching 100%. In FXS males, NBS FREE2m strongly correlated with intellectual functioning and autism features, however associations were not as strong for FXS females. Fragile X mental retardation 1 gene (FMR1) mRNA levels in blood were correlated with FREE2m in both NBS and DBS, for both sexes. In females, DNAm was significantly increased at birth with a decrease in childhood. The findings support the use of FREE2m analysis in newborns for screening, diagnostic and prognostic testing in FXS.
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Affiliation(s)
- Claudine M Kraan
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
| | - Emma K Baker
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
- School of Psychology and Public Health, La Trobe University, Bundoora VIC 3086, Australia
| | - Marta Arpone
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
- Brain and Mind, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville VIC 3052, Australia
| | - Minh Bui
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne VIC 3052, Australia;
| | - Ling Ling
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
| | - Dinusha Gamage
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
| | - Lesley Bretherton
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
| | - Carolyn Rogers
- Genetics of Learning Disability Service (GOLD service), Hunter Genetics, Newcastle NSW 2298, Australia; (C.R.); (M.J.F.)
| | - Michael J Field
- Genetics of Learning Disability Service (GOLD service), Hunter Genetics, Newcastle NSW 2298, Australia; (C.R.); (M.J.F.)
| | - Tiffany L Wotton
- New South Wales Newborn Screening Program, Children’s Hospital at Westmead, Sydney NSW 2145, Australia;
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia;
| | - Matt F Hunter
- Monash Genetics, Monash Health, Clayton, VIC 3168, Australia;
| | - Jonathan Cohen
- Centre for Developmental Disability Health Victoria, Monash University, Doveton VIC 3177, Australia;
- Fragile X Alliance Inc., North Caulfield VIC 3161, Australia
| | - David J Amor
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
| | - David E Godler
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne VIC 3052, Australia; (C.M.K.); (E.K.B.); (M.A.); (L.L.); (D.G.); (L.B.); (D.J.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville VIC 3052, Australia
- Correspondence: ; Tel.: +613-8341-6496
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Møller Johansen L, Gerra MC, Arendt-Nielsen L. Time course of DNA methylation in pain conditions: From experimental models to humans. Eur J Pain 2020; 25:296-312. [PMID: 33063322 DOI: 10.1002/ejp.1674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND OBJECTIVE Throughout the last decade, research has uncovered associations between pain and epigenetic alterations caused by environmental factors. Specifically, studies have demonstrated correlations between pain conditions and altered DNA methylation patterns. Thus, DNA methylation has been revealed as a possible modulator or contributor to pain conditions, providing a potential therapeutic target for treatment by DNA methylation modification. To develop such treatments, it is necessary to clarify a wide number of aspects on how DNA methylation affects pain perception; first and foremost, the temporal dynamics. The objective of the present review is to provide an overview of current knowledge on temporal dynamics of DNA methylation in response to pain, and to investigate if a timeframe can be established based on the data of currently published studies. DATABASES AND DATA TREATMENT PubMed, MEDLINE, Google Scholar and Embase were searched comprehensively for studies of DNA methylation in neuropathic, inflammatory and alternative animal pain models, and in chronic pain patients including Complex Regional Pain Syndrome, chronic postsurgical pain, chronic widespread pain, fibromyalgia and Crohn's disease. RESULTS We identified 34 articles highlighting variations in temporal dynamics of DNA methylation across species and between different types of pain. These studies represent a starting point to uncover new insights in the DNA methylation time course in pain. CONCLUSIONS No timeframe can currently be made for the DNA methylation response to pain in any of the reviewed conditions, highlighting an important focus area for future research.
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Affiliation(s)
- Lonnie Møller Johansen
- Department of Health Science and Technology, The Faculty of Medicine, Aalborg University, Aalborg, Denmark
| | - Maria Carla Gerra
- Center for Neuroplasticity and Pain (CNAP), SMI®, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Lars Arendt-Nielsen
- Center for Neuroplasticity and Pain (CNAP), SMI®, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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Choi YJ, Lee YA, Hong YC, Cho J, Lee KS, Shin CH, Kim BN, Kim JI, Park SJ, Bisgaard H, Bønnelykke K, Lim YH. Effect of prenatal bisphenol A exposure on early childhood body mass index through epigenetic influence on the insulin-like growth factor 2 receptor (IGF2R) gene. ENVIRONMENT INTERNATIONAL 2020; 143:105929. [PMID: 32645488 DOI: 10.1016/j.envint.2020.105929] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVES Epigenetic mechanisms have been suggested to play a role in the link between in utero exposure to bisphenol A (BPA) and pediatric obesity; however, there is little evidence regarding this mechanism in humans. We obtained data on obesity-associated CpG sites from a previous epigenome-wide association study, and then examined whether methylation at those CpG sites was influenced by prenatal BPA exposure. We then evaluated the relationship between CpG methylation status and body mass index (BMI) in a prospective children's cohort at ages 2, 4, 6, and 8 years. METHODS Methylation profiles of 59 children were longitudinally analyzed at ages 2 and 6 years using the Infinium Human Methylation BeadChip. A total of 594 CpG sites known to be BMI or obesity-associated sites were tested for an association with prenatal BPA levels, categorized into low and high exposure groups based on the 80th percentile of maternal BPA levels (2.68 μg/g creatinine), followed by an analysis of the association between DNA methylation and BMI from ages 2-8. RESULTS There was a significant increase in the methylation levels of cg19196862 (IGF2R) in the high BPA group at age 2 years (p = 0.00030, false discovery rate corrected p < 0.10) but not at age 6. With one standard deviation increase of methylation at cg19196862 (IGF2R) at age 2 years, the linear mixed model analysis revealed that BMI during ages 2-8 years significantly increased by 0.49 (95% confidence interval; 0.08, 0.90) in girls, but not in boys. The indirect effect of prenatal BPA exposure on early childhood BMI through methylation at cg19196862 (IGF2R) at age 2 years was marginally significant. CONCLUSIONS Prenatal exposure to BPA may influence differential methylation of IGF2R at age 2. This result indicates that a possible sensitive period of DNA methylation occurs earlier during development, which may affect BMI until later childhood in a sex-specific manner.
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Affiliation(s)
- Yoon-Jung Choi
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Environmental Health Center, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Young Ah Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Environmental Health Center, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
| | - Jinwoo Cho
- Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
| | - Kyung-Shin Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Environmental Health Center, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Bung-Nyun Kim
- Division of Children and Adolescent Psychiatry, Department of Psychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Johanna Inhyang Kim
- Department of Psychiatry, Hanyang University Medical Center, Seoul 04763, Republic of Korea
| | - Soo Jin Park
- Department of Surgery, Wonkwang University Sanbon Hospital, Gunpo 15865, Republic of Korea
| | - Hans Bisgaard
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, 2820, Gentofte, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, 2820, Gentofte, Copenhagen, Denmark
| | - Youn-Hee Lim
- Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea; Section of Environmental Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen 1014, Denmark.
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Stonawski V, Roetner J, Goecke TW, Fasching PA, Beckmann MW, Kornhuber J, Kratz O, Moll GH, Eichler A, Heinrich H, Frey S. Genome-Wide DNA Methylation Patterns in Children Exposed to Nonpharmacologically Treated Prenatal Depressive Symptoms: Results From 2 Independent Cohorts. Epigenet Insights 2020; 13:2516865720932146. [PMID: 32596638 PMCID: PMC7298426 DOI: 10.1177/2516865720932146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/01/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Maternal depressive symptoms are a common phenomenon during pregnancy and are related to negative outcomes for child development and health. Modifications in child DNA methylation are discussed as an underlying mechanism for the association between prenatal depressive symptoms and alterations in child outcomes. However, formerly reported genome-wide associations have yet to be replicated. METHODS In an epigenome-wide association study (EWAS), alterations of DNA methylation related to maternal prenatal depressive symptoms were investigated in buccal cell samples from 174 children (n = 52 exposed to prenatal depressive symptoms; 6-9 years old) of the German longitudinal study FRAMES-FRANCES. Whole blood samples from the independent, age-comparable ARIES subsample of the ARIES/ALSPAC study (n = 641; n = 159 exposed to prenatal depressive symptoms; 7-8 years old) were examined as a confirmation sample. Depressive symptoms were assessed with the Edinburgh Postnatal Depression Scale. DNA methylation was analyzed with the Infinium Human Methylation 450k BeadChip. Modifications in single CpGs, regions, and biological pathways were investigated. Results were adjusted for age and birth outcomes as well as postnatal and current maternal depressive symptoms. Analyses were performed for the whole sample as well as separated for sex. RESULTS The EWAS yielded no differentially methylated CpG or region as well as no accordance between samples withstanding correction for multiple testing. In pathway analyses, no overlapping functional domain was found to be enriched for either sample. A comparison of current and former findings suggests some overlapping methylation modifications from infancy to childhood. Results suggest that there might be sex-specific differential methylation, which should be further investigated in additional studies. CONCLUSIONS The current, mainly nonsignificant, results challenge the assumption of consistent modifications of DNA methylation in children exposed to prenatal depressive symptoms. Despite the relatively small sample size used in this study, this lack of significant results may reflect diverse issues of environmental epigenetic studies, which need to be addressed in future research.
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Affiliation(s)
- Valeska Stonawski
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jakob Roetner
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Tamme W Goecke
- Department of Gynecology and Obstetrics,
University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg
(FAU), Erlangen, Germany
- Department of Obstetrics and
Gynaecology, RoMed Hospital Rosenheim, Rosenheim, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics,
University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg
(FAU), Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics,
University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg
(FAU), Erlangen, Germany
| | - Johannes Kornhuber
- Department of Psychiatry and
Psychotherapy, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Oliver Kratz
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Gunther H Moll
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Anna Eichler
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | | | - Stefan Frey
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
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Stoffel M, Gardini E, Ehrenthal J, Abbruzzese E, Ditzen B. Evaluation of Stress Management and Stress Prevention Using Epigenetic Markers. VERHALTENSTHERAPIE 2020. [DOI: 10.1159/000506323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Stoffel M, Gardini E, Ehrenthal J, Abbruzzese E, Ditzen B. Evaluation von Stressprävention und Stressbewältigung mittels epigenetischer Marker. VERHALTENSTHERAPIE 2020. [DOI: 10.1159/000505595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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38
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Cuvertino S, Hartill V, Colyer A, Garner T, Nair N, Al-Gazali L, Canham N, Faundes V, Flinter F, Hertecant J, Holder-Espinasse M, Jackson B, Lynch SA, Nadat F, Narasimhan VM, Peckham M, Sellers R, Seri M, Montanari F, Southgate L, Squeo GM, Trembath R, van Heel D, Venuto S, Weisberg D, Stals K, Ellard S, Barton A, Kimber SJ, Sheridan E, Merla G, Stevens A, Johnson CA, Banka S. A restricted spectrum of missense KMT2D variants cause a multiple malformations disorder distinct from Kabuki syndrome. Genet Med 2020; 22:867-877. [PMID: 31949313 PMCID: PMC7200597 DOI: 10.1038/s41436-019-0743-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/24/2019] [Indexed: 12/19/2022] Open
Abstract
Purpose To investigate if specific exon 38 or 39 KMT2D missense variants (MVs) cause a condition distinct from
Kabuki syndrome type 1 (KS1). Methods Multiple individuals, with MVs in exons 38 or 39 of KMT2D that encode a highly conserved region of 54
amino acids flanked by Val3527 and Lys3583, were identified and phenotyped.
Functional tests were performed to study their pathogenicity and understand the
disease mechanism. Results The consistent clinical features of the affected individuals, from
seven unrelated families, included choanal atresia, athelia or hypoplastic
nipples, branchial sinus abnormalities, neck pits, lacrimal duct anomalies,
hearing loss, external ear malformations, and thyroid abnormalities. None of the
individuals had intellectual disability. The frequency of clinical features,
objective software-based facial analysis metrics, and genome-wide peripheral
blood DNA methylation patterns in these patients were significantly different
from that of KS1. Circular dichroism spectroscopy indicated that these MVs
perturb KMT2D secondary structure through an increased disordered to ɑ-helical
transition. Conclusion KMT2D MVs located in a specific
region spanning exons 38 and 39 and affecting highly conserved residues cause a
novel multiple malformations syndrome distinct from KS1. Unlike KMT2D haploinsufficiency in KS1, these MVs likely
result in disease through a dominant negative mechanism.
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Affiliation(s)
- Sara Cuvertino
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Verity Hartill
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK.,Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Alice Colyer
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Terence Garner
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Nisha Nair
- Centre of Genetics & Genomics Versus Arthritis, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine & Health Sciences, United Arab University, Al-Ain, UAE
| | - Natalie Canham
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK.,North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Victor Faundes
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.,Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Frances Flinter
- Department of Clinical Genetics, Guy's & St Thomas NHS Foundation Trust, London, UK
| | | | | | - Brian Jackson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Sally Ann Lynch
- Temple street Children's University Hospital, Dublin, Ireland
| | - Fatima Nadat
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | | | - Michelle Peckham
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Robert Sellers
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Marco Seri
- Medical Genetics Unit, St. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Francesca Montanari
- Medical Genetics Unit, St. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Laura Southgate
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK.,Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Gabriella Maria Squeo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Richard Trembath
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | | | - Santina Venuto
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Daniel Weisberg
- Clinical Psychology Department, Royal Manchester Children's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester, UK
| | - Karen Stals
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Sian Ellard
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | | | - Anne Barton
- Centre of Genetics & Genomics Versus Arthritis, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Eamonn Sheridan
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK.,Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Giuseppe Merla
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Adam Stevens
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Colin A Johnson
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK. .,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester, UK.
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Ciuculete DM, Voisin S, Kular L, Welihinda N, Jonsson J, Jagodic M, Mwinyi J, Schiöth HB. Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression. Epigenetics 2019; 15:646-663. [PMID: 31852353 PMCID: PMC7574381 DOI: 10.1080/15592294.2019.1700628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Unrecognized depression during adolescence can result in adult suicidal behaviour. The aim of this study was to identify, replicate and characterize DNA methylation (DNAm) shifts in depression aetiology, using a longitudinal, multi-tissue (blood and brain) and multi-layered (genetics, epigenetics, transcriptomics) approach. We measured genome-wide blood DNAm data at baseline and one-year follow-up, and imputed genetic variants, in 59 healthy adolescents comprising the discovery cohort. Depression and suicidal symptoms were determined using the Development and Well-Being Assessment (DAWBA) depression band, Montgomery-Åsberg Depression Rating Scale-Self (MADRS-S) and SUicide Assessment Scale (SUAS). DNAm levels at follow-up were regressed against depression scores, adjusting for sex, age and the DNAm residuals at baseline. Higher methylation levels of 5% and 13% at cg24627299 within the MET gene were associated with higher depression scores (praw<1e-4) and susceptibility for suicidal symptoms (padj.<0.005). The nearby rs39748 was discovered to be a methylation and expression quantitative trait locus in blood cells. mRNA levels of hepatocyte growth factor (HGF) expression, known to strongly interact with MET, were inversely associated with methylation levels at cg24627299, in an independent cohort of 1180 CD14+ samples. In an open-access dataset of brain tissue, lower methylation at cg24627299 was found in 45 adults diagnosed with major depressive disorder compared with matched controls (padj.<0.05). Furthermore, lower MET expression was identified in the hippocampus of depressed individuals compared with controls in a fourth, independent cohort. Our findings reveal methylation changes at MET in the pathology of depression, possibly involved in downregulation of HGF/c-MET signalling the hippocampal region.
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Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University , Footscray, Australian
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Nipuni Welihinda
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Jörgen Jonsson
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University , Moscow, Russia
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40
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Maternal and Post-weaning High-Fat Diets Produce Distinct DNA Methylation Patterns in Hepatic Metabolic Pathways within Specific Genomic Contexts. Int J Mol Sci 2019; 20:ijms20133229. [PMID: 31262088 PMCID: PMC6651091 DOI: 10.3390/ijms20133229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023] Open
Abstract
Calorie-dense high-fat diets (HF) are associated with detrimental health outcomes, including obesity, cardiovascular disease, and diabetes. Both pre- and post-natal HF diets have been hypothesized to negatively impact long-term metabolic health via epigenetic mechanisms. To understand how the timing of HF diet intake impacts DNA methylation and metabolism, male Sprague–Dawley rats were exposed to either maternal HF (MHF) or post-weaning HF diet (PHF). At post-natal week 12, PHF rats had similar body weights but greater hepatic lipid accumulation compared to the MHF rats. Genome-wide DNA methylation was evaluated, and analysis revealed 1744 differentially methylation regions (DMRs) between the groups with the majority of the DMR located outside of gene-coding regions. Within differentially methylated genes (DMGs), intragenic DNA methylation closer to the transcription start site was associated with lower gene expression, whereas DNA methylation further downstream was positively correlated with gene expression. The insulin and phosphatidylinositol (PI) signaling pathways were enriched with 25 DMRs that were associated with 20 DMGs, including PI3 kinase (Pi3k), pyruvate kinase (Pklr), and phosphodiesterase 3 (Pde3). Together, these results suggest that the timing of HF diet intake determines DNA methylation and gene expression patterns in hepatic metabolic pathways that target specific genomic contexts.
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Imeh-Nathaniel A, Orfanakos V, Wormack L, Huber R, Nathaniel TI. The crayfish model (Orconectes rusticus), epigenetics and drug addiction research. Pharmacol Biochem Behav 2019; 183:38-45. [PMID: 31202808 DOI: 10.1016/j.pbb.2019.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/16/2019] [Accepted: 06/12/2019] [Indexed: 12/15/2022]
Abstract
Fundamental signs of epigenetic effects are variations in the expression of genes or phenotypic traits among isogenic mates. Therefore, genetically identical animals are in high demand for epigenetic research. There are many genetically identical animals, including natural parthenogens and inbred laboratory lineages or clones. However, most parthenogenetic animal taxa are very small in combined epigenetic and drug addiction research. Orconectes rusticus has a unique phylogenetic position, with 2-3 years of life span, which undergoes metamorphosis that creates developmental stages with distinctly different morphologies, unique lifestyles, and broad behavioral traits, even among isogenic mates reared in the same environment offer novel inroads for epigenetics studies. Moreover, the establishment of crayfish as a novel system for drug addiction with evidence of an automated, operant self-administration and conditioned-reward, withdrawal, reinstatement of the conditioned drug-induced reward sets the stage to investigate epigenetic mechanisms of drug addiction. We discuss behavioral, pharmacological and molecular findings from laboratory studies that document a broad spectrum of molecular and, behavioral evidence including potential hypotheses that can be tested with the crayfish model for epigenetic study in drug addiction research.
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Affiliation(s)
| | | | - Leah Wormack
- University of South Carolina School of Medicine, SC, USA
| | - Robert Huber
- J.P Scott Center for Neuroscience, Mind and Behavior, Bowling Green State University, Bowling Green, OH, USA
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