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Morgan RK, Wang K, Svoboda LK, Rygiel CA, Lalancette C, Cavalcante R, Bartolomei MS, Prasasya R, Neier K, Perera BPU, Jones TR, Colacino JA, Sartor MA, Dolinoy DC. Effects of Developmental Lead and Phthalate Exposures on DNA Methylation in Adult Mouse Blood, Brain, and Liver: A Focus on Genomic Imprinting by Tissue and Sex. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:67003. [PMID: 38833407 DOI: 10.1289/ehp14074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
BACKGROUND Maternal exposure to environmental chemicals can cause adverse health effects in offspring. Mounting evidence supports that these effects are influenced, at least in part, by epigenetic modifications. It is unknown whether epigenetic changes in surrogate tissues such as the blood are reflective of similar changes in target tissues such as cortex or liver. OBJECTIVE We examined tissue- and sex-specific changes in DNA methylation (DNAm) associated with human-relevant lead (Pb) and di(2-ethylhexyl) phthalate (DEHP) exposure during perinatal development in cerebral cortex, blood, and liver. METHODS Female mice were exposed to human relevant doses of either Pb (32 ppm ) via drinking water or DEHP (5 mg / kg-day ) via chow for 2 weeks prior to mating through offspring weaning. Whole genome bisulfite sequencing (WGBS) was utilized to examine DNAm changes in offspring cortex, blood, and liver at 5 months of age. Metilene and methylSig were used to identify differentially methylated regions (DMRs). Annotatr and ChIP-enrich were used for genomic annotations and gene set enrichment tests of DMRs, respectively. RESULTS The cortex contained the majority of DMRs associated with Pb (66%) and DEHP (57%) exposure. The cortex also contained the greatest degree of overlap in DMR signatures between sexes (n = 13 and 8 DMRs with Pb and DEHP exposure, respectively) and exposure types (n = 55 and 39 DMRs in males and females, respectively). In all tissues, detected DMRs were preferentially found at genomic regions associated with gene expression regulation (e.g., CpG islands and shores, 5' UTRs, promoters, and exons). An analysis of GO terms associated with DMR-containing genes identified imprinted genes to be impacted by both Pb and DEHP exposure. Of these, Gnas and Grb10 contained DMRs across tissues, sexes, and exposures, with some signatures replicated between target and surrogate tissues. DMRs were enriched in the imprinting control regions (ICRs) of Gnas and Grb10, and we again observed a replication of DMR signatures between blood and target tissues. Specifically, we observed hypermethylation of the Grb10 ICR in both blood and liver of Pb-exposed male animals. CONCLUSIONS These data provide preliminary evidence that imprinted genes may be viable candidates in the search for epigenetic biomarkers of toxicant exposure in target tissues. Additional research is needed on allele- and developmental stage-specific effects, as well as whether other imprinted genes provide additional examples of this relationship. https://doi.org/10.1289/EHP14074.
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Affiliation(s)
- Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Christine A Rygiel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Claudia Lalancette
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Raymond Cavalcante
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rexxi Prasasya
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kari Neier
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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2
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Yeung E, Biedrzycki RJ, Gómez Herrera LC, Issarapu P, Dou J, Marques IF, Mansuri SR, Page CM, Harbs J, Khodasevich D, Poisel E, Niu Z, Allard C, Casey E, Berstein FM, Mancano G, Elliott HR, Richmond R, He Y, Ronkainen J, Sebert S, Bell EM, Sharp G, Mumford SL, Schisterman EF, Chandak GR, Fall CHD, Sahariah SA, Silver MJ, Prentice AM, Bouchard L, Domellof M, West C, Holland N, Cardenas A, Eskenazi B, Zillich L, Witt SH, Send T, Breton C, Bakulski KM, Fallin MD, Schmidt RJ, Stein DJ, Zar HJ, Jaddoe VWV, Wright J, Grazuleviciene R, Gutzkow KB, Sunyer J, Huels A, Vrijheid M, Harlid S, London S, Hivert MF, Felix J, Bustamante M, Guan W. Maternal age is related to offspring DNA methylation: A meta-analysis of results from the PACE consortium. Aging Cell 2024:e14194. [PMID: 38808605 DOI: 10.1111/acel.14194] [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: 10/24/2023] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/30/2024] Open
Abstract
Worldwide trends to delay childbearing have increased parental ages at birth. Older parental age may harm offspring health, but mechanisms remain unclear. Alterations in offspring DNA methylation (DNAm) patterns could play a role as aging has been associated with methylation changes in gametes of older individuals. We meta-analyzed epigenome-wide associations of parental age with offspring blood DNAm of over 9500 newborns and 2000 children (5-10 years old) from the Pregnancy and Childhood Epigenetics consortium. In newborns, we identified 33 CpG sites in 13 loci with DNAm associated with maternal age (PFDR < 0.05). Eight of these CpGs were located near/in the MTNR1B gene, coding for a melatonin receptor. Regional analysis identified them together as a differentially methylated region consisting of 9 CpGs in/near MTNR1B, at which higher DNAm was associated with greater maternal age (PFDR = 6.92 × 10-8) in newborns. In childhood blood samples, these differences in blood DNAm of MTNR1B CpGs were nominally significant (p < 0.05) and retained the same positive direction, suggesting persistence of associations. Maternal age was also positively associated with higher DNA methylation at three CpGs in RTEL1-TNFRSF6B at birth (PFDR < 0.05) and nominally in childhood (p < 0.0001). Of the remaining 10 CpGs also persistent in childhood, methylation at cg26709300 in YPEL3/BOLA2B in external data was associated with expression of ITGAL, an immune regulator. While further study is needed to establish causality, particularly due to the small effect sizes observed, our results potentially support offspring DNAm as a mechanism underlying associations of maternal age with child health.
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Affiliation(s)
- Edwina Yeung
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Richard J Biedrzycki
- Division of Intramural Research, Glotech Inc., Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura C Gómez Herrera
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Prachand Issarapu
- MRC Unit the Gambia at the London School of Hygiene and Tropical Medicine (LSHTM), Banjul, The Gambia
| | - John Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Irene Fontes Marques
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Sohail Rafik Mansuri
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Christian Magnus Page
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Justin Harbs
- Department of Diagnostics and Intervention, Oncology, Umeå University, Umeå, Sweden
| | - Dennis Khodasevich
- Environmental Health Sciences, Berkeley Public Health, CERCH, University of California, Berkeley, California, USA
| | - Eric Poisel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Zhongzheng Niu
- Department of Population and Public Health Science, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, Quebec, Canada
| | - Emma Casey
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Fernanda Morales Berstein
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
| | - Giulia Mancano
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
| | - Hannah R Elliott
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
| | - Rebecca Richmond
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol Medical School Population Health Sciences, University of Bristol, Bristol, UK
| | - Yiyan He
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | | | - Sylvain Sebert
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | - Erin M Bell
- Department of Environmental Health Sciences and Epidemiology and Biostatistics, University at Albany School of Public Health, Albany, New York, USA
| | - Gemma Sharp
- Department of Psychology, University of Exeter, Exeter, UK
| | - Sunni L Mumford
- Department of Biostatistics, Epidemiology and Informatics and Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Enrique F Schisterman
- Department of Biostatistics, Epidemiology and Informatics and Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Caroline H D Fall
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK, UK
| | | | - Matt J Silver
- MRC Unit the Gambia at the London School of Hygiene and Tropical Medicine (LSHTM), Banjul, The Gambia
| | - Andrew M Prentice
- MRC Unit the Gambia at the London School of Hygiene and Tropical Medicine (LSHTM), Banjul, The Gambia
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Centre intégré Universitaire de santé et de Services Sociaux (CIUSSS) du Saguenay-Lac-St-Jean, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Department of Laboratory Medicine, CIUSSS du Saguenay-Lac-Saint-Jean - Hôpital de Chicoutimi, Chicoutimi, Quebec, Canada
| | - Magnus Domellof
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Christina West
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Nina Holland
- Environmental Health Sciences, Berkeley Public Health, CERCH, University of California, Berkeley, California, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University, Stanford, California, USA
| | - Brenda Eskenazi
- Environmental Health Sciences, Berkeley Public Health, CERCH, University of California, Berkeley, California, USA
| | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Tabea Send
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Carrie Breton
- Department of Population and Public Health Science, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - M Daniele Fallin
- Dean's Office, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, California, USA
| | - Dan J Stein
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - Vincent W V Jaddoe
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - John Wright
- Bradford Institute for Health Research, Temple Bank House, Bradford Royal Infirmary, Bradford, UK
| | | | - Kristine Bjerve Gutzkow
- Division of Climate and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jordi Sunyer
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM-Parc Salut Mar, Barcelona, Spain
| | - Anke Huels
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Martine Vrijheid
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Sophia Harlid
- Department of Diagnostics and Intervention, Oncology, Umeå University, Umeå, Sweden
| | - Stephanie London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina, USA
| | - Marie-France Hivert
- Division of Chronic Disease Research across the Lifecourse (CoRAL); Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Janine Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mariona Bustamante
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
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3
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Campbell KA, Colacino JA, Dou J, Dolinoy DC, Park SK, Loch-Caruso R, Padmanabhan V, Bakulski KM. Placental and Immune Cell DNA Methylation Reference Panel for Bulk Tissue Cell Composition Estimation in Epidemiological Studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.588886. [PMID: 38766167 PMCID: PMC11100803 DOI: 10.1101/2024.05.06.588886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
To distinguish DNA methylation (DNAm) from cell proportion changes in whole placental tissue research, we developed a robust cell type-specific DNAm reference to estimate cell composition. We collated newly collected and existing cell type DNAm profiles quantified via Illumina EPIC or 450k microarrays. To estimate cell composition, we deconvoluted whole placental samples (n=36) with robust partial correlation based on the top 50 hyper- and hypomethylated sites per cell type. To test deconvolution performance, we evaluated RMSE in predicting principal component one of DNAm variation in 204 external placental samples. We analyzed DNAm profiles (n=368,435 sites) from 12 cell types: cytotrophoblasts (n=18), endothelial cells (n=19), Hofbauer cells (n=26), stromal cells (n=21), syncytiotrophoblasts (n=4), six lymphocyte types (n=36), and nucleated red blood cells (n=11). Median cell composition was consistent with placental biology: 60.4% syncytiotrophoblast, 17.1% stromal, 8.8% endothelial, 4.5% cytotrophoblast, 3.9% Hofbauer, 1.7% nucleated red blood cells, and 1.2% neutrophils. Our expanded reference outperformed an existing reference in predicting DNAm variation (15.4% variance explained, IQR=21.61) with cell composition estimates (RMSE:10.51 vs. 11.43, p-value<0.001). This cell type reference can robustly estimate cell composition from whole placental DNAm data to detect important cell types, reveal biological mechanisms, and improve casual inference.
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Affiliation(s)
- Kyle A. Campbell
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - John Dou
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sung Kyun Park
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rita Loch-Caruso
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vasantha Padmanabhan
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kelly M. Bakulski
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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4
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Petroff RL, Dolinoy DC, Wang K, Montrose L, Padmanabhan V, Peterson KE, Ruden DM, Sartor MA, Svoboda LK, Téllez-Rojo MM, Goodrich JM. Translational toxicoepigenetic Meta-Analyses identify homologous gene DNA methylation reprogramming following developmental phthalate and lead exposure in mouse and human offspring. ENVIRONMENT INTERNATIONAL 2024; 186:108575. [PMID: 38507935 DOI: 10.1016/j.envint.2024.108575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/26/2024] [Accepted: 03/09/2024] [Indexed: 03/22/2024]
Abstract
Although toxicology uses animal models to represent real-world human health scenarios, a critical translational gap between laboratory-based studies and epidemiology remains. In this study, we aimed to understand the toxicoepigenetic effects on DNA methylation after developmental exposure to two common toxicants, the phthalate di(2-ethylhexyl) phthalate (DEHP) and the metal lead (Pb), using a translational paradigm that selected candidate genes from a mouse study and assessed them in four human birth cohorts. Data from mouse offspring developmentally exposed to DEHP, Pb, or control were used to identify genes with sex-specific sites with differential DNA methylation at postnatal day 21. Associations of human infant DNA methylation in homologous mouse genes with prenatal DEHP or Pb were examined with a meta-analysis. Differential methylation was observed on 6 cytosines (adjusted-p < 0.05) and 90 regions (adjusted-p < 0.001). This translational approach offers a unique method that can detect conserved epigenetic differences that are developmentally susceptible to environmental toxicants.
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Affiliation(s)
- Rebekah L Petroff
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Kai Wang
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Luke Montrose
- Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Vasantha Padmanabhan
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA; Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Karen E Peterson
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Douglas M Ruden
- Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Maureen A Sartor
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA; Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Laurie K Svoboda
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Martha M Téllez-Rojo
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca, Mexico
| | - Jaclyn M Goodrich
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA.
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5
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Mulder RH, Neumann A, Felix JF, Suderman M, Cecil CAM. What makes clocks tick? Characterizing developmental dynamics of adult epigenetic clock sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584597. [PMID: 38559237 PMCID: PMC10979995 DOI: 10.1101/2024.03.12.584597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
DNA methylation (DNAm) at specific sites can be used to calculate 'epigenetic clocks', which in adulthood are used as indicators of age(ing). However, little is known about how these clock sites 'behave' during development and what factors influence their variability in early life. This knowledge could be used to optimize healthy aging well before the onset of age-related conditions. Here, we leveraged results from two longitudinal population-based cohorts (N=5,019 samples from 2,348 individuals) to characterize trajectories of adult clock sites from birth to early adulthood. We find that clock sites (i) diverge widely in their developmental trajectories, often showing non-linear change over time; (ii) are substantially more likely than non-clock sites to vary between individuals already from birth, differences that are predictive of DNAm variation at later ages; and (iii) show enrichment for genetic and prenatal environmental exposures, supporting an early-origins perspective to epigenetic aging.
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Affiliation(s)
- Rosa H. Mulder
- Department of Child and Adolescent Psychiatry / Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alexander Neumann
- Department of Child and Adolescent Psychiatry / Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F. Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Charlotte A. M. Cecil
- Department of Child and Adolescent Psychiatry / Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
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6
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Saucedo-Cuevas L, Ma MPQ, Le AH, Akin N, Pham TD, Ho TM, Pita G, Gonzalez-Neira A, De Vos M, Smitz J, Anckaert E, Vuong LN. Epigenetic variation in neonatal tissues in infants conceived using capacitation-in vitro maturation vs. in vitro fertilization. Fertil Steril 2024; 121:506-518. [PMID: 38052376 DOI: 10.1016/j.fertnstert.2023.11.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023]
Abstract
OBJECTIVE To investigate alterations of the global DNA methylation profile in placenta, cord blood, and neonatal buccal smears in infants conceived using in vitro maturation (IVM) with a prematuration step (capacitation-IVM [CAPA-IVM]) vs. in vitro fertilization (IVF). DESIGN Analysis of data from the offspring of participants in a randomized controlled trial. SETTING Private clinic. PATIENTS Forty-six women with polycystic ovary syndrome and/or high antral follicle count and their offspring (58 newborns). INTERVENTION(S) Women with polycystic ovary syndrome and/or a high antral follicle count participating in the clinical trial were randomized to undergo CAPA-IVM or conventional IVF. MAIN OUTCOME MEASURE(S) At delivery, biological samples including cord blood, placental tissue, and a neonatal buccal smear were collected. Genome-wide DNA methylation was determined using the Illumina Infinium MethylationEPIC BeadChip. Variability in methylation was also considered, and mean variances for the two treatment categories were compared. RESULTS In neonatal buccal smears, there were no significant differences between the CAPA-IVM and conventional IVF groups on the basis of the CpG probe after linear regression analysis using a significant cut-off of false-discovery rate <0.05 and |Δβ|≥0.05. In cord blood, only one CpG site showed a significant gain of methylation in the CAPA-IVM group. In the placenta, CAPA-IVM was significantly associated with changes in methylation at five CpG sites. Significantly more variable DNA methylation was found in five probes in the placenta, 54 in cord blood, and two in buccal smears after IVM of oocytes. In cord blood samples, 20 CpG sites had more variable methylation in the conventional IVF vs. IVM group. Isolated CpG sites showing differences in methylation in cord blood were not associated with changes in gene expression of the overlapping genes. CONCLUSION(S) Capacitation-IVM appeared to be associated with only a small amount of epigenetic variation in cord blood, placental tissue, and neonate buccal smears. CLINICAL TRIAL REGISTRATION NUMBER NCT03405701 (www. CLINICALTRIALS gov).
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Affiliation(s)
- Laura Saucedo-Cuevas
- Follicle Biology Laboratory, UZ Brussel, Vrije Universiteit Brussel, Brussel, Belgium
| | - Mai P Q Ma
- IVFMD, My Duc Hospital, Ho Chi Minh City, Vietnam; HOPE Research Center, My Duc Hospital, Ho Chi Minh City, Vietnam
| | - Anh H Le
- IVFMD, My Duc Hospital, Ho Chi Minh City, Vietnam; HOPE Research Center, My Duc Hospital, Ho Chi Minh City, Vietnam
| | - Nazli Akin
- Follicle Biology Laboratory, UZ Brussel, Vrije Universiteit Brussel, Brussel, Belgium
| | - Toan D Pham
- IVFMD, My Duc Hospital, Ho Chi Minh City, Vietnam; HOPE Research Center, My Duc Hospital, Ho Chi Minh City, Vietnam
| | - Tuong M Ho
- IVFMD, My Duc Hospital, Ho Chi Minh City, Vietnam; HOPE Research Center, My Duc Hospital, Ho Chi Minh City, Vietnam
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Anna Gonzalez-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Michel De Vos
- Centre for Reproductive Medicine, Universitair Ziekenhuis Brussel, Brussels, Belgium; Department of Obstetrics, Gynecology, Perinatology, and Reproductology, Institute of Professional Education, Sechenov University, Moscow, Russia
| | - Johan Smitz
- Follicle Biology Laboratory, UZ Brussel, Vrije Universiteit Brussel, Brussel, Belgium
| | - Ellen Anckaert
- Follicle Biology Laboratory, UZ Brussel, Vrije Universiteit Brussel, Brussel, Belgium
| | - Lan N Vuong
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam.
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7
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Bozack AK, Rifas-Shiman SL, Baccarelli AA, Wright RO, Gold DR, Oken E, Hivert MF, Cardenas A. Associations of prenatal one-carbon metabolism nutrients and metals with epigenetic aging biomarkers at birth and in childhood in a US cohort. Aging (Albany NY) 2024; 16:3107-3136. [PMID: 38412256 PMCID: PMC10929819 DOI: 10.18632/aging.205602] [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: 10/31/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
Epigenetic gestational age acceleration (EGAA) at birth and epigenetic age acceleration (EAA) in childhood may be biomarkers of the intrauterine environment. We investigated the extent to which first-trimester folate, B12, 5 essential, and 7 non-essential metals in maternal circulation are associated with EGAA and EAA in early life. Bohlin EGAA and Horvath pan-tissue and skin and blood EAA were calculated using DNA methylation measured in cord blood (N=351) and mid-childhood blood (N=326; median age = 7.7 years) in the Project Viva pre-birth cohort. A one standard deviation increase in individual essential metals (copper, manganese, and zinc) was associated with 0.94-1.2 weeks lower Horvath EAA at birth, and patterns of exposures identified by exploratory factor analysis suggested that a common source of essential metals was associated with Horvath EAA. We also observed evidence nonlinear associations of zinc with Bohlin EGAA, magnesium and lead with Horvath EAA, and cesium with skin and blood EAA at birth. Overall, associations at birth did not persist in mid-childhood; however, arsenic was associated with greater EAA at birth and in childhood. Prenatal metals, including essential metals and arsenic, are associated with epigenetic aging in early life, which might be associated with future health.
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Affiliation(s)
- Anne K. Bozack
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sheryl L. Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York City, NY 10032, USA
| | - Robert O. Wright
- Department of Environmental Medicine and Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Diane R. Gold
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
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8
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Laubach ZM, Bozack A, Aris IM, Slopen N, Tiemeier H, Hivert MF, Cardenas A, Perng W. Maternal prenatal social experiences and offspring epigenetic age acceleration from birth to mid-childhood. Ann Epidemiol 2024; 90:28-34. [PMID: 37839726 PMCID: PMC10842218 DOI: 10.1016/j.annepidem.2023.10.003] [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: 07/12/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
PURPOSE Investigate associations of maternal social experiences with offspring epigenetic age acceleration (EAA) from birth through mid-childhood among 205 mother-offspring dyads of minoritized racial and ethnic groups. METHODS We used linear regression to examine associations of maternal experiences of racial bias or discrimination (0 = none, 1-2 = intermediate, or 3+ = high), social support (tertile 1 = low, 2 = intermediate, 3 = high), and socioeconomic status index (tertile 1 = low, 2 = intermediate, 3 = high) during the prenatal period with offspring EAA according to Horvath's Pan-Tissue, Horvath's Skin and Blood, and Intrinsic EAA clocks at birth, 3 years, and 7 years. RESULTS In comparison to children of women who did not experience any racial bias or discrimination, those whose mothers reported highest levels of racial bias or discrimination had lower Pan-Tissue clock EAA in early (-0.50 years; 90% CI: -0.91, -0.09) and mid-childhood (-0.75 years; -1.41, -0.08). We observed similar associations for the Skin and Blood clock and Intrinsic EAA. Maternal experiences of discrimination were not associated with Pan-Tissue EAA at birth. Neither maternal social support nor socioeconomic status predicted offspring EAA. CONCLUSIONS Children whose mothers experienced higher racial bias or discrimination exhibited slower EAA. Future studies are warranted to confirm these findings and establish associations of early-life EAA with long-term health outcomes.
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Affiliation(s)
- Zachary M Laubach
- Department of Ecology and Evolutionary Biology (EBIO), University of Colorado Boulder
| | - Anne Bozack
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA
| | - Izzuddin M Aris
- Division of Chronic Disease Research Across the Lifecourse (CORAL), Department of Population Medicine, Harvard Medical School, Boston, MA
| | - Natalie Slopen
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Henning Tiemeier
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse (CORAL), Department of Population Medicine, Harvard Medical School, Boston, MA; Diabetes Unit, Massachusetts General Hospital, Boston, MA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA
| | - Wei Perng
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD Center), Department of Epidemiology, Colorado School of Public Health, Aurora, CO.
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9
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Song AY, Bulka CM, Niemiec SS, Kechris K, Boyle KE, Marsit CJ, O’Shea TM, Fry RC, Lyall K, Fallin MD, Volk HE, Ladd-Acosta C. Accelerated epigenetic age at birth and child emotional and behavioura development in early childhood: a meta-analysis of four prospective cohort studies in ECHO. Epigenetics 2023; 18:2254971. [PMID: 37691382 PMCID: PMC10496525 DOI: 10.1080/15592294.2023.2254971] [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: 02/15/2023] [Revised: 08/16/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023] Open
Abstract
Background: 'Epigenetic clocks' have been developed to accurately predict chronologic gestational age and have been associated with child health outcomes in prior work.Methods: We meta-analysed results from four prospective U.S cohorts investigating the association between epigenetic age acceleration estimated using blood DNA methylation collected at birth and preschool age Childhood Behavior Checklist (CBCL) scores.Results: Epigenetic ageing was not significantly associated with CBCL total problem scores (β = 0.33, 95% CI: -0.95, 0.28) and DSM-oriented pervasive development problem scores (β = -0.23, 95% CI: -0.61, 0.15). No associations were observed for other DSM-oriented subscales.Conclusions: The meta-analysis results suggest that epigenetic gestational age acceleration is not associated with child emotional and behavioural functioning for preschool age group. These findings may relate to our study population, which includes two cohorts enriched for ASD and one preterm birth cohort.; future work should address the role of epigenetic age in child health in other study populations.Abbreviations: DNAm: DNA methylation; CBCL: Child Behavioral Checklist; ECHO: Environmental Influences on Child Health Outcomes; EARLI: Early Autism Risk Longitudinal Investigation; MARBLES: Markers of Autism Risk in Babies - Learning Early Signs; ELGAN: Extremely Low Gestational Age Newborns; ASD: autism spectrum disorder; BMI: body mass index; DSM: Diagnostic and Statistical Manual of Mental Disorders.
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Affiliation(s)
- Ashley Y. Song
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Sierra S. Niemiec
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kristen E. Boyle
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Carmen J. Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - T. Michael O’Shea
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kristen Lyall
- A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA, USA
| | | | - Heather E. Volk
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christine Ladd-Acosta
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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10
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Vellame DS, Shireby G, MacCalman A, Dempster EL, Burrage J, Gorrie-Stone T, Schalkwyk LS, Mill J, Hannon E. Uncertainty quantification of reference-based cellular deconvolution algorithms. Epigenetics 2023; 18:2137659. [PMID: 36539387 PMCID: PMC9980651 DOI: 10.1080/15592294.2022.2137659] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/12/2022] [Indexed: 12/24/2022] Open
Abstract
The majority of epigenetic epidemiology studies to date have generated genome-wide profiles from bulk tissues (e.g., whole blood) however these are vulnerable to confounding from variation in cellular composition. Proxies for cellular composition can be mathematically derived from the bulk tissue profiles using a deconvolution algorithm; however, there is no method to assess the validity of these estimates for a dataset where the true cellular proportions are unknown. In this study, we describe, validate and characterize a sample level accuracy metric for derived cellular heterogeneity variables. The CETYGO score captures the deviation between a sample's DNA methylation profile and its expected profile given the estimated cellular proportions and cell type reference profiles. We demonstrate that the CETYGO score consistently distinguishes inaccurate and incomplete deconvolutions when applied to reconstructed whole blood profiles. By applying our novel metric to >6,300 empirical whole blood profiles, we find that estimating accurate cellular composition is influenced by both technical and biological variation. In particular, we show that when using a common reference panel for whole blood, less accurate estimates are generated for females, neonates, older individuals and smokers. Our results highlight the utility of a metric to assess the accuracy of cellular deconvolution, and describe how it can enhance studies of DNA methylation that are reliant on statistical proxies for cellular heterogeneity. To facilitate incorporating our methodology into existing pipelines, we have made it freely available as an R package (https://github.com/ds420/CETYGO).
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Affiliation(s)
| | - Gemma Shireby
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Ailsa MacCalman
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Emma L Dempster
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Tyler Gorrie-Stone
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | | | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
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11
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Rabotnick MH, Ehlinger J, Haidari A, Goodrich JM. Prenatal exposures to endocrine disrupting chemicals: The role of multi-omics in understanding toxicity. Mol Cell Endocrinol 2023; 578:112046. [PMID: 37598796 PMCID: PMC10592024 DOI: 10.1016/j.mce.2023.112046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are a diverse group of toxicants detected in populations globally. Prenatal EDC exposures impact birth and childhood outcomes. EDCs work through persistent changes at the molecular, cellular, and organ level. Molecular and biochemical signals or 'omics' can be measured at various functional levels - including the epigenome, transcriptome, proteome, metabolome, and the microbiome. In this narrative review, we introduce each omics and give examples of associations with prenatal EDC exposures. There is substantial research on epigenomic modifications in offspring exposed to EDCs during gestation, and a growing number of studies evaluating the transcriptome, proteome, metabolome, or microbiome in response to these exposures. Multi-omics, integrating data across omics layers, may improve understanding of disrupted function pathways related to early life exposures. We highlight several data integration methods to consider in multi-omics studies. Information from multi-omics can improve understanding of the biological processes and mechanisms underlying prenatal EDC toxicity.
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Affiliation(s)
- Margaret H Rabotnick
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Jessa Ehlinger
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Ariana Haidari
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
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12
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Knihtilä HM, Kachroo P, Shadid I, Raissadati A, Peng C, McElrath TF, Litonjua AA, Demeo DL, Loscalzo J, Weiss ST, Mirzakhani H. Cord blood DNA methylation signatures associated with preeclampsia are enriched for cardiovascular pathways: insights from the VDAART trial. EBioMedicine 2023; 98:104890. [PMID: 37995466 PMCID: PMC10709000 DOI: 10.1016/j.ebiom.2023.104890] [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: 06/22/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Preeclampsia has been associated with maternal epigenetic changes, in particular DNA methylation changes in the placenta. It has been suggested that preeclampsia could also cause DNA methylation changes in the neonate. We examined DNA methylation in relation to gene expression in the cord blood of offspring born to mothers with preeclampsia. METHODS This study included 128 mother-child pairs who participated in the Vitamin D Antenatal Asthma Reduction Trial (VDAART), where assessment of preeclampsia served as secondary outcome. We performed an epigenome-wide association study of preeclampsia and cord blood DNA methylation (Illumina 450 K chip). We then examined gene expression of the same subjects for validation and replicated the gene signatures in independent DNA methylation datasets. Lastly, we applied functional enrichment and network analyses to identify biological pathways that could potentially be involved in preeclampsia. FINDINGS In the cord blood samples (n = 128), 263 CpGs were differentially methylated (FDR <0.10) in preeclampsia (n = 16), of which 217 were annotated. Top pathways in the functional enrichment analysis included apelin signaling pathway and other endothelial and cardiovascular pathways. Of the 217 genes, 13 showed differential expression (p's < 0.001) in preeclampsia and 11 had been previously related to preeclampsia (p's < 0.0001). These genes were linked to apelin, cGMP and Notch signaling pathways, all having a role in angiogenic process and cardiovascular function. INTERPRETATION Preeclampsia is related to differential cord blood DNA methylation signatures of cardiovascular pathways, including the apelin signaling pathway. The association of these cord blood DNA methylation signatures with offspring's long-term morbidities due to preeclampsia should be further investigated. FUNDING VDAART is funded by National Heart, Lung, and Blood Institute grants of R01HL091528 and UH3OD023268. HMK is supported by Jane and Aatos Erkko Foundation, Paulo Foundation, and the Pediatric Research Foundation. HM is supported by K01 award from NHLBI (1K01HL146977-01A1). PK is supported by K99HL159234 from NIH/NHLBI.
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Affiliation(s)
- Hanna M Knihtilä
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Iskander Shadid
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alireza Raissadati
- Department of Pediatric Cardiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cheng Peng
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas F McElrath
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Augusto A Litonjua
- Division of Pediatric Pulmonary Medicine, Golisano Children's Hospital, University of Rochester Medical Center, Rochester, NY, USA
| | - Dawn L Demeo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hooman Mirzakhani
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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13
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Ng JWY, Felix JF, Olson DM. A novel approach to risk exposure and epigenetics-the use of multidimensional context to gain insights into the early origins of cardiometabolic and neurocognitive health. BMC Med 2023; 21:466. [PMID: 38012757 PMCID: PMC10683259 DOI: 10.1186/s12916-023-03168-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Each mother-child dyad represents a unique combination of genetic and environmental factors. This constellation of variables impacts the expression of countless genes. Numerous studies have uncovered changes in DNA methylation (DNAm), a form of epigenetic regulation, in offspring related to maternal risk factors. How these changes work together to link maternal-child risks to childhood cardiometabolic and neurocognitive traits remains unknown. This question is a key research priority as such traits predispose to future non-communicable diseases (NCDs). We propose viewing risk and the genome through a multidimensional lens to identify common DNAm patterns shared among diverse risk profiles. METHODS We identified multifactorial Maternal Risk Profiles (MRPs) generated from population-based data (n = 15,454, Avon Longitudinal Study of Parents and Children (ALSPAC)). Using cord blood HumanMethylation450 BeadChip data, we identified genome-wide patterns of DNAm that co-vary with these MRPs. We tested the prospective relation of these DNAm patterns (n = 914) to future outcomes using decision tree analysis. We then tested the reproducibility of these patterns in (1) DNAm data at age 7 and 17 years within the same cohort (n = 973 and 974, respectively) and (2) cord DNAm in an independent cohort, the Generation R Study (n = 686). RESULTS We identified twenty MRP-related DNAm patterns at birth in ALSPAC. Four were prospectively related to cardiometabolic and/or neurocognitive childhood outcomes. These patterns were replicated in DNAm data from blood collected at later ages. Three of these patterns were externally validated in cord DNAm data in Generation R. Compared to previous literature, DNAm patterns exhibited novel spatial distribution across the genome that intersects with chromatin functional and tissue-specific signatures. CONCLUSIONS To our knowledge, we are the first to leverage multifactorial population-wide data to detect patterns of variability in DNAm. This context-based approach decreases biases stemming from overreliance on specific samples or variables. We discovered molecular patterns demonstrating prospective and replicable relations to complex traits. Moreover, results suggest that patterns harbour a genome-wide organisation specific to chromatin regulation and target tissues. These preliminary findings warrant further investigation to better reflect the reality of human context in molecular studies of NCDs.
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Affiliation(s)
- Jane W Y Ng
- Department of Pediatrics, Cummings School of Medicine, University of Calgary, 28 Oki Drive NW, Calgary, AB, T3B 6A8, Canada
| | - Janine F Felix
- The Generation F Study Group, Erasmus MC University Medical Center Rotterdam, Postbus, 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - David M Olson
- Departments of Obstetrics and Gynecology, Physiology, and Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, 220 HMRC, Edmonton, AB, T6G2S2, Canada.
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14
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Collender P, Bozack AK, Veazie S, Nwanaji-Enwerem JC, Van Der Laan L, Kogut K, Riddell C, Eskenazi B, Holland N, Deardorff J, Cardenas A. Maternal adverse childhood experiences (ACEs) and DNA methylation of newborns in cord blood. Clin Epigenetics 2023; 15:162. [PMID: 37845746 PMCID: PMC10577922 DOI: 10.1186/s13148-023-01581-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/07/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Adverse childhood experiences (ACEs) increase the risk of poor health outcomes later in life. Psychosocial stressors may also have intergenerational health effects by which parental ACEs are associated with mental and physical health of children. Epigenetic programming may be one mechanism linking parental ACEs to child health. This study aimed to investigate epigenome-wide associations of maternal preconception ACEs with DNA methylation patterns of children. In the Center for the Health Assessment of Mothers and Children of Salinas study, cord blood DNA methylation was measured using the Illumina HumanMethylation450 BeadChip. Preconception ACEs, which occurred during the mothers' childhoods, were collected using a standard ACE questionnaire including 10 ACE indicators. Maternal ACE exposures were defined in this study as (1) the total number of ACEs; (2) the total number of ACEs categorized as 0, 1-3, and > 4; and (3) individual ACEs. Associations of ACE exposures with differential methylated positions, regions, and CpG modules determined using weighted gene co-expression network analysis were evaluated adjusting for covariates. RESULTS Data on maternal ACEs and cord blood DNA methylation were available for 196 mother/newborn pairs. One differential methylated position was associated with maternal experience of emotional abuse (cg05486260/FAM135B gene; q value < 0.05). Five differential methylated regions were significantly associated with the total number of ACEs, and 36 unique differential methylated regions were associated with individual ACEs (Šidák p value < 0.05). Fifteen CpG modules were significantly correlated with the total number of ACEs or individual ACEs, of which 8 remained significant in fully adjusted models (p value < 0.05). Significant modules were enriched for pathways related to neurological and immune development and function. CONCLUSIONS Maternal ACEs prior to conception were associated with cord blood DNA methylation of offspring at birth. Although there was limited overlap between differential methylated regions and CpGs in modules associated with ACE exposures, statistically significant regions and networks were related to genes involved in neurological and immune function. Findings may provide insights to pathways linking psychosocial stressors to health. Further research is needed to understand the relationship between changes in DNA methylation and child health.
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Affiliation(s)
- Phillip Collender
- Division of Environmental Health Sciences, University of California, Berkeley, CA, USA
| | - Anne K Bozack
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Research Park, 1701 Page Mill Road, Stanford, CA, 94304, USA
| | - Stephanie Veazie
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Jamaji C Nwanaji-Enwerem
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Department of Emergency Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Lars Van Der Laan
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Katherine Kogut
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
- Center for Environmental Research of Community Health, CERCH, School of Public Health, University of California, Berkeley, CA, USA
| | - Corinne Riddell
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research of Community Health, CERCH, School of Public Health, University of California, Berkeley, CA, USA
- Division of Community Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Nina Holland
- Division of Environmental Health Sciences, University of California, Berkeley, CA, USA
- Center for Environmental Research of Community Health, CERCH, School of Public Health, University of California, Berkeley, CA, USA
| | - Julianna Deardorff
- Center for Environmental Research of Community Health, CERCH, School of Public Health, University of California, Berkeley, CA, USA
- Division of Community Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Research Park, 1701 Page Mill Road, Stanford, CA, 94304, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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15
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Morgan RK, Wang K, Svoboda LK, Rygiel CA, Lalancette C, Cavalcante R, Bartolomei MS, Prasasya R, Neier K, Perera BP, Jones TR, Colacino JA, Sartor MA, Dolinoy DC. Effects of Developmental Lead and Phthalate Exposures on DNA Methylation in Adult Mouse Blood, Brain, and Liver Identifies Tissue- and Sex-Specific Changes with Implications for Genomic Imprinting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560131. [PMID: 37873115 PMCID: PMC10592650 DOI: 10.1101/2023.09.29.560131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background Maternal exposure to environmental chemicals can cause adverse health effects in offspring. Mounting evidence supports that these effects are influenced, at least in part, by epigenetic modifications. Objective We examined tissue- and sex-specific changes in DNA methylation (DNAm) associated with human-relevant lead (Pb) and di(2-ethylhexyl) phthalate (DEHP) exposure during perinatal development in cerebral cortex, blood, and liver. Methods Female mice were exposed to human relevant doses of either Pb (32ppm) via drinking water or DEHP (5 mg/kg-day) via chow for two weeks prior to mating through offspring weaning. Whole genome bisulfite sequencing (WGBS) was utilized to examine DNAm changes in offspring cortex, blood, and liver at 5 months of age. Metilene and methylSig were used to identify differentially methylated regions (DMRs). Annotatr and Chipenrich were used for genomic annotations and geneset enrichment tests of DMRs, respectively. Results The cortex contained the majority of DMRs associated with Pb (69%) and DEHP (58%) exposure. The cortex also contained the greatest degree of overlap in DMR signatures between sexes (n = 17 and 14 DMRs with Pb and DEHP exposure, respectively) and exposure types (n = 79 and 47 DMRs in males and females, respectively). In all tissues, detected DMRs were preferentially found at genomic regions associated with gene expression regulation (e.g., CpG islands and shores, 5' UTRs, promoters, and exons). An analysis of GO terms associated with DMR-containing genes identified imprinted genes to be impacted by both Pb and DEHP exposure. Of these, Gnas and Grb10 contained DMRs across tissues, sexes, and exposures. DMRs were enriched in the imprinting control regions (ICRs) of Gnas and Grb10, with 15 and 17 ICR-located DMRs across cortex, blood, and liver in each gene, respectively. The ICRs were also the location of DMRs replicated across target and surrogate tissues, suggesting epigenetic changes these regions may be potentially viable biomarkers. Conclusions We observed Pb- and DEHP-specific DNAm changes in cortex, blood, and liver, and the greatest degree of overlap in DMR signatures was seen between exposures followed by sex and tissue type. DNAm at imprinted control regions was altered by both Pb and DEHP, highlighting the susceptibility of genomic imprinting to these exposures during the perinatal window of development.
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Affiliation(s)
- Rachel K. Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Claudia Lalancette
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raymond Cavalcante
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi Prasasya
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Neier
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bambarendage P.U. Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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Ehlinger JV, Goodrich JM, Dolinoy DC, Watkins DJ, Cantoral A, Mercado-García A, Téllez-Rojo MM, Peterson KE. Associations between blood leukocyte DNA methylation and sustained attention in mid-to-late childhood. Epigenomics 2023; 15:965-981. [PMID: 37942546 PMCID: PMC10718163 DOI: 10.2217/epi-2023-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023] Open
Abstract
Aims: To identify associations between DNA methylation (DNAm) across the epigenome and symptoms related to attention-deficit/hyperactivity disorder in a population of Hispanic children. Materials & methods: Among 517 participants in the ELEMENT study aged 9-18 years, we conducted an epigenome-wide association study examining associations between blood leukocyte DNAm and performance on the Conners' continuous performance test (CPT3). Results: DNAm at loci in or near ZNF814, ELF4 and OR6K6 and functional enrichment for gene pathways pertaining to ferroptosis, inflammation, immune response and neurotransmission were significantly related to CPT3 scores. Conclusion: DNAm was associated with CPT3 performance. Further analysis is warranted to understand how these genes and enriched pathways contribute to attention-deficit/hyperactivity disorder.
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Affiliation(s)
- Jessa V Ehlinger
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jaclyn M Goodrich
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Deborah J Watkins
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | - Karen E Peterson
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan, Ann Arbor, MI 48109, USA
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17
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Kadalayil L, Alam MZ, White CH, Ghantous A, Walton E, Gruzieva O, Merid SK, Kumar A, Roy RP, Solomon O, Huen K, Eskenazi B, Rzehak P, Grote V, Langhendries JP, Verduci E, Ferre N, Gruszfeld D, Gao L, Guan W, Zeng X, Schisterman EF, Dou JF, Bakulski KM, Feinberg JI, Soomro MH, Pesce G, Baiz N, Isaevska E, Plusquin M, Vafeiadi M, Roumeliotaki T, Langie SAS, Standaert A, Allard C, Perron P, Bouchard L, van Meel ER, Felix JF, Jaddoe VWV, Yousefi PD, Ramlau-Hansen CH, Relton CL, Tobi EW, Starling AP, Yang IV, Llambrich M, Santorelli G, Lepeule J, Salas LA, Bustamante M, Ewart SL, Zhang H, Karmaus W, Röder S, Zenclussen AC, Jin J, Nystad W, Page CM, Magnus M, Jima DD, Hoyo C, Maguire RL, Kvist T, Czamara D, Räikkönen K, Gong T, Ullemar V, Rifas-Shiman SL, Oken E, Almqvist C, Karlsson R, Lahti J, Murphy SK, Håberg SE, London S, Herberth G, Arshad H, Sunyer J, Grazuleviciene R, Dabelea D, Steegers-Theunissen RPM, Nohr EA, Sørensen TIA, Duijts L, Hivert MF, Nelen V, Popovic M, Kogevinas M, Nawrot TS, Herceg Z, Annesi-Maesano I, Fallin MD, Yeung E, Breton CV, Koletzko B, Holland N, Wiemels JL, Melén E, Sharp GC, Silver MJ, Rezwan FI, Holloway JW. Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude. Clin Epigenetics 2023; 15:148. [PMID: 37697338 PMCID: PMC10496224 DOI: 10.1186/s13148-023-01542-5] [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: 02/13/2023] [Accepted: 07/27/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Seasonal variations in environmental exposures at birth or during gestation are associated with numerous adult traits and health outcomes later in life. Whether DNA methylation (DNAm) plays a role in the molecular mechanisms underlying the associations between birth season and lifelong phenotypes remains unclear. METHODS We carried out epigenome-wide meta-analyses within the Pregnancy And Childhood Epigenetic Consortium to identify associations of DNAm with birth season, both at differentially methylated probes (DMPs) and regions (DMRs). Associations were examined at two time points: at birth (21 cohorts, N = 9358) and in children aged 1-11 years (12 cohorts, N = 3610). We conducted meta-analyses to assess the impact of latitude on birth season-specific associations at both time points. RESULTS We identified associations between birth season and DNAm (False Discovery Rate-adjusted p values < 0.05) at two CpGs at birth (winter-born) and four in the childhood (summer-born) analyses when compared to children born in autumn. Furthermore, we identified twenty-six differentially methylated regions (DMR) at birth (winter-born: 8, spring-born: 15, summer-born: 3) and thirty-two in childhood (winter-born: 12, spring and summer: 10 each) meta-analyses with few overlapping DMRs between the birth seasons or the two time points. The DMRs were associated with genes of known functions in tumorigenesis, psychiatric/neurological disorders, inflammation, or immunity, amongst others. Latitude-stratified meta-analyses [higher (≥ 50°N), lower (< 50°N, northern hemisphere only)] revealed differences in associations between birth season and DNAm by birth latitude. DMR analysis implicated genes with previously reported links to schizophrenia (LAX1), skin disorders (PSORS1C, LTB4R), and airway inflammation including asthma (LTB4R), present only at birth in the higher latitudes (≥ 50°N). CONCLUSIONS In this large epigenome-wide meta-analysis study, we provide evidence for (i) associations between DNAm and season of birth that are unique for the seasons of the year (temporal effect) and (ii) latitude-dependent variations in the seasonal associations (spatial effect). DNAm could play a role in the molecular mechanisms underlying the effect of birth season on adult health outcomes.
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Affiliation(s)
- Latha Kadalayil
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Md Zahangir Alam
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Cory Haley White
- Merck Exploratory Science Center in Cambridge MA, Merck Research Laboratories, Cambridge, MA, 02141, USA
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Esther Walton
- Department of Psychology, University of Bath, Bath, UK
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Simon Kebede Merid
- Centre for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Ashish Kumar
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Ritu P Roy
- Helen Diller Family Comprehensive Cancer Center University of California, San Francisco, CA, 94143, USA
- Computational Biology and Informatics Core, University of California, San Francisco, CA, 94143, USA
| | - Olivia Solomon
- Children's Environmental Health Laboratory, University of California, Berkeley, CA, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, University of California, Berkeley, CA, USA
| | - Brenda Eskenazi
- Children's Environmental Health Laboratory, University of California, Berkeley, CA, USA
| | - Peter Rzehak
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | | | - Elvira Verduci
- Department of Pediatrics, Vittore Buzzi Children Hospital, University of Milan, Milan, Italy
| | - Natalia Ferre
- Pediatric Nutrition and Human Development Research Unit, Universitat Rovira i Virgili, IISPV, Reus, Spain
| | - Darek Gruszfeld
- Neonatal Department, Children's Memorial Health Institute, Warsaw, Poland
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, MMC 303, 420 Delaware St. SE, Minneapolis, MN, 55455, USA
| | | | - Enrique F Schisterman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Drive, Philadelphia, PA, 19104, USA
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Jason I Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities Johns Hopkins University, Baltimore, MD, USA
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Munawar Hussain Soomro
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris Cedex 12, France
- Department of Community Medicine and Public Health, SMBB Medical University, Larkana, Pakistan
| | - Giancarlo Pesce
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris Cedex 12, France
| | - Nour Baiz
- Institut Desbrest de Santé Publique (IDESP), INSERM and Montpellier University, Montpellier, France
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, CPO Piemonte, Italy
| | - Michelle Plusquin
- Center for Environmental Sciences, University of Hasselt, 3590, Diepenbeek, Belgium
| | - Marina Vafeiadi
- Department of Social Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Theano Roumeliotaki
- Department of Social Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Sabine A S Langie
- Unit Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Faculty of Sciences, Hasselt University, Diepenbeek, Belgium
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Limburg, The Netherlands
| | - Arnout Standaert
- Unit Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Canada
| | - Patrice Perron
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, Canada
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Universite de Sherbrooke, Sherbrooke, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-Saint-Jean - Hôpital de Chicoutimi, Chicoutimi, Canada
| | - Evelien R van Meel
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Paul D Yousefi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Elmar W Tobi
- Periconceptional Epidemiology, Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Anne P Starling
- Life Course Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ivana V Yang
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Maria Llambrich
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | | | - Johanna Lepeule
- Institute for Advanced Biosciences, University Grenoble-Alpes, INSERM, CNRS, Grenoble, France
| | - Lucas A Salas
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
- Center for Molecular Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
- Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Lebanon, NH, USA
| | - Mariona Bustamante
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan L Ewart
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Stefan Röder
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ana Claudia Zenclussen
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jianping Jin
- 2530 Meridian Pkwy, Suite 200, Durham, NC 27713, USA
| | - Wenche Nystad
- Department of Chronic Diseases and Ageing, Norwegian Institute of Public Health, Oslo, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Section for Statistics and Data Science, Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Maria Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Obstetrics and Gynaecology, Duke University Medical Center, Durham, NC, USA
| | - Tuomas Kvist
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, 80804, Munich, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Tong Gong
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sheryl L Rifas-Shiman
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, USA
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, USA
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Susan K Murphy
- Department of Obstetrics and Gynaecology, Duke University Medical Center, Durham, NC, USA
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, NC, 27709, USA
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
- NIHR Southampton Biomedical Research Centre, Southampton General Hospital, Southampton, UK
| | - Jordi Sunyer
- Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Regina Grazuleviciene
- Department of Environmental Science, Vytautas Magnus University, 44248, Kaunas, Lithuania
| | - Dana Dabelea
- Life Course Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Régine P M Steegers-Theunissen
- Periconceptional Epidemiology, Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Ellen A Nohr
- Department of Clinical Research, Odense Universitetshospital, Odense, Denmark
| | - Thorkild I A Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Division of Neonatology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Vera Nelen
- Provincial Institute for Hygiene, Antwerp, Belgium
| | - Maja Popovic
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, CPO Piemonte, Italy
| | | | - Tim S Nawrot
- Center for Environmental Sciences, University of Hasselt, 3590, Diepenbeek, Belgium
- Department of Public Health and Primary Care, Leuven University, Louvain, Belgium
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Isabella Annesi-Maesano
- Institut Desbrest de Santé Publique (IDESP), INSERM and Montpellier University, Montpellier, France
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities Johns Hopkins University, Baltimore, MD, USA
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Edwina Yeung
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 6710B Rockledge Dr, MSC 7004, Bethesda, MD, USA
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Nina Holland
- Children's Environmental Health Laboratory, CERCH, Berkeley Public Health, University of California, 2121 Berkeley Way #5216, Berkeley, CA, 94720, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, 90033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Psychology, University of Exeter, Exeter, UK
| | - Matt J Silver
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Medical Research Council Unit, The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
- Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
- NIHR Southampton Biomedical Research Centre, Southampton General Hospital, Southampton, UK.
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18
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Liu W, Yang X, Mao Z, Du Y, Lassiter C, AlAkwaa FM, Benny PA, Garmire LX. Severe preeclampsia is not associated with significant DNA methylation changes but cell proportion changes in the cord blood - caution on the importance of confounding adjustment. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.31.23294898. [PMID: 37693517 PMCID: PMC10491383 DOI: 10.1101/2023.08.31.23294898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Epigenome-wide DNA methylation analysis (EWAS) is an important approach to identify biomarkers for early disease detection and prognosis prediction, yet its results could be confounded by other factors such as cell-type heterogeneity and patient characteristics. In this study, we address the importance of confounding adjustment by examining DNA methylation patterns in cord blood exposed to severe preeclampsia (PE), a prevalent and potentially fatal pregnancy complication. Without such adjustment, a misleading global hypomethylation pattern is obtained. However, after adjusting cell type proportions and patient clinical characteristics, most of the so-called significant CpG methylation changes associated with severe PE disappear. Rather, the major effect of PE on cord blood is through the proportion changes in different cell types. These results are validated using a previously published cord blood DNA methylation dataset, where global hypomethylation pattern was also wrongfully obtained without confounding adjustment. Additionally, several cell types significantly change as gestation progress (eg. granulocyte, nRBC, CD4T, and B cells), further confirming the importance of cell type adjustment in EWAS study of cord blood tissues. Our study urges the community to perform confounding adjustments in EWAS studies, based on cell type heterogeneity and other patient characteristics.
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Affiliation(s)
- Wenting Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Xiaotong Yang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Zhixin Mao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Yuheng Du
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | | | - Fadhl M AlAkwaa
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Paula A Benny
- University of Hawaii Cancer Center, Epidemiology, Honolulu, HI
| | - Lana X Garmire
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
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Si J, Meir AY, Hong X, Wang G, Huang W, Pearson C, Adams WG, Wang X, Liang L. Maternal pre-pregnancy BMI, offspring epigenome-wide DNA methylation, and childhood obesity: findings from the Boston Birth Cohort. BMC Med 2023; 21:317. [PMID: 37612641 PMCID: PMC10463574 DOI: 10.1186/s12916-023-03003-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/25/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Maternal pre-pregnancy obesity is an established risk factor for childhood obesity. Investigating epigenetic alterations induced by maternal obesity during fetal development could gain mechanistic insight into the developmental origins of childhood obesity. While obesity disproportionately affects underrepresented racial and ethnic mothers and children in the USA, few studies investigated the role of prenatal epigenetic programming in intergenerational obesity of these high-risk populations. METHODS This study included 903 mother-child pairs from the Boston Birth Cohort, a predominantly urban, low-income minority birth cohort. Mother-infant dyads were enrolled at birth and the children were followed prospectively to age 18 years. Infinium Methylation EPIC BeadChip was used to measure epigenome-wide methylation level of cord blood. We performed an epigenome-wide association study of maternal pre-pregnancy body mass index (BMI) and cord blood DNA methylation (DNAm). To quantify the degree to which cord blood DNAm mediates the maternal BMI-childhood obesity, we further investigated whether maternal BMI-associated DNAm sites impact birthweight or childhood overweight or obesity (OWO) from age 1 to age 18 and performed corresponding mediation analyses. RESULTS The study sample contained 52.8% maternal pre-pregnancy OWO and 63.2% offspring OWO at age 1-18 years. Maternal BMI was associated with cord blood DNAm at 8 CpG sites (genome-wide false discovery rate [FDR] < 0.05). After accounting for the possible interplay of maternal BMI and smoking, 481 CpG sites were discovered for association with maternal BMI. Among them 123 CpGs were associated with childhood OWO, ranging from 42% decrease to 87% increase in OWO risk for each SD increase in DNAm. A total of 14 identified CpG sites showed a significant mediation effect on the maternal BMI-child OWO association (FDR < 0.05), with mediating proportion ranging from 3.99% to 25.21%. Several of these 14 CpGs were mapped to genes in association with energy balance and metabolism (AKAP7) and adulthood metabolic syndrome (CAMK2B). CONCLUSIONS This prospective birth cohort study in a high-risk yet understudied US population found that maternal pre-pregnancy OWO significantly altered DNAm in newborn cord blood and provided suggestive evidence of epigenetic involvement in the intergenerational risk of obesity.
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Affiliation(s)
- Jiahui Si
- Departments of Epidemiology and Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anat Yaskolka Meir
- Departments of Epidemiology and Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xiumei Hong
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Guoying Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Wanyu Huang
- Department of Civil and Systems Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - Colleen Pearson
- Department of Pediatrics, Boston University Chobanian & Avedisian School of Medicine and Boston Medical Center, Boston, MA, USA
| | - William G Adams
- Department of Pediatrics, Boston University Chobanian & Avedisian School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Xiaobin Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Liming Liang
- Departments of Epidemiology and Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Li Y, Hong X, Liang L, Wang X, Ladd-Acosta C. Association between acetaminophen metabolites and CYP2E1 DNA methylation level in neonate cord blood in the Boston Birth Cohort. Clin Epigenetics 2023; 15:132. [PMID: 37596607 PMCID: PMC10439592 DOI: 10.1186/s13148-023-01551-4] [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: 03/08/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Acetaminophen is a commonly used medication by pregnant women and is known to cross the placenta. However, little is known about the biological mechanisms that regulate acetaminophen in the developing offspring. Cytochrome 2E1 (CYP2E1) is the primary enzyme responsible for the conversion of acetaminophen to its toxic metabolite. Ex vivo studies have shown that the CYP2E1 gene expression in human fetal liver and placenta is largely controlled by DNA methylation (DNAm) at CpG sites located in the gene body of CYP2E1 at the 5' end. To date, no population studies have examined the association between acetaminophen metabolite and fetal DNAm of CYP2E1 at birth. METHODS We utilized data from the Boston Birth Cohort (BBC) which represents an urban, low-income, racially and ethnically diverse population in Boston, Massachusetts. Acetaminophen metabolites were measured in the cord plasma of newborns enrolled in BBC between 2003 and 2013 using liquid chromatography-tandem mass spectrometry. DNAm at 28 CpG sites of CYP2E1 was measured by Illumina Infinium MethylationEPIC BeadChip. We used linear regression to identify differentially methylated CpG sites and the "DiffVar" method to identify differences in methylation variation associated with the detection of acetaminophen, adjusting for cell heterogeneity and batch effects. The false discovery rate (FDR) was calculated to account for multiple comparisons. RESULTS Among the 570 newborns included in this study, 96 (17%) had detectable acetaminophen in cord plasma. We identified 7 differentially methylated CpGs (FDR < 0.05) associated with the detection of acetaminophen and additional 4 CpGs showing a difference in the variation of methylation (FDR < 0.05). These CpGs were all located in the gene body of CYP2E1 at the 5' end and had a 3-6% lower average methylation level among participants with detectable acetaminophen compared to participants without. The CpG sites we identified overlap with previously identified DNase hypersensitivity and open chromatin regions in the ENCODE project, suggesting potential regulatory functions. CONCLUSIONS In a US birth cohort, we found detection of cord biomarkers of acetaminophen was associated with DNAm level of CYP2E1 in cord blood. Our findings suggest that DNA methylation of CYP2E1 may be an important regulator of acetaminophen levels in newborns.
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Affiliation(s)
- Yijun Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street W6509, Baltimore, MD, 21205, USA
| | - Xiumei Hong
- Center on the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xiaobin Wang
- Center on the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street W6509, Baltimore, MD, 21205, USA.
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21
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Niemiec SS, Kechris K, Pattee J, Yang IV, Adgate JL, Calafat AM, Dabelea D, Starling AP. Prenatal exposures to per- and polyfluoroalkyl substances and epigenetic aging in umbilical cord blood: The Healthy Start study. ENVIRONMENTAL RESEARCH 2023; 231:116215. [PMID: 37224946 PMCID: PMC10330919 DOI: 10.1016/j.envres.2023.116215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/19/2023] [Accepted: 05/20/2023] [Indexed: 05/26/2023]
Abstract
BACKGROUND Per- and polyfluoroalkyl substances (PFAS) are ubiquitous, environmentally persistent chemicals, and prenatal exposures have been associated with adverse child health outcomes. Prenatal PFAS exposure may lead to epigenetic age acceleration (EAA), defined as the discrepancy between an individual's chronologic and epigenetic or biological age. OBJECTIVES We estimated associations of maternal serum PFAS concentrations with EAA in umbilical cord blood DNA methylation using linear regression, and a multivariable exposure-response function of the PFAS mixture using Bayesian kernel machine regression. METHODS Five PFAS were quantified in maternal serum (median: 27 weeks of gestation) among 577 mother-infant dyads from a prospective cohort. Cord blood DNA methylation data were assessed with the Illumina HumanMethylation450 array. EAA was calculated as the residuals from regressing gestational age on epigenetic age, calculated using a cord-blood specific epigenetic clock. Linear regression tested for associations between each maternal PFAS concentration with EAA. Bayesian kernel machine regression with hierarchical selection estimated an exposure-response function for the PFAS mixture. RESULTS In single pollutant models we observed an inverse relationship between perfluorodecanoate (PFDA) and EAA (-0.148 weeks per log-unit increase, 95% CI: -0.283, -0.013). Mixture analysis with hierarchical selection between perfluoroalkyl carboxylates and sulfonates indicated the carboxylates had the highest group posterior inclusion probability (PIP), or relative importance. Within this group, PFDA had the highest conditional PIP. Univariate predictor-response functions indicated PFDA and perfluorononanoate were inversely associated with EAA, while perfluorohexane sulfonate had a positive association with EAA. CONCLUSIONS Maternal mid-pregnancy serum concentrations of PFDA were negatively associated with EAA in cord blood, suggesting a pathway by which prenatal PFAS exposures may affect infant development. No significant associations were observed with other PFAS. Mixture models suggested opposite directions of association between perfluoroalkyl sulfonates and carboxylates. Future studies are needed to determine the importance of neonatal EAA for later child health outcomes.
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Affiliation(s)
- Sierra S Niemiec
- Center for Innovative Design and Analysis, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Katerina Kechris
- Center for Innovative Design and Analysis, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jack Pattee
- Center for Innovative Design and Analysis, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ivana V Yang
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - John L Adgate
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Antonia M Calafat
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Anne P Starling
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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22
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Rahimi S, Shao X, Chan D, Martel J, Bérard A, Fraser WD, Simon MM, Kwan T, Bourque G, Trasler J. Capturing sex-specific and hypofertility-linked effects of assisted reproductive technologies on the cord blood DNA methylome. Clin Epigenetics 2023; 15:82. [PMID: 37170172 PMCID: PMC10176895 DOI: 10.1186/s13148-023-01497-7] [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: 09/12/2022] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Children conceived through assisted reproduction are at an increased risk for growth and genomic imprinting disorders, often linked to DNA methylation defects. It has been suggested that assisted reproductive technology (ART) and underlying parental infertility can induce epigenetic instability, specifically interfering with DNA methylation reprogramming events during germ cell and preimplantation development. To date, human studies exploring the association between ART and DNA methylation defects have reported inconsistent or inconclusive results, likely due to population heterogeneity and the use of technologies with limited coverage of the epigenome. In our study, we explored the epigenetic risk of ART by comprehensively profiling the DNA methylome of 73 human cord blood samples of singleton pregnancies (n = 36 control group, n = 37 ART/hypofertile group) from a human prospective longitudinal birth cohort, the 3D (Design, Develop, Discover) Study, using a high-resolution sequencing-based custom capture panel that examines over 2.4 million autosomal CpGs in the genome. RESULTS We identified evidence of sex-specific effects of ART/hypofertility on cord blood DNA methylation patterns. Our genome-wide analyses identified ~ 46% more CpGs affected by ART/hypofertility in female than in male infant cord blood. We performed a detailed analysis of three imprinted genes which have been associated with altered DNA methylation following ART (KCNQ1OT1, H19/IGF2 and GNAS) and found that female infant cord blood was associated with DNA hypomethylation. When compared to less invasive procedures such as intrauterine insemination, more invasive ARTs (in vitro fertilization, intracytoplasmic sperm injection, embryo culture) resulted in more marked and distinct effects on the cord blood DNA methylome. In the in vitro group, we found a close to fourfold higher proportion of significantly enriched Gene Ontology terms involved in development than in the in vivo group. CONCLUSIONS Our study highlights the ability of a sensitive, targeted, sequencing-based approach to uncover DNA methylation perturbations in cord blood associated with hypofertility and ART and influenced by offspring sex and ART technique invasiveness.
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Affiliation(s)
- Sophia Rahimi
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Donovan Chan
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Josée Martel
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Anick Bérard
- Research Unit On Medications and Pregnancy, Research Centre, CHU Sainte-Justine, Montreal, Canada
- Faculty of Pharmacy, Université de Montréal, Montreal, QC, Canada
- Faculty of Medicine, Université Claude Bernard Lyon 1, Lyon, France
| | - William D Fraser
- Department of Obstetrics and Gynecology, Université de Sherbrooke and Centre de Recherche du CHUS, Sherbrooke, QC, Canada
| | | | - Tony Kwan
- McGill University Genome Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Guillaume Bourque
- McGill University Genome Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jacquetta Trasler
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada.
- Department of Pediatrics, McGill University, Montreal, QC, Canada.
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23
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Meir AY, Huang W, Cao T, Hong X, Wang G, Pearson C, Adams WG, Wang X, Liang L. Umbilical cord DNA methylation is associated with body mass index trajectories from birth to adolescence. EBioMedicine 2023; 91:104550. [PMID: 37088033 PMCID: PMC10141503 DOI: 10.1016/j.ebiom.2023.104550] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 02/27/2023] [Accepted: 03/15/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND DNA methylation (DNAm) in cord blood has been associated with various prenatal factors and birth outcomes. This study sought to fill an important knowledge gap: the link of cord DNAm with child postnatal growth trajectories from birth to age 18 years (y). METHODS Using data from a US predominantly urban, low-income, multi-ethnic birth cohort (N = 831), we first applied non-parametric methods to identify body-mass-index percentile (BMIPCT) trajectories from birth to age 18 y (the outcome); then, conducted epigenome-wide association study (EWAS) of the outcome, interrogating over 700,000 CpG sites profiled by the Illumina Infinium MethylationEPIC BeadChip. Multivariate linear regression models and likelihood ratio tests (LRT) were applied to examine the DNAm-outcome association in the overall sample and sex strata. FINDINGS We identified four distinct patterns of BMIPCT trajectories: normal weight (NW), Early overweight or obesity (OWO), Late OWO, and normal to very late OWO. DNAm at CpG18582997 annotated to TPGS1, CpG15241084 of TLR7, and cg24350936 of RAB31 were associated with BMIPCT at birth-to-3 y, 10 y, and 14 y, respectively (LRT FDR < 0.05 for all). INTERPRETATION In this prospective birth cohort study, we identified 4 distinct and robust patterns of growth trajectories from birth to 18 y, which were associated with variations in cord blood DNAm at genes implicated in inflammation induction pathways. These findings, if further replicated, raise the possibility that these DNAm markers along with early assessment of BMIPCT trajectories may help identify young children at high-risk for obesity later in life. FUNDING Detailed in the Acknowledgements section.
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Affiliation(s)
- Anat Yaskolka Meir
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building II, 2nd Floor, Boston, MA 02115, USA
| | - Wanyu Huang
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, John Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Civil and Systems Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Tingyi Cao
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building II, 4th Floor, Boston, MA 02115, USA
| | - Xiumei Hong
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, John Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Guoying Wang
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, John Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Colleen Pearson
- Department of Pediatrics, Boston University School of Medicine and Boston Medical Center, 1 Boston Medical Center Pl, Boston, MA 02118, USA
| | - William G Adams
- Department of Pediatrics, Boston University School of Medicine and Boston Medical Center, 1 Boston Medical Center Pl, Boston, MA 02118, USA
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, John Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building II, 2nd Floor, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building II, 4th Floor, Boston, MA 02115, USA.
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24
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Romanowska J, Nustad HE, Page CM, Denault WRP, Lee Y, Magnus MC, Haftorn KL, Gjerdevik M, Novakovic B, Saffery R, Gjessing HK, Lyle R, Magnus P, Håberg SE, Jugessur A. The X-factor in ART: does the use of assisted reproductive technologies influence DNA methylation on the X chromosome? Hum Genomics 2023; 17:35. [PMID: 37085889 PMCID: PMC10122315 DOI: 10.1186/s40246-023-00484-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Assisted reproductive technologies (ART) may perturb DNA methylation (DNAm) in early embryonic development. Although a handful of epigenome-wide association studies of ART have been published, none have investigated CpGs on the X chromosome. To bridge this knowledge gap, we leveraged one of the largest collections of mother-father-newborn trios of ART and non-ART (natural) conceptions to date to investigate sex-specific DNAm differences on the X chromosome. The discovery cohort consisted of 982 ART and 963 non-ART trios from the Norwegian Mother, Father, and Child Cohort Study (MoBa). To verify our results from the MoBa cohort, we used an external cohort of 149 ART and 58 non-ART neonates from the Australian 'Clinical review of the Health of adults conceived following Assisted Reproductive Technologies' (CHART) study. The Illumina EPIC array was used to measure DNAm in both datasets. In the MoBa cohort, we performed a set of X-chromosome-wide association studies ('XWASs' hereafter) to search for sex-specific DNAm differences between ART and non-ART newborns. We tested several models to investigate the influence of various confounders, including parental DNAm. We also searched for differentially methylated regions (DMRs) and regions of co-methylation flanking the most significant CpGs. Additionally, we ran an analogous model to our main model on the external CHART dataset. RESULTS In the MoBa cohort, we found more differentially methylated CpGs and DMRs in girls than boys. Most of the associations persisted after controlling for parental DNAm and other confounders. Many of the significant CpGs and DMRs were in gene-promoter regions, and several of the genes linked to these CpGs are expressed in tissues relevant for both ART and sex (testis, placenta, and fallopian tube). We found no support for parental DNAm-dependent features as an explanation for the observed associations in the newborns. The most significant CpG in the boys-only analysis was in UBE2DNL, which is expressed in testes but with unknown function. The most significant CpGs in the girls-only analysis were in EIF2S3 and AMOT. These three loci also displayed differential DNAm in the CHART cohort. CONCLUSIONS Genes that co-localized with the significant CpGs and DMRs associated with ART are implicated in several key biological processes (e.g., neurodevelopment) and disorders (e.g., intellectual disability and autism). These connections are particularly compelling in light of previous findings indicating that neurodevelopmental outcomes differ in ART-conceived children compared to those naturally conceived.
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Affiliation(s)
- Julia Romanowska
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.
| | - Haakon E Nustad
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- DeepInsight, 0154, Oslo, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - William R P Denault
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristine L Haftorn
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Miriam Gjerdevik
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Computer Science, Electrical Engineering and Mathematical Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Boris Novakovic
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Robert Lyle
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
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25
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Bozack AK, Rifas-Shiman SL, Gold DR, Laubach ZM, Perng W, Hivert MF, Cardenas A. DNA methylation age at birth and childhood: performance of epigenetic clocks and characteristics associated with epigenetic age acceleration in the Project Viva cohort. Clin Epigenetics 2023; 15:62. [PMID: 37046280 PMCID: PMC10099681 DOI: 10.1186/s13148-023-01480-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/05/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Epigenetic age acceleration (EAA) and epigenetic gestational age acceleration (EGAA) are biomarkers of physiological development and may be affected by the perinatal environment. The aim of this study was to evaluate performance of epigenetic clocks and to identify biological and sociodemographic correlates of EGAA and EAA at birth and in childhood. In the Project Viva pre-birth cohort, DNA methylation was measured in nucleated cells in cord blood (leukocytes and nucleated red blood cells, N = 485) and leukocytes in early (N = 120, median age = 3.2 years) and mid-childhood (N = 460, median age = 7.7 years). We calculated epigenetic gestational age (EGA; Bohlin and Knight clocks) and epigenetic age (EA; Horvath and skin & blood clocks), and respective measures of EGAA and EAA. We evaluated the performance of clocks relative to chronological age using correlations and median absolute error. We tested for associations of maternal-child characteristics with EGAA and EAA using mutually adjusted linear models controlling for estimated cell type proportions. We also tested associations of Horvath EA at birth with childhood EAA. RESULTS Bohlin EGA was strongly correlated with chronological gestational age (Bohlin EGA r = 0.82, p < 0.001). Horvath and skin & blood EA were weakly correlated with gestational age, but moderately correlated with chronological age in childhood (r = 0.45-0.65). Maternal smoking during pregnancy was associated with higher skin & blood EAA at birth [B (95% CI) = 1.17 weeks (- 0.09, 2.42)] and in early childhood [0.34 years (0.03, 0.64)]. Female newborns and children had lower Bohlin EGAA [- 0.17 weeks (- 0.30, - 0.04)] and Horvath EAA at birth [B (95% CI) = - 2.88 weeks (- 4.41, - 1.35)] and in childhood [early childhood: - 0.3 years (- 0.60, 0.01); mid-childhood: - 0.48 years (- 0.77, - 0.18)] than males. When comparing self-reported Asian, Black, Hispanic, and more than one race or other racial/ethnic groups to White, we identified significant differences in EGAA and EAA at birth and in mid-childhood, but associations varied across clocks. Horvath EA at birth was positively associated with childhood Horvath and skin & blood EAA. CONCLUSIONS Maternal smoking during pregnancy and child sex were associated with EGAA and EAA at multiple timepoints. Further research may provide insight into the relationship between perinatal factors, pediatric epigenetic aging, and health and development across the lifespan.
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Affiliation(s)
- Anne K Bozack
- Department of Epidemiology and Population Health, Stanford University, Research Park, 1701 Page Mill Road, Stanford, CA, USA
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Diane R Gold
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Zachary M Laubach
- Department of Ecology and Evolutionary Biology (EEB), University of Colorado Boulder, Boulder, CO, USA
| | - Wei Perng
- Department of Epidemiology, Colorado School of Public Health and Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University, Research Park, 1701 Page Mill Road, Stanford, CA, USA.
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Wang G, Xu R, Zhang B, Hong X, Bartell TR, Pearson C, Liang L, Wang X. Impact of intrauterine exposure to maternal diabetes on preterm birth: fetal DNA methylation alteration is an important mediator. Clin Epigenetics 2023; 15:59. [PMID: 37029435 PMCID: PMC10082529 DOI: 10.1186/s13148-023-01473-1] [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: 01/08/2023] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND In utero exposure to diabetes has been shown to contribute to preterm birth, though the underlying biological mechanisms are yet to be fully elucidated. Fetal epigenetic variations established in utero may be a possible pathway. This study aimed to investigate whether in utero exposure to diabetes was associated with a change in newborn DNA methylation, and whether the identified CpG sites mediate the association between diabetes and preterm birth in a racially diverse birth cohort population. METHODS This study included 954 mother-newborn pairs. Methylation levels in the cord blood were determined using the Illumina Infinium MethylationEPIC BeadChip 850 K array platform. In utero exposure to diabetes was defined by the presence of maternal pregestational or gestational diabetes. Preterm birth was defined as gestational age at birth less than 37 weeks. Linear regression analysis was employed to identify differentially methylated CpG sites. Differentially methylated regions were identified using the DMRcate Package. RESULTS 126 (13%) newborns were born to mothers with diabetes in pregnancy and 173 (18%) newborns were born preterm, while 41 newborns were born both preterm and to mothers with diabetes in pregnancy. Genomic-wide CpG analysis found that eighteen CpG sites in cord blood were differentially methylated by maternal diabetes status at an FDR threshold of 5%. These significant CpG sites were mapped to 12 known genes, one of which was annotated to gene Major Histocompatibility Complex, Class II, DM Beta (HLA-DMB). Consistently, one of the two identified significant methylated regions overlapped with HLA-DMB. The identified differentially methylated CpG sites mediated the association between diabetes in pregnancy and preterm birth by 61%. CONCLUSIONS In this US birth cohort, we found that maternal diabetes was associated with altered fetal DNA methylation patterns, which substantially explained the link between diabetes and preterm birth.
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Affiliation(s)
- Guoying Wang
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205-2179, USA.
| | - Richard Xu
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Boyang Zhang
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Xiumei Hong
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205-2179, USA
| | - Tami R Bartell
- Patrick M. Magoon Institute for Healthy Communities, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Colleen Pearson
- Department of Pediatrics, Boston University Chobanian & Avedisian School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xiaobin Wang
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205-2179, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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27
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Parsons E, Rifas-Shiman SL, Bozack AK, Baccarelli AA, DeMeo DL, Hivert MF, Godderis L, Duca RC, Oken E, Cardenas A. Prenatal trimester-specific intake of micronutrients: global DNA methylation and hydroxymethylation at birth and persistence in childhood. J Dev Orig Health Dis 2023; 14:311-318. [PMID: 36515010 PMCID: PMC9998337 DOI: 10.1017/s2040174422000642] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The prenatal environment may program health and disease susceptibility via epigenetic mechanisms. We evaluated associations of maternal trimester-specific intake of micronutrients with global DNA methylation (%5mC) and 5-hydroxymethylation (%5hmC) at birth in cord blood and tested for persistence into childhood. We quantified global %5mC and %5hmC in cord blood cells (n = 434) and in leukocytes collected in early (n = 108) and mid-childhood (n = 390) from children in Project Viva, a pre-birth cohort from Boston, MA. Validated food frequency questionnaires estimated maternal first- and second-trimester intakes of vitamin B2, vitamin B6, vitamin B12, folate, betaine, choline, methionine, iron, and zinc. Mean (SD) cord blood %5mC and %5hmC was 5.62% (2.04) and 0.25% (0.15), respectively. Each μg increase in first-trimester B12 intake was associated with 0.002 lower %5hmC in cord blood (95% CI: -0.005, -0.0003), and this association persisted in early childhood (β = -0.007; 95% CI: -0.01, -0.001) but not mid-childhood. Second-trimester iron (mg) was associated with 0.01 lower %5mC (95% CI: -0.02, -0.002) and 0.001 lower %5hmC (95% CI: -0.01, -0.00001) in cord blood only. Increased second-trimester zinc (mg) intake was associated with 0.003 greater %5hmC in early childhood (β = 0.003; 95% CI: 0.0004, 0.006). Second-trimester folate was positively associated with %5hmC in early childhood only (β = 0.08, 95% CI: 0.003, 0.16). Associations did not survive multiple testing adjustment; future replication is needed. Trimester-specific nutrients may impact various sensitive windows of epigenetic programming some with lasting effects in childhood. Further research is needed to understand the role of gene-specific epigenetic changes and how global DNA methylation measures relate to child health.
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Affiliation(s)
- Ella Parsons
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sheryl L. Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Anne K. Bozack
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lode Godderis
- Centre for Environment & Health, Department of Public Health & Primary Care, University of Leuven (KU Leuven), Belgium
- IDEWE, External service for prevention and protection at work, Heverlee, Belgium
| | - Radu-Corneliu Duca
- Centre for Environment & Health, Department of Public Health & Primary Care, University of Leuven (KU Leuven), Belgium
- Environmantal Hygiene and Biological Surveillance at the National Health Laboratory (LNS), Luxembourg
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
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28
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Petroff RL, Cavalcante RG, Langen ES, Dolinoy DC, Padmanabhan V, Goodrich JM. Mediation effects of DNA methylation and hydroxymethylation on birth outcomes after prenatal per- and polyfluoroalkyl substances (PFAS) exposure in the Michigan mother-infant Pairs cohort. Clin Epigenetics 2023; 15:49. [PMID: 36964604 PMCID: PMC10037903 DOI: 10.1186/s13148-023-01461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/05/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND Per- and polyfluoroalkyl substances (PFAS) are chemicals that are resistant to degradation and ubiquitous in our environments. PFAS may impact the developing epigenome, but current human evidence is limited to assessments of total DNA methylation. We assessed associations between first trimester PFAS exposures with newborn DNA methylation, including 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC). DNA methylation mediation of associations between PFAS and birth outcomes were explored in the Michigan Mother Infant Pairs cohort. Nine PFAS were measured in maternal first trimester blood. Seven were highly detected and included for analysis: PFHxS, PFOA, PFOS, PFNA, PFDA, PFUnDA, and MeFOSAA. Bisulfite-converted cord blood DNA (n = 141) and oxidative-bisulfite-converted cord blood (n = 70) were assayed on Illumina MethylationEPIC BeadChips to measure total DNA methylation (5-mC + 5-hmC) and 5-mC/5-hmC. Correcting for multiple comparisons, beta regressions were used to assess associations between levels of PFAS and total methylation, 5-mC, or 5-hmC. Nonlinear mediation analyses were used to assess the epigenetic meditation effect between PFAS and birth outcomes. RESULTS PFAS was significantly associated with total methylation (q < 0.05: PFHxS-12 sites; PFOS-19 sites; PFOA-2 sites; PFNA-3 sites; PFDA-4 sites). In 72 female infants and 69 male infants, there were sex-specific associations between five PFAS and DNA methylation. 5-mC and 5-hmC were each significantly associated with thousands of sites for PFHxS, PFOS, PFNA, PFDA, PFUnDA, and MeFOSAA (q < 0.05). Clusters of 5-mC and 5-hmC sites were significant mediators between PFNA and PFUnDA and decreased gestational age (q < 0.05). CONCLUSIONS This study demonstrates the mediation role of specific types of DNA methylation on the relationship between PFAS exposure and birth outcomes. These results suggest that 5-mC and 5-hmC may be more sensitive to the developmental impacts of PFAS than total DNA methylation.
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Affiliation(s)
- Rebekah L Petroff
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Raymond G Cavalcante
- Epigenomics Core, Biomedical Research Core Facilities, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Elizabeth S Langen
- Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
- Epigenomics Core, Biomedical Research Core Facilities, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
- Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pediatrics Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
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29
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Kupsco A, Bloomquist TR, Hu H, Reddam A, Tang D, Goldsmith J, Rundle AG, Baccarelli AA, Herbstman JB. Mitochondrial DNA copy number dynamics and associations with the prenatal environment from birth through adolescence in a population of Dominican and African American children. Mitochondrion 2023; 69:140-146. [PMID: 36804466 PMCID: PMC10006332 DOI: 10.1016/j.mito.2023.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/17/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
Mitochondrial DNA copy number (mtDNAcn) dynamics throughout childhood are poorly understood. We profiled mtDNAcn from birth through adolescence and evaluated how the prenatal environment influences mtDNAcn across childhood. Data were collected from children from New York City followed through 18 years. Using duplexed qRT-PCR, we quantified mtDNAcn relative to nuclear DNA in blood collected from the umbilical cord (n = 450), children aged 5-7 (n = 510), and adolescents aged 15-18 (n = 278). We examined mtDNAcn across childhood with linear mixed-effects models (LMM). Relative mtDNAcn was lowest at birth (mean ± SD: 0.67 ± 0.35) and increased in childhood (1.24 ± 0.50) then slightly declined in adolescence (1.13 ± 0.44). We observed no differences in mtDNAcn by sex or race/ethnicity. mtDNAcn was positively associated with prenatal environmental tobacco smoke exposure (0.077 [ 0.01, 0.14] change in relative mtDNAcn) but negatively associated with maternal completion of high school (-0.066 [-0.13, 0.00]), with the receipt of public assistance at birth (-0.074 [-0.14, -0.01]), and when mother born outside the U.S (-0.061 [-0.13, 0.003]). Infant birth outcomes were not associated with mtDNAcn. MtDNAcn levels were dynamic through childhood and associated with some prenatal factors, underscoring the need for the investigation of longitudinal mtDNAcn for human health research.
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Affiliation(s)
- Allison Kupsco
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States.
| | - Tessa R Bloomquist
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Heng Hu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Aalekhya Reddam
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Deliang Tang
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Jeff Goldsmith
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Andrew G Rundle
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Julie B Herbstman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
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30
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Apsley AT, Etzel L, Hastings WJ, Heim CC, Noll JG, O'Donnell KJ, Schreier HMC, Shenk CE, Ye Q, Shalev I. Investigating the effects of maltreatment and acute stress on the concordance of blood and DNA methylation methods of estimating immune cell proportions. Clin Epigenetics 2023; 15:33. [PMID: 36855187 PMCID: PMC9976543 DOI: 10.1186/s13148-023-01437-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/05/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Immune cell proportions can be used to detect pathophysiological states and are also critical covariates in genomic analyses. The complete blood count (CBC) is the most common method of immune cell proportion estimation, but immune cell proportions can also be estimated using whole-genome DNA methylation (DNAm). Although the concordance of CBC and DNAm estimations has been validated in various adult and clinical populations, less is known about the concordance of existing estimators among stress-exposed individuals. As early life adversity and acute psychosocial stress have both been associated with unique DNAm alterations, the concordance of CBC and DNAm immune cell proportion needs to be validated in various states of stress. RESULTS We report the correlation and concordance between CBC and DNAm estimates of immune cell proportions using the Illumina EPIC DNAm array within two unique studies: Study 1, a high-risk pediatric cohort of children oversampled for exposure to maltreatment (N = 365, age 8 to 14 years), and Study 2, a sample of young adults who have participated in an acute laboratory stressor with four pre- and post-stress measurements (N = 28, number of observations = 100). Comparing CBC and DNAm proportions across both studies, estimates of neutrophils (r = 0.948, p < 0.001), lymphocytes (r = 0.916, p < 0.001), and eosinophils (r = 0.933, p < 0.001) were highly correlated, while monocyte estimates were moderately correlated (r = 0.766, p < 0.001) and basophil estimates were weakly correlated (r = 0.189, p < 0.001). In Study 1, we observed significant deviations in raw values between the two approaches for some immune cell subtypes; however, the observed differences were not significantly predicted by exposure to child maltreatment. In Study 2, while significant changes in immune cell proportions were observed in response to acute psychosocial stress for both CBC and DNAm estimates, the observed changes were similar for both approaches. CONCLUSIONS Although significant differences in immune cell proportion estimates between CBC and DNAm exist, as well as stress-induced changes in immune cell proportions, neither child maltreatment nor acute psychosocial stress alters the concordance of CBC and DNAm estimation methods. These results suggest that the agreement between CBC and DNAm estimators of immune cell proportions is robust to exposure to child maltreatment and acute psychosocial stress.
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Affiliation(s)
- Abner T Apsley
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
- Department of Molecular, Cellular, and Integrated Biosciences, The Pennsylvania State University, University Park, PA, USA
| | - Laura Etzel
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Waylon J Hastings
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Christine C Heim
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
- Corporate Member of Freie Universität Berlin, and Humboldt-Universität Zu Berlin, Berlin Institute of Health (BIH), Institute of Medical Psychology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jennie G Noll
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
| | - Kieran J O'Donnell
- Yale Child Study Center, Yale School of Medicine, Yale University, New Haven, CT, USA
- Department of Obstetrics Gynecology and Reproductive Sciences, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Hannah M C Schreier
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Chad E Shenk
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Qiaofeng Ye
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Idan Shalev
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA.
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Louise J, Deussen AR, Dodd JM. Data processing choices can affect findings in differential methylation analyses: an investigation using data from the LIMIT RCT. PeerJ 2023; 11:e14786. [PMID: 36755865 PMCID: PMC9901304 DOI: 10.7717/peerj.14786] [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: 10/11/2022] [Accepted: 01/03/2023] [Indexed: 02/05/2023] Open
Abstract
Objective A wide array of methods exist for processing and analysing DNA methylation data. We aimed to perform a systematic comparison of the behaviour of these methods, using cord blood DNAm from the LIMIT RCT, in relation to detecting hypothesised effects of interest (intervention and pre-pregnancy maternal BMI) as well as effects known to be spurious, and known to be present. Methods DNAm data, from 645 cord blood samples analysed using Illumina 450K BeadChip arrays, were normalised using three different methods (with probe filtering undertaken pre- or post- normalisation). Batch effects were handled with a supervised algorithm, an unsupervised algorithm, or adjustment in the analysis model. Analysis was undertaken with and without adjustment for estimated cell type proportions. The effects estimated included intervention and BMI (effects of interest in the original study), infant sex and randomly assigned groups. Data processing and analysis methods were compared in relation to number and identity of differentially methylated probes, rankings of probes by p value and log-fold-change, and distributions of p values and log-fold-change estimates. Results There were differences corresponding to each of the processing and analysis choices. Importantly, some combinations of data processing choices resulted in a substantial number of spurious 'significant' findings. We recommend greater emphasis on replication and greater use of sensitivity analyses.
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Affiliation(s)
- Jennie Louise
- Discipline of Obstetrics & Gynaecology and The Robinson Research Institute, The University of Adelaide, Adelaide, Australia,Adelaide Health Technology Asseessment, The University of Adelaide, Adelaide, Australia
| | - Andrea R. Deussen
- Discipline of Obstetrics & Gynaecology and The Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Jodie M. Dodd
- Discipline of Obstetrics & Gynaecology and The Robinson Research Institute, The University of Adelaide, Adelaide, Australia,Department of Perinatal Medicine, Women’s and Babies Division, The Women’s and Children’s Hospital, Adelaide, South Australia, Australia
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32
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Alfano R, Zugna D, Barros H, Bustamante M, Chatzi L, Ghantous A, Herceg Z, Keski-Rahkonen P, de Kok TM, Nawrot TS, Relton CL, Robinson O, Roumeliotaki T, Scalbert A, Vrijheid M, Vineis P, Richiardi L, Plusquin M. Cord blood epigenome-wide meta-analysis in six European-based child cohorts identifies signatures linked to rapid weight growth. BMC Med 2023; 21:17. [PMID: 36627699 PMCID: PMC9831885 DOI: 10.1186/s12916-022-02685-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/29/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Rapid postnatal growth may result from exposure in utero or early life to adverse conditions and has been associated with diseases later in life and, in particular, with childhood obesity. DNA methylation, interfacing early-life exposures and subsequent diseases, is a possible mechanism underlying early-life programming. METHODS Here, a meta-analysis of Illumina HumanMethylation 450K/EPIC-array associations of cord blood DNA methylation at single CpG sites and CpG genomic regions with rapid weight growth at 1 year of age (defined with reference to WHO growth charts) was conducted in six European-based child cohorts (ALSPAC, ENVIRONAGE, Generation XXI, INMA, Piccolipiù, and RHEA, N = 2003). The association of gestational age acceleration (calculated using the Bohlin epigenetic clock) with rapid weight growth was also explored via meta-analysis. Follow-up analyses of identified DNA methylation signals included prediction of rapid weight growth, mediation of the effect of conventional risk factors on rapid weight growth, integration with transcriptomics and metabolomics, association with overweight in childhood (between 4 and 8 years), and comparison with previous findings. RESULTS Forty-seven CpGs were associated with rapid weight growth at suggestive p-value <1e-05 and, among them, three CpGs (cg14459032, cg25953130 annotated to ARID5B, and cg00049440 annotated to KLF9) passed the genome-wide significance level (p-value <1.25e-07). Sixteen differentially methylated regions (DMRs) were identified as associated with rapid weight growth at false discovery rate (FDR)-adjusted/Siddak p-values < 0.01. Gestational age acceleration was associated with decreasing risk of rapid weight growth (p-value = 9.75e-04). Identified DNA methylation signals slightly increased the prediction of rapid weight growth in addition to conventional risk factors. Among the identified signals, three CpGs partially mediated the effect of gestational age on rapid weight growth. Both CpGs (N=3) and DMRs (N=3) were associated with differential expression of transcripts (N=10 and 7, respectively), including long non-coding RNAs. An AURKC DMR was associated with childhood overweight. We observed enrichment of CpGs previously reported associated with birthweight. CONCLUSIONS Our findings provide evidence of the association between cord blood DNA methylation and rapid weight growth and suggest links with prenatal exposures and association with childhood obesity providing opportunities for early prevention.
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Affiliation(s)
- Rossella Alfano
- Medical Research Council Centre for Environment and Health, Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Daniela Zugna
- Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Henrique Barros
- Institute of Public Health, University of Porto, Porto, Portugal
| | - Mariona Bustamante
- ISGlobal, Institute of Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Leda Chatzi
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Akram Ghantous
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Pekka Keski-Rahkonen
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Theo M de Kok
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Caroline L Relton
- Μedical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Oliver Robinson
- Medical Research Council Centre for Environment and Health, Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
- Mohn Centre for Children's Health and Well-being, The School of Public Health, Imperial College London, London, UK
| | - Theano Roumeliotaki
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Augustin Scalbert
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Martine Vrijheid
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Paolo Vineis
- Medical Research Council Centre for Environment and Health, Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
| | - Lorenzo Richiardi
- Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium.
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McCabe CF, Goodrich JM, Bakulski KM, Domino SE, Jones TR, Colacino J, Dolinoy DC, Padmanabhan V. Probing prenatal bisphenol exposures and tissue-specific DNA methylation responses in cord blood, cord tissue, and placenta. Reprod Toxicol 2023; 115:74-84. [PMID: 36473650 PMCID: PMC9851062 DOI: 10.1016/j.reprotox.2022.11.005] [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: 10/03/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
The early-gestational fetal epigenome establishes the landscape for fetal development and is susceptible to disruption via environmental stressors including chemical exposures. Research has explored how cell- and tissue-type-specific epigenomic signatures contribute to human disease, but how the epigenome in each tissue comparatively responds to environmental exposures is largely unknown. This pilot study compared DNA methylation in four previously identified genes across matched cord blood (CB), cord tissue (CT), and placental (PL) samples from 28 mother-infant pairs in tthe Michigan Mother Infant Pairs study; evaluated association between prenatal exposure to bisphenols (BPA, BPF, and BPS) and DNA methylation (DNAm) by tissue type; compared epigenome-wide DNAm of CB and PL; and explored associations between prenatal bisphenol exposures and epigenome-wide DNAm in PL. Bisphenol concentrations were quantified in first-trimester maternal urine. DNAm was assessed at four genes via pyrosequencing in three tissues; epigenome-wide DNAm analysis via Infinium MethylationEPIC array was completed on CB and PL. Candidate gene analysis revealed tissue-specific differences across all genes. In adjusted linear regression, BPA and BPF were associated with DNAm across candidate genes in PL but not CB and CT. Epigenome-wide comparison of matched CB and PL DNAm revealed tissue-specific differences at most CpG sites and modest associations between maternal first-trimester bisphenol exposures and PL but not CB DNAm. These data endorse inclusion of a variety of tissues in prenatal exposure studies. Overlapping and divergent responses in CB, CT, and PL demonstrate their utility in combination to capture a fuller picture of the epigenetic effect of developmental exposures.
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Affiliation(s)
- Carolyn F McCabe
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Steven E Domino
- Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Justin Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA; Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA; Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA.
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Nikolaienko O, Lønning PE, Knappskog S. epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data. Gigascience 2022; 12:giad087. [PMID: 37919976 PMCID: PMC10622323 DOI: 10.1093/gigascience/giad087] [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: 06/01/2023] [Revised: 08/03/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023] Open
Abstract
Low-level mosaic epimutations within the BRCA1 gene promoter occur in 5-8% of healthy individuals and are associated with a significantly elevated risk of breast and ovarian cancer. Similar events may also affect other tumor suppressor genes, potentially being a significant contributor to cancer burden. While this opens a new area for translational research, detection of low-level mosaic epigenetic events requires highly sensitive and robust methodology for methylation analysis. We here present epialleleR, a computational framework for sensitive detection, quantification, and visualization of mosaic epimutations in methylation sequencing data. Analyzing simulated and real data sets, we provide in-depth assessments of epialleleR performance and show that linkage to epihaplotype data is necessary to detect low-level methylation events. The epialleleR is freely available at https://github.com/BBCG/epialleleR and https://bioconductor.org/packages/epialleleR/ as an open-source R/Bioconductor package.
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Affiliation(s)
- Oleksii Nikolaienko
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | - Per Eystein Lønning
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Department of Oncology, Haukeland University Hospital, Bergen 5021, Norway
| | - Stian Knappskog
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Department of Oncology, Haukeland University Hospital, Bergen 5021, Norway
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Wang Y, Tzeng JY, Huang Y, Maguire R, Hoyo C, Allen TK. Duration of exposure to epidural anesthesia at delivery, DNA methylation in umbilical cord blood and their association with offspring asthma in Non-Hispanic Black women. ENVIRONMENTAL EPIGENETICS 2022; 9:dvac026. [PMID: 36694712 PMCID: PMC9854336 DOI: 10.1093/eep/dvac026] [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] [Received: 08/02/2022] [Revised: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Epidural anesthesia is an effective pain relief modality, widely used for labor analgesia. Childhood asthma is one of the commonest chronic medical illnesses in the USA which places a significant burden on the health-care system. We recently demonstrated a negative association between the duration of epidural anesthesia and the development of childhood asthma; however, the underlying molecular mechanisms still remain unclear. In this study of 127 mother-child pairs comprised of 75 Non-Hispanic Black (NHB) and 52 Non-Hispanic White (NHW) from the Newborn Epigenetic Study, we tested the hypothesis that umbilical cord blood DNA methylation mediates the association between the duration of exposure to epidural anesthesia at delivery and the development of childhood asthma and whether this differed by race/ethnicity. In the mother-child pairs of NHB ancestry, the duration of exposure to epidural anesthesia was associated with a marginally lower risk of asthma (odds ratio = 0.88, 95% confidence interval = 0.76-1.01) for each 1-h increase in exposure to epidural anesthesia. Of the 20 CpGs in the NHB population showing the strongest mediation effect, 50% demonstrated an average mediation proportion of 52%, with directional consistency of direct and indirect effects. These top 20 CpGs mapped to 21 genes enriched for pathways engaged in antigen processing, antigen presentation, protein ubiquitination and regulatory networks related to the Major Histocompatibility Complex (MHC) class I complex and Nuclear Factor Kappa-B (NFkB) complex. Our findings suggest that DNA methylation in immune-related pathways contributes to the effects of the duration of exposure to epidural anesthesia on childhood asthma risk in NHB offspring.
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Affiliation(s)
- Yaxu Wang
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA
| | - Jung-Ying Tzeng
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695-7633, USA
- Department of Statistics, North Carolina State University, Raleigh, NC 27607, USA
| | - Yueyang Huang
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27607, USA
| | - Rachel Maguire
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695-7633, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Terrence K Allen
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC 27710, USA
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DeVries A, McCauley K, Fadrosh D, Fujimura KE, Stern DA, Lynch SV, Vercelli D. Maternal prenatal immunity, neonatal trained immunity, and early airway microbiota shape childhood asthma development. Allergy 2022; 77:3617-3628. [PMID: 35841380 PMCID: PMC9712226 DOI: 10.1111/all.15442] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/25/2022] [Accepted: 06/11/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND The path to childhood asthma is thought to initiate in utero and be further promoted by postnatal exposures. However, the underlying mechanisms remain underexplored. We hypothesized that prenatal maternal immune dysfunction associated with increased childhood asthma risk (revealed by low IFN-γ:IL-13 secretion during the third trimester of pregnancy) alters neonatal immune training through epigenetic mechanisms and promotes early-life airway colonization by asthmagenic microbiota. METHODS We examined epigenetic, immunologic, and microbial features potentially related to maternal prenatal immunity (IFN-γ:IL-13 ratio) and childhood asthma in a birth cohort of mother-child dyads sampled pre-, peri-, and postnatally (N = 155). Epigenome-wide DNA methylation and cytokine production were assessed in cord blood mononuclear cells (CBMC) by array profiling and ELISA, respectively. Nasopharyngeal microbiome composition was characterized at age 2-36 months by 16S rRNA sequencing. RESULTS Maternal prenatal immune status related to methylome profiles in neonates born to non-asthmatic mothers. A module of differentially methylated CpG sites enriched for microbe-responsive elements was associated with childhood asthma. In vitro responsiveness to microbial products was impaired in CBMCs from neonates born to mothers with the lowest IFN-γ:IL-13 ratio, suggesting defective neonatal innate immunity in those who developed asthma during childhood. These infants exhibited a distinct pattern of upper airway microbiota development characterized by early-life colonization by Haemophilus that transitioned to a Moraxella-dominated microbiota by age 36 months. CONCLUSIONS Maternal prenatal immune status shapes asthma development in her child by altering the epigenome and trained innate immunity at birth, and is associated with pathologic upper airway microbial colonization in early life.
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Affiliation(s)
- Avery DeVries
- Asthma and Airway Disease Research CenterThe University of ArizonaTucsonArizonaUSA
- The BIO5 InstituteThe University of ArizonaTucsonArizonaUSA
| | - Kathryn McCauley
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Benioff Center for Microbiome MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Douglas Fadrosh
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Kei E. Fujimura
- Genetic Disease LabCalifornia Department of Public HealthRichmondCaliforniaUSA
| | - Debra A. Stern
- Asthma and Airway Disease Research CenterThe University of ArizonaTucsonArizonaUSA
| | - Susan V. Lynch
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Benioff Center for Microbiome MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Donata Vercelli
- Asthma and Airway Disease Research CenterThe University of ArizonaTucsonArizonaUSA
- The BIO5 InstituteThe University of ArizonaTucsonArizonaUSA
- Department of Cellular and Molecular MedicineThe University of ArizonaTucsonArizonaUSA
- Arizona Center for the Biology of Complex DiseasesThe University of ArizonaTucsonArizonaUSA
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Wheatley LM, Holloway JW, Svanes C, Sears MR, Breton C, Fedulov AV, Nilsson E, Vercelli D, Zhang H, Togias A, Arshad SH. The role of epigenetics in multi-generational transmission of asthma: An NIAID workshop report-based narrative review. Clin Exp Allergy 2022; 52:1264-1275. [PMID: 36073598 PMCID: PMC9613603 DOI: 10.1111/cea.14223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 01/26/2023]
Abstract
There is mounting evidence that environmental exposures can result in effects on health that can be transmitted across generations, without the need for a direct exposure to the original factor, for example, the effect of grandparental smoking on grandchildren. Hence, an individual's health should be investigated with the knowledge of cross-generational influences. Epigenetic factors are molecular factors or processes that regulate genome activity and may impact cross-generational effects. Epigenetic transgenerational inheritance has been demonstrated in plants and animals, but the presence and extent of this process in humans are currently being investigated. Experimental data in animals support transmission of asthma risk across generations from a single exposure to the deleterious factor and suggest that the nature of this transmission is in part due to changes in DNA methylation, the most studied epigenetic process. The association of father's prepuberty exposure with offspring risk of asthma and lung function deficit may also be mediated by epigenetic processes. Multi-generational birth cohorts are ideal to investigate the presence and impact of transfer of disease susceptibility across generations and underlying mechanisms. However, multi-generational studies require recruitment and assessment of participants over several decades. Investigation of adult multi-generation cohorts is less resource intensive but run the risk of recall bias. Statistical analysis is challenging given varying degrees of longitudinal and hierarchical data but path analyses, structural equation modelling and multilevel modelling can be employed, and directed networks addressing longitudinal effects deserve exploration as an effort to study causal pathways.
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Affiliation(s)
- Lisa M. Wheatley
- National Institute of Allergy and Infectious DiseaseNational Institutes of HealthBethesdaMarylandUSA
| | - John W. Holloway
- Faculty of Medicine, Human Development and HealthUniversity of SouthamptonSouthamptonUK
| | - Cecilie Svanes
- Department of Global Public Health and Primary CareUniversity of BergenBergenNorway
| | | | - Carrie Breton
- University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Alexey V. Fedulov
- Warren Alpert Medical School of Brown University, Rhode Island HospitalProvidenceRhode IslandUSA
| | - Eric Nilsson
- Washington State University PullmanPullmanWashingtonUSA
| | | | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public HealthUniversity of MemphisMemphisTennesseeUSA
| | - Alkis Togias
- National Institute of Allergy and Infectious DiseaseNational Institutes of HealthBethesdaMarylandUSA
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
- The David Hide Asthma and Allergy CentreSt Mary's HospitalNewportUK
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Wang C, Alfano R, Reimann B, Hogervorst J, Bustamante M, De Vivo I, Plusquin M, Nawrot TS, Martens DS. Genetic regulation of newborn telomere length is mediated and modified by DNA methylation. Front Genet 2022; 13:934277. [PMID: 36267401 PMCID: PMC9576874 DOI: 10.3389/fgene.2022.934277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022] Open
Abstract
Telomere length at birth determines later life telomere length and potentially predicts ageing-related diseases. However, the genetic and epigenetic settings of telomere length in newborns have not been analyzed. In addition, no study yet has reported how the interplay between genetic variants and genome-wide cytosine methylation explains the variation in early-life telomere length. In this study based on 281 mother-newborn pairs from the ENVIRONAGE birth cohort, telomere length and whole-genome DNA methylation were assessed in cord blood and 26 candidate single nucleotide polymorphism related to ageing or telomere length were genotyped. We identified three genetic variants associated with cord blood telomere length and 57 cis methylation quantitative trait loci (cis-mQTLs) of which 22 mQTLs confirmed previous findings and 35 were newly identified. Five SNPs were found to have significant indirect effects on cord blood telomere length via the mediating CpGs. The association between rs911874 (SOD2) and newborn telomere length was modified by nearby DNA methylation indicated by a significant statistical interaction. Our results suggest that DNA methylation in cis might have a mediation or modification effect on the genetic difference in newborn telomere length. This novel approach warrants future follow-up studies that are needed to further confirm and extend these findings.
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Affiliation(s)
- Congrong Wang
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Brigitte Reimann
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | | | - Mariona Bustamante
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Madrid, Spain
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Immaculata De Vivo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA, United States
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Tim S. Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
- Department of Public Health and Primary Care, Leuven University, Leuven, Belgium
| | - Dries S. Martens
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
- *Correspondence: Dries S. Martens,
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Ma Z, Wang Y, Quan Y, Wang Z, Liu Y, Ding Z. Maternal obesity alters methylation level of cytosine in CpG island for epigenetic inheritance in fetal umbilical cord blood. Hum Genomics 2022; 16:34. [PMID: 36045397 PMCID: PMC9429776 DOI: 10.1186/s40246-022-00410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over the past few decades, global maternal obesity prevalence has rapidly increased. This condition may induce long-lasting pathophysiological effects on either fetal or infant health that could be attributable to unknown unique changes in the umbilical blood composition. METHODS A total of 34 overweight/obese and 32 normal-weight pregnant women were recruited. Fifteen umbilical blood samples including 8 overweight/obese subjects and 7 normal weight women were sequenced using Targeted Bisulfite Sequencing technology to detect the average methylation level of cytosine and identify the differentially methylated region (DMR). GO and KEGG analyses were then employed to perform pathway enrichment analysis of DMR-related genes and promoters. Moreover, the mRNA levels of methylation-related genes histone deacetylases (HDACs) and DNA methyltransferases (DNMTs) were characterized in the samples obtained from these two groups. RESULTS Average methylated cytosine levels in both the CpG islands (CGI) and promoter significantly decreased in overweight/obese groups. A total of 1669 DMRs exhibited differences in their DNA methylation status between the overweight/obese and control groups. GO and KEGG analyses revealed that DMR-related genes and promoters were enriched in the metabolism, cancer and cardiomyopathy signaling pathways. Furthermore, the HDACs and DNMTs mRNA levels trended to decline in overweight/obese groups. CONCLUSIONS Decreased methylated cytosine levels in overweight/obese women induce the gene expression activity at a higher level than in the control group. DMRs between these two groups in the fetal blood may contribute to the changes in gene transcription that underlie the increased risk of metabolic disorders, cancers and cardiomyopathy in their offspring.
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Affiliation(s)
- Zhuoyao Ma
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China
| | - Yingjin Wang
- Department of Obstetrics and Gynecology, Shanghai Eighth People's Hospital, Shanghai, 200235, China
| | - Yanmei Quan
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China
| | - Zhijie Wang
- Department of Obstetrics and Gynecology, Shanghai Eighth People's Hospital, Shanghai, 200235, China.
| | - Yue Liu
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China.
| | - Zhide Ding
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China.
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40
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Reimann B, Martens DS, Wang C, Ghantous A, Herceg Z, Plusquin M, Nawrot TS. Interrelationships and determinants of aging biomarkers in cord blood. J Transl Med 2022; 20:353. [PMID: 35945616 PMCID: PMC9361565 DOI: 10.1186/s12967-022-03541-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Increasing evidence supports the concept of prenatal programming as an early factor in the aging process. DNA methylation age (DNAm age), global genome-wide DNA methylation (global methylation), telomere length (TL), and mitochondrial DNA content (mtDNA content) have independently been shown to be markers of aging, but their interrelationship and determinants at birth remain uncertain. METHODS We assessed the inter-correlation between the aging biomarkers DNAm age, global methylation, TL and mtDNA content using Pearson's correlation in 190 cord blood samples of the ENVIRONAGE birth cohort. TL and mtDNA content was measured via qPCR, while the DNA methylome was determined using the human 450K methylation Illumina microarray. Subsequently, DNAm age was calculated according to Horvath's epigenetic clock, and mean global, promoter, gene-body, and intergenic DNA methylation were determined. Path analysis, a form of structural equation modeling, was performed to disentangle the complex causal relationships among the aging biomarkers and their potential determinants. RESULTS DNAm age was inversely correlated with global methylation (r = -0.64, p < 0.001) and mtDNA content (r = - 0.16, p = 0.027). Cord blood TL was correlated with mtDNA content (r = 0.26, p < 0.001) but not with global methylation or DNAm age. Path analysis showed the strongest effect for global methylation on DNAm age with a decrease of 0.64 standard deviations (SD) in DNAm age for each SD (0.01%) increase in global methylation (p < 0.001). Among the applied covariates, newborn sex and season of delivery were the strongest determinants of aging biomarkers. CONCLUSIONS We provide insight into molecular aging signatures at the start of life, including their interrelations and determinants, showing that cord blood DNAm age is inversely associated with global methylation and mtDNA content but not with newborn telomere length. Our findings demonstrate that cord blood TL and DNAm age relate to different pathways/mechanisms of biological aging and can be influenced by environmental factors already at the start of life. These findings are relevant for understanding fetal programming and for the early prevention of noncommunicable diseases.
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Affiliation(s)
- Brigitte Reimann
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Congrong Wang
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), Lyon, France
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium.
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
- School of Public Health, Occupational and Environmental Medicine, KU Leuven, Leuven, Belgium
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Dou JF, Middleton LYM, Zhu Y, Benke KS, Feinberg JI, Croen LA, Hertz-Picciotto I, Newschaffer CJ, LaSalle JM, Fallin D, Schmidt RJ, Bakulski KM. Prenatal vitamin intake in first month of pregnancy and DNA methylation in cord blood and placenta in two prospective cohorts. Epigenetics Chromatin 2022; 15:28. [PMID: 35918756 PMCID: PMC9344645 DOI: 10.1186/s13072-022-00460-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Prenatal vitamin use is recommended before and during pregnancies for normal fetal development. Prenatal vitamins do not have a standard formulation, but many contain calcium, folic acid, iodine, iron, omega-3 fatty acids, zinc, and vitamins A, B6, B12, and D, and usually they contain higher concentrations of folic acid and iron than regular multivitamins in the US Nutrient levels can impact epigenetic factors such as DNA methylation, but relationships between maternal prenatal vitamin use and DNA methylation have been relatively understudied. We examined use of prenatal vitamins in the first month of pregnancy in relation to cord blood and placenta DNA methylation in two prospective pregnancy cohorts: the Early Autism Risk Longitudinal Investigation (EARLI) and Markers of Autism Risk Learning Early Signs (MARBLES) studies. RESULTS In placenta, prenatal vitamin intake was marginally associated with -0.52% (95% CI -1.04, 0.01) lower mean array-wide DNA methylation in EARLI, and associated with -0.60% (-1.08, -0.13) lower mean array-wide DNA methylation in MARBLES. There was little consistency in the associations between prenatal vitamin intake and single DNA methylation site effect estimates across cohorts and tissues, with only a few overlapping sites with correlated effect estimates. However, the single DNA methylation sites with p-value < 0.01 (EARLI cord nCpGs = 4068, EARLI placenta nCpGs = 3647, MARBLES cord nCpGs = 4068, MARBLES placenta nCpGs = 9563) were consistently enriched in neuronal developmental pathways. CONCLUSIONS Together, our findings suggest that prenatal vitamin intake in the first month of pregnancy may be related to lower placental global DNA methylation and related to DNA methylation in brain-related pathways in both placenta and cord blood.
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Affiliation(s)
- John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, USA
| | - Lauren Y M Middleton
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, USA
| | - Yihui Zhu
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Kelly S Benke
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jason I Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Lisa A Croen
- Kaiser Permanente Northern California, Oakland, CA, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Craig J Newschaffer
- College of Health and Human Development, Penn State University, State College, PA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, USA.
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Epigenetic profiling of social communication trajectories and co-occurring mental health problems: a prospective, methylome-wide association study. Dev Psychopathol 2022; 34:854-863. [PMID: 33494854 PMCID: PMC8622455 DOI: 10.1017/s0954579420001662] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
While previous studies suggest that both genetic and environmental factors play an important role in the development of autism-related traits, little is known about potential biological mechanisms underlying these associations. Using data from the Avon Longitudinal Study of Parents and Children (ALSPAC), we examined prospective associations between DNA methylation (DNAm: nbirth = 804, nage 7 = 877) and trajectories of social communication deficits at age 8-17 years. Methylomic variation at three loci across the genome (false discovery rate = 0.048) differentiated children following high (n = 80) versus low (n = 724) trajectories of social communication deficits. This differential DNAm was specific to the neonatal period and not observed at 7 years of age. Associations between DNAm and trajectory membership remained robust after controlling for co-occurring mental health problems (i.e., hyperactivity/inattention, conduct problems). The three loci identified at birth were not replicated in the Generation R Study. However, to the best of our knowledge, ALSPAC is the only study to date that is prospective enough to examine DNAm in relation to longitudinal trajectories of social communication deficits from childhood to adolescence. Although the present findings might point to potentially novel sites that differentiate between a high versus low trajectory of social communication deficits, the results should be considered tentative until further replicated.
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Daredia S, Huen K, Van Der Laan L, Collender PA, Nwanaji-Enwerem JC, Harley K, Deardorff J, Eskenazi B, Holland N, Cardenas A. Prenatal and birth associations of epigenetic gestational age acceleration in the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) cohort. Epigenetics 2022; 17:2006-2021. [PMID: 35912433 DOI: 10.1080/15592294.2022.2102846] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Gestational age (GA) is an important determinant of child health and disease risk. Two epigenetic GA clocks have been developed using DNA methylation (DNAm) patterns in cord blood. We investigate the accuracy of GA clocks and determinants of epigenetic GA acceleration (GAA), a biomarker of biological ageing. We hypothesize that prenatal and birth characteristics are associated with altered GAA, thereby disrupting foetal biological ageing. We examined 372 mother-child pairs from the Center for the Health Assessment of Mothers and Children of Salinas study of primarily Latino farmworkers in California. Chronological GA was robustly correlated with epigenetic GA (DNAm GA) estimated by the Knight (r = 0.48, p < 2.2x10-16) and Bohlin clocks (r = 0.67, p < 2.2x10-16) using the Illumina 450K array in cord blood samples collected at birth. GA clock performance was robust, though slightly lower, using DNAm profiles from the Illumina EPIC array in a smaller subsample (Knight: r = 0.39, p < 3.5x10-5; Bohlin: r = 0.60, p < 7.7x10-12). After adjusting for confounders, high maternal serum triglyceride levels (Bohlin: β = -0.01 days per mg/dL, p = 0.03), high maternal serum lipid levels (Bohlin: β = -4.31x10-3 days per mg/dL, p = 0.04), preterm delivery (Bohlin: β = -4.03 days, p = 9.64x10-4), greater maternal parity (Knight: β = -4.07 days, p = 0.01; Bohlin: β = -2.43 days, p = 0.01), and male infant sex (Knight: β = -3.15 days, p = 3.10x10-3) were associated with decreased GAA.Prenatal and birth characteristics affect GAA in newborns. Understanding factors that accelerate or delay biological ageing at birth may identify early-life targets for disease prevention and improve ageing across the life-course. Future research should test the impact of altered GAA on the long-term burden of age-related diseases.
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Affiliation(s)
- Saher Daredia
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | - Karen Huen
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA.,Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, Berkeley, CA, USA
| | - Lars Van Der Laan
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Philip A Collender
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Jamaji C Nwanaji-Enwerem
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Kim Harley
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, Berkeley, CA, USA.,Division of Community Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Julianna Deardorff
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, Berkeley, CA, USA.,Division of Community Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Brenda Eskenazi
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA.,Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA.,Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, Berkeley, CA, USA
| | - Nina Holland
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA.,Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, Berkeley, CA, USA
| | - Andres Cardenas
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA.,Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA.,Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, Berkeley, CA, USA.,Center for Computational Biology, University of California, Berkeley, CA, USA
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44
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Sammallahti S, Koopman-Verhoeff ME, Binter AC, Mulder RH, Cabré-Riera A, Kvist T, Malmberg ALK, Pesce G, Plancoulaine S, Heiss JA, Rifas-Shiman SL, Röder SW, Starling AP, Wilson R, Guerlich K, Haftorn KL, Page CM, Luik AI, Tiemeier H, Felix JF, Raikkonen K, Lahti J, Relton CL, Sharp GC, Waldenberger M, Grote V, Heude B, Annesi-Maesano I, Hivert MF, Zenclussen AC, Herberth G, Dabelea D, Grazuleviciene R, Vafeiadi M, Håberg SE, London SJ, Guxens M, Richmond RC, Cecil CAM. Longitudinal associations of DNA methylation and sleep in children: a meta-analysis. Clin Epigenetics 2022; 14:83. [PMID: 35790973 PMCID: PMC9258202 DOI: 10.1186/s13148-022-01298-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sleep is important for healthy functioning in children. Numerous genetic and environmental factors, from conception onwards, may influence this phenotype. Epigenetic mechanisms such as DNA methylation have been proposed to underlie variation in sleep or may be an early-life marker of sleep disturbances. We examined if DNA methylation at birth or in school age is associated with parent-reported and actigraphy-estimated sleep outcomes in children. METHODS We meta-analysed epigenome-wide association study results. DNA methylation was measured from cord blood at birth in 11 cohorts and from peripheral blood in children (4-13 years) in 8 cohorts. Outcomes included parent-reported sleep duration, sleep initiation and fragmentation problems, and actigraphy-estimated sleep duration, sleep onset latency and wake-after-sleep-onset duration. RESULTS We found no associations between DNA methylation at birth and parent-reported sleep duration (n = 3658), initiation problems (n = 2504), or fragmentation (n = 1681) (p values above cut-off 4.0 × 10-8). Lower methylation at cg24815001 and cg02753354 at birth was associated with longer actigraphy-estimated sleep duration (p = 3.31 × 10-8, n = 577) and sleep onset latency (p = 8.8 × 10-9, n = 580), respectively. DNA methylation in childhood was not cross-sectionally associated with any sleep outcomes (n = 716-2539). CONCLUSION DNA methylation, at birth or in childhood, was not associated with parent-reported sleep. Associations observed with objectively measured sleep outcomes could be studied further if additional data sets become available.
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Affiliation(s)
- Sara Sammallahti
- grid.5645.2000000040459992XDepartment of Adolescent and Child Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.7737.40000 0004 0410 2071Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - M. Elisabeth Koopman-Verhoeff
- grid.5645.2000000040459992XDepartment of Adolescent and Child Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.5645.2000000040459992XGeneration R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.5132.50000 0001 2312 1970Institute of Education and Child Studies, Leiden University, Leiden, The Netherlands
| | - Anne-Claire Binter
- Barcelona Institute for Global Health, ISGlobal, Campus Mar, Doctor Aiguader, 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain. .,Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.
| | - Rosa H. Mulder
- grid.5645.2000000040459992XDepartment of Adolescent and Child Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.5645.2000000040459992XGeneration R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alba Cabré-Riera
- grid.434607.20000 0004 1763 3517Barcelona Institute for Global Health, ISGlobal, Campus Mar, Doctor Aiguader, 88, 08003 Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra, Barcelona, Spain ,grid.413448.e0000 0000 9314 1427Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Tuomas Kvist
- grid.7737.40000 0004 0410 2071Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Anni L. K. Malmberg
- grid.7737.40000 0004 0410 2071Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Giancarlo Pesce
- grid.462844.80000 0001 2308 1657INSERM UMR-S 1136, Team of Epidemiology of Allergic and Respiratory Diseases (EPAR), Institute Pierre Louis of Epidemiology and Public Health (IPLESP), Sorbonne University, Paris, France
| | - Sabine Plancoulaine
- grid.508487.60000 0004 7885 7602CRESS, Inserm, INRAE, Université de Paris Cité, Paris, France
| | - Jonathan A. Heiss
- grid.59734.3c0000 0001 0670 2351Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Sheryl L. Rifas-Shiman
- grid.67104.340000 0004 0415 0102Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA USA
| | - Stefan W. Röder
- grid.7492.80000 0004 0492 3830Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Anne P. Starling
- grid.430503.10000 0001 0703 675XDepartment of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO USA ,grid.430503.10000 0001 0703 675XCenter for Lifecourse Epidemiology of Adiposity and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO USA ,grid.10698.360000000122483208Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Rory Wilson
- grid.4567.00000 0004 0483 2525Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria Germany
| | - Kathrin Guerlich
- grid.411095.80000 0004 0477 2585Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital Munich, Munich, Germany
| | - Kristine L. Haftorn
- grid.418193.60000 0001 1541 4204Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway ,grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway ,grid.5510.10000 0004 1936 8921Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Christian M. Page
- grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway ,grid.5510.10000 0004 1936 8921Department of Mathematics, University of Oslo, Oslo, Norway
| | - Annemarie I. Luik
- grid.5645.2000000040459992XDepartment of Adolescent and Child Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.5645.2000000040459992XDepartment of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Henning Tiemeier
- grid.5645.2000000040459992XDepartment of Adolescent and Child Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.5645.2000000040459992XGeneration R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.38142.3c000000041936754XDepartment of Social and Behavioral Science, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Janine F. Felix
- grid.5645.2000000040459992XGeneration R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.5645.2000000040459992XDepartment of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Katri Raikkonen
- grid.7737.40000 0004 0410 2071Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- grid.7737.40000 0004 0410 2071Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Caroline L. Relton
- grid.5337.20000 0004 1936 7603MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK ,grid.5337.20000 0004 1936 7603Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gemma C. Sharp
- grid.5337.20000 0004 1936 7603MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK ,grid.5337.20000 0004 1936 7603Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Melanie Waldenberger
- grid.4567.00000 0004 0483 2525Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria Germany
| | - Veit Grote
- grid.411095.80000 0004 0477 2585Division of Metabolic and Nutritional Medicine, Department of Pediatrics, Dr. Von Hauner Children’s Hospital, LMU University Hospital Munich, Munich, Germany
| | - Barbara Heude
- grid.508487.60000 0004 7885 7602CRESS, Inserm, INRAE, Université de Paris Cité, Paris, France
| | - Isabella Annesi-Maesano
- grid.121334.60000 0001 2097 0141IDESP, University of Montpellier and INSERM, Montpellier, France
| | - Marie-France Hivert
- grid.67104.340000 0004 0415 0102Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA USA
| | - Ana C. Zenclussen
- grid.7492.80000 0004 0492 3830Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Perinatal Immunology Group, Saxonian Incubator for Clinical Translation - SIKT, Leipzig University, Leipzig, Germany
| | - Gunda Herberth
- grid.7492.80000 0004 0492 3830Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Dana Dabelea
- grid.430503.10000 0001 0703 675XDepartment of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO USA ,grid.430503.10000 0001 0703 675XCenter for Lifecourse Epidemiology of Adiposity and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO USA ,grid.430503.10000 0001 0703 675XDepartment of Pediatrics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Regina Grazuleviciene
- grid.19190.300000 0001 2325 0545Department of Environmental Science, Vytautas Magnus University, Kaunas, Lithuania
| | - Marina Vafeiadi
- grid.8127.c0000 0004 0576 3437Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Crete Greece
| | - Siri E. Håberg
- grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie J. London
- grid.280664.e0000 0001 2110 5790Epidemiology Branch, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC USA
| | - Mònica Guxens
- grid.5645.2000000040459992XDepartment of Adolescent and Child Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.434607.20000 0004 1763 3517Barcelona Institute for Global Health, ISGlobal, Campus Mar, Doctor Aiguader, 88, 08003 Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra, Barcelona, Spain ,grid.413448.e0000 0000 9314 1427Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Rebecca C. Richmond
- grid.5337.20000 0004 1936 7603MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK ,grid.5337.20000 0004 1936 7603Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Charlotte A. M. Cecil
- grid.5645.2000000040459992XDepartment of Adolescent and Child Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.5645.2000000040459992XGeneration R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.5645.2000000040459992XDepartment of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands ,grid.10419.3d0000000089452978Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands ,grid.13097.3c0000 0001 2322 6764Department of Psychology, Institute of Psychology, Psychiatry and Neuroscience, King’s College London, London, UK
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45
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Xu K, Li S, Muskens IS, Elliott N, Myint SS, Pandey P, Hansen HM, Morimoto LM, Kang AY, Ma X, Metayer C, Mueller BA, Roberts I, Walsh K, Horvath S, Wiemels JL, de Smith AJ. Accelerated epigenetic aging in newborns with Down syndrome. Aging Cell 2022; 21:e13652. [PMID: 35661546 PMCID: PMC9282838 DOI: 10.1111/acel.13652] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/11/2022] [Accepted: 05/18/2022] [Indexed: 01/07/2023] Open
Abstract
Accelerated aging is a hallmark of Down syndrome (DS), with adults experiencing early-onset Alzheimer's disease and premature aging of the skin, hair, and immune and endocrine systems. Accelerated epigenetic aging has been found in the blood and brain tissue of adults with DS but when premature aging in DS begins remains unknown. We investigated whether accelerated aging in DS is already detectable in blood at birth. We assessed the association between age acceleration and DS using five epigenetic clocks in 346 newborns with DS and 567 newborns without DS using Illumina MethylationEPIC DNA methylation array data. We compared two epigenetic aging clocks (DNAmSkinBloodClock and pan-tissue DNAmAge) and three epigenetic gestational age clocks (Haftorn, Knight, and Bohlin) between DS and non-DS newborns using linear regression adjusting for observed age, sex, batch, deconvoluted blood cell proportions, and genetic ancestry. Targeted sequencing of GATA1 was performed in a subset of 184 newborns with DS to identify somatic mutations associated with transient abnormal myelopoiesis. DS was significantly associated with increased DNAmSkinBloodClock (effect estimate = 0.2442, p < 0.0001), with an epigenetic age acceleration of 244 days in newborns with DS after adjusting for potential confounding factors (95% confidence interval: 196-292 days). We also found evidence of epigenetic age acceleration associated with somatic GATA1 mutations among newborns with DS (p = 0.015). DS was not associated with epigenetic gestational age acceleration. We demonstrate that accelerated epigenetic aging in the blood of DS patients begins prenatally, with implications for the pathophysiology of immunosenescence and other aging-related traits in DS.
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Affiliation(s)
- Keren Xu
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Ivo S. Muskens
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Natalina Elliott
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular MedicineOxford University and BRC Blood Theme, NIHR Oxford Biomedical CentreOxfordUK
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Priyatama Pandey
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Helen M. Hansen
- Department of Neurological SurgeryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Libby M. Morimoto
- School of Public HealthUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Alice Y. Kang
- School of Public HealthUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Xiaomei Ma
- Department of Chronic Disease EpidemiologyYale School of Public HealthNew HavenConnecticutUSA
| | - Catherine Metayer
- School of Public HealthUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Beth A. Mueller
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, and Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Irene Roberts
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular MedicineOxford University and BRC Blood Theme, NIHR Oxford Biomedical CentreOxfordUK
| | - Kyle M. Walsh
- Department of NeurosurgeryDuke UniversityDurhamNorth CarolinaUSA
| | - Steve Horvath
- Department of Human GeneticsDavid Geffen School of Medicine, University of CaliforniaLos AngelesCaliforniaUSA
| | - Joseph L. Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Adam J. de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health SciencesKeck School of Medicine of the University of Southern CaliforniaLos AngelesCaliforniaUSA
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46
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Kallak TK, Fransson E, Bränn E, Berglund H, Lager S, Comasco E, Lyle R, Skalkidou A. Maternal prenatal depressive symptoms and toddler behavior: an umbilical cord blood epigenome-wide association study. Transl Psychiatry 2022; 12:186. [PMID: 35513368 PMCID: PMC9072531 DOI: 10.1038/s41398-022-01954-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/09/2022] Open
Abstract
Children of mothers with prenatal depressive symptoms (PND) have a higher risk of behavioral problems; fetal programming through DNA methylation is a possible underlying mechanism. This study investigated DNA methylation in cord blood to identify possible "at birth" signatures that may indicate susceptibility to behavioral problems at 18 months of age. Cord blood was collected from 256 children of mothers who had self-reported on symptoms of depression during pregnancy and the behavior of their child at 18 months of age. Whole genome DNA methylation was assessed using Illumina MethylationEPIC assay. The mother and child pairs were categorized into four groups, based on both self-reported depressive symptoms, PND or Healthy control (HC), and scores from the Child Behavior checklist (high or low for internalizing, externalizing, and total scores). Adjustments were made for batch effects, cell-type, and clinical covariates. Differentially methylated sites were identified using Kruskal-Wallis test, and Benjamini-Hochberg adjusted p values < 0.05 were considered significant. The analysis was also stratified by sex of the child. Among boys, we observed higher and correlated DNA methylation of one CpG-site in the promoter region of TPP1 in the HC group, with high externalizing scores compared to HC with low externalizing scores. Boys in the PND group showed lower DNA methylation in NUDT15 among those with high, compared to low, internalizing scores; the DNA methylation levels of CpGs in this gene were positively correlated with the CBCL scores. Hence, the differentially methylated CpG sites could be of interest for resilience, regardless of maternal mental health during pregnancy. The findings are in a relatively healthy study cohort, thus limiting the possibility of detecting strong effects associated with behavioral difficulties. This is the first investigation of cord blood DNA methylation signs of fetal programming of PND on child behavior at 18 months of age and thus calls for independent replications.
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Affiliation(s)
| | - Emma Fransson
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Emma Bränn
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Hanna Berglund
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Susanne Lager
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Erika Comasco
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Robert Lyle
- Department of Medical Genetics and Norwegian Sequencing Centre (NSC), Oslo University Hospital, Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Alkistis Skalkidou
- grid.8993.b0000 0004 1936 9457Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
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47
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Gliga AR, Malin Igra A, Hellberg A, Engström K, Raqib R, Rahman A, Vahter M, Kippler M, Broberg K. Maternal exposure to cadmium during pregnancy is associated with changes in DNA methylation that are persistent at 9 years of age. ENVIRONMENT INTERNATIONAL 2022; 163:107188. [PMID: 35334376 DOI: 10.1016/j.envint.2022.107188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/10/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Cadmium (Cd) exposure during gestation has been associated with altered DNA methylation at birth, but it is not known if the changes in methylation persist into childhood. OBJECTIVES To evaluate whether gestational Cd-related changes of DNA methylation persist from birth to 9 years of age. METHODS We studied mother-child dyads in a longitudinal cohort in rural Bangladesh. Cadmium concentrations in maternal blood (erythrocyte fraction; Ery-Cd) at gestational week 14 and in child urine (U-Cd, long-term exposure marker) at 9 years were measured using inductively coupled plasma mass spectrometry. The epigenome-wide DNA methylation was measured in mononuclear cells (PBMCs) prepared from cord blood and peripheral blood at 9 years in 71 children (hereafter referred to as the explorative group) by Infinium HumanMethylation450K BeadChip. Replication of one differentially methylated region (DMR; 9 CpG sites) was performed in PBMCs of 160 9-year-old children (validation group) by EpiTyper MALDI-TOF mass spectrometry. RESULTS The median maternal Ery-Cd concentration was 1.24 µg/kg (range 0.35, 4.55) in the explorative group and 0.83 µg/kg (0.08, 2.97) in the validation group. The median U-Cd concentration in the 9-year-old children was 0.26 µg/L (0.09, 1.06) in the explorative group and 0.32 µg/L (0.07, 1.33) in the validation group. In the explorative group, we identified ten DMRs, both in cord blood and in PBMCs at 9 years, that were associated with maternal Ery-Cd. Eight out of the ten DMRs were hypomethylated and three of the hypomethylated DMRs were located in the HLA region on chromosome 6. One of the DMRs (hypomethylated) in the HLA region (upstream of the zinc finger protein 57 homolog, ZFP57 gene) was replicated in the validation group, and we found that it was hypomethylated in relation to maternal Ery-Cd, but not child U-Cd. CONCLUSION Gestational exposure to Cd appears to be associated with regional changes, especially hypomethylated, in DNA methylation that linger from birth up to prepubertal age.
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Affiliation(s)
- Anda R Gliga
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77 Stockholm, Sweden.
| | - Annachiara Malin Igra
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77 Stockholm, Sweden
| | - Alexander Hellberg
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77 Stockholm, Sweden
| | - Karin Engström
- EPI@LUND, Division of Occupational and Environmental Medicine, Lund University, Sweden
| | - Rubhana Raqib
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Anisur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Marie Vahter
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77 Stockholm, Sweden
| | - Maria Kippler
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77 Stockholm, Sweden
| | - Karin Broberg
- Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77 Stockholm, Sweden
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Wang X, Cho HY, Campbell MR, Panduri V, Coviello S, Caballero MT, Sambandan D, Kleeberger SR, Polack FP, Ofman G, Bell DA. Epigenome-wide association study of bronchopulmonary dysplasia in preterm infants: results from the discovery-BPD program. Clin Epigenetics 2022; 14:57. [PMID: 35484630 PMCID: PMC9052529 DOI: 10.1186/s13148-022-01272-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/06/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Bronchopulmonary dysplasia (BPD) is a lung disease in premature infants caused by therapeutic oxygen supplemental and characterized by impaired pulmonary development which persists into later life. While advances in neonatal care have improved survival rates of premature infants, cases of BPD have been increasing with limited therapeutic options for prevention and treatment. This study was designed to explore the relationship between gestational age (GA), birth weight, and estimated blood cell-type composition in premature infants and to elucidate early epigenetic biomarkers associated with BPD. METHODS Cord blood DNA from preterm neonates that went on to develop BPD (n = 14) or not (non-BPD, n = 93) was applied to Illumina 450 K methylation arrays. Blood cell-type compositions were estimated using DNA methylation profiles. Multivariable robust regression analysis elucidated CpGs associated with BPD risk. cDNA microarray analysis of cord blood RNA identified differentially expressed genes in neonates who later developed BPD. RESULTS The development of BPD and the need for oxygen supplementation were strongly associated with GA (BPD, p < 1.0E-04; O2 supplementation, p < 1.0E-09) and birth weight (BPD, p < 1.0E-02; O2 supplementation, p < 1.0E-07). The estimated nucleated red blood cell (NRBC) percent was negatively associated with birth weight and GA, positively associated with hypomethylation of the tobacco smoke exposure biomarker cg05575921, and high-NRBC blood samples displayed a hypomethylation profile. Epigenome-wide association study (EWAS) identified 38 (Bonferroni) and 275 (false discovery rate 1%) differentially methylated CpGs associated with BPD. BPD-associated CpGs in cord blood were enriched for lung maturation and hematopoiesis pathways. Stochastic epigenetic mutation burden at birth was significantly elevated among those who developed BPD (adjusted p = 0.02). Transcriptome changes in cord blood cells reflected cell cycle, development, and pulmonary disorder events in BPD. CONCLUSIONS While results must be interpreted with caution because of the small size of this study, NRBC content strongly impacted DNA methylation profiles in preterm cord blood and EWAS analysis revealed potential insights into biological pathways involved in BPD pathogenesis.
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Affiliation(s)
- Xuting Wang
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Hye-Youn Cho
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Michelle R Campbell
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Vijayalakshmi Panduri
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | | | - Mauricio T Caballero
- Fundación INFANT, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Deepa Sambandan
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
- The Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, 27606, USA
| | - Steven R Kleeberger
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
| | - Fernando P Polack
- Fundación INFANT, Buenos Aires, Argentina
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Gaston Ofman
- Fundación INFANT, Buenos Aires, Argentina
- Section of Neonatal-Perinatal Medicine, Center for Pregnancy and Newborn Research, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Douglas A Bell
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Building 101, MD C3-03, PO Box 12233, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA.
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49
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Caramaschi D, Neumann A, Cardenas A, Tindula G, Alemany S, Zillich L, Pesce G, Lahti JMT, Havdahl A, Mulder R, Felix JF, Tiemeier H, Sirignano L, Frank J, Witt SH, Rietschel M, Deuschle M, Huen K, Eskenazi B, Send TS, Ferrer M, Gilles M, de Agostini M, Baïz N, Rifas-Shiman SL, Kvist T, Czamara D, Tuominen ST, Relton CL, Rai D, London SJ, Räikkönen K, Holland N, Annesi-Maesano I, Streit F, Hivert MF, Oken E, Sunyer J, Cecil CAM, Sharp G. Meta-analysis of epigenome-wide associations between DNA methylation at birth and childhood cognitive skills. Mol Psychiatry 2022; 27:2126-2135. [PMID: 35145228 PMCID: PMC9126809 DOI: 10.1038/s41380-022-01441-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 01/11/2022] [Indexed: 12/21/2022]
Abstract
Cognitive skills are a strong predictor of a wide range of later life outcomes. Genetic and epigenetic associations across the genome explain some of the variation in general cognitive abilities in the general population and it is plausible that epigenetic associations might arise from prenatal environmental exposures and/or genetic variation early in life. We investigated the association between cord blood DNA methylation at birth and cognitive skills assessed in children from eight pregnancy cohorts within the Pregnancy And Childhood Epigenetics (PACE) Consortium across overall (total N = 2196), verbal (total N = 2206) and non-verbal cognitive scores (total N = 3300). The associations at single CpG sites were weak for all of the cognitive domains investigated. One region near DUSP22 on chromosome 6 was associated with non-verbal cognition in a model adjusted for maternal IQ. We conclude that there is little evidence to support the idea that variation in cord blood DNA methylation at single CpG sites is associated with cognitive skills and further studies are needed to confirm the association at DUSP22.
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Affiliation(s)
- Doretta Caramaschi
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK.
- Department of Psychology, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.
| | - Alexander Neumann
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Gwen Tindula
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Silvia Alemany
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Giancarlo Pesce
- Epidemiology of Allergic and Respiratory Diseases Team (EPAR), Institute Pierre Louis of Epidemiology and Public Health, UMR-S 1136 INSERM and Sorbonne Université, Paris, France
| | - Jari M T Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alexandra Havdahl
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK
- Department of Mental Disorders, Norwegian Institute of Public Health and Nic Waals Institute of Lovisenberg Diaconal Hospital, Oslo, Norway
| | - Rosa Mulder
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lea Sirignano
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Michael Deuschle
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Karen Huen
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, Berkeley, CA, USA
| | - Tabea Sarah Send
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Muriel Ferrer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
| | - Maria Gilles
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Maria de Agostini
- Inserm, Centre for Research in Epidemiology and StatisticS (CRESS), Research Team on Early Life Origins of Health (EAROH), Villejuif, France
| | - Nour Baïz
- Epidemiology of Allergic and Respiratory Diseases Team (EPAR), Institute Pierre Louis of Epidemiology and Public Health, UMR-S 1136 INSERM and Sorbonne Université, Paris, France
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Tuomas Kvist
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Samuli T Tuominen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK
| | - Dheeraj Rai
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK
| | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nina Holland
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Isabella Annesi-Maesano
- Epidemiology of Allergic and Respiratory Diseases Team (EPAR), Institute Pierre Louis of Epidemiology and Public Health, UMR-S 1136 INSERM and Sorbonne Université, Paris, France
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Jordi Sunyer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Gemma Sharp
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), Bristol Medical School, Population Health Science, University of Bristol, Bristol, UK
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50
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van Weelden W, Seed PT, Antoun E, Godfrey KM, Kitaba NT, Lillycrop KA, Dalrymple KV, Sobczyńska-Malefora A, Painter RC, Poston L, White SL, Flynn AC. Folate and vitamin B12 status: associations with maternal glucose and neonatal DNA methylation sites related to dysglycaemia, in pregnant women with obesity. J Dev Orig Health Dis 2022; 13:168-176. [PMID: 33972006 PMCID: PMC7612506 DOI: 10.1017/s2040174421000246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Recent studies implicate maternal gestational diabetes mellitus (GDM) in differential methylation of infant DNA. Folate and vitamin B12 play a role in DNA methylation, and these vitamins may also influence GDM risk. The aims of this study were to determine folate and vitamin B12 status in obese pregnant women and investigate associations between folate and vitamin B12 status, maternal dysglycaemia and neonatal DNA methylation at cytosine-phosphate-guanine sites previously observed to be associated with dysglycaemia. Obese pregnant women who participated in the UK Pregnancies Better Eating and Activity Trial were included. Serum folate and vitamin B12 were measured at the oral glucose tolerance test (OGTT) visit. Cord blood DNA methylation was assessed using the Infinium MethylationEPIC BeadChip. Regression models with adjustment for confounders were used to examine associations. Of the 951 women included, 356 (37.4%) were vitamin B12 deficient, and 44 (4.6%) were folate deficient. Two-hundred and seventy-one women (28%) developed GDM. Folate and vitamin B12 concentrations were not associated with neonatal DNA methylation. Higher folate was positively associated with 1-h plasma glucose after OGTT (β = 0.031, 95% CI 0.001-0.061, p = 0.045). There was no relationship between vitamin B12 and glucose concentrations post OGTT or between folate or vitamin B12 and GDM. In summary, we found no evidence to link folate and vitamin B12 status with the differential methylation of neonatal DNA previously observed in association with dysglycaemia. We add to the evidence that folate status may be related to maternal glucose homoeostasis although replication in other maternal cohorts is required for validation.
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Affiliation(s)
- Wenneke van Weelden
- Amsterdam University Medical Center – location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul T. Seed
- Department of Women and Children’s Health, School of Life Course Sciences, King’s College London
| | - Elie Antoun
- Human Development and Health, Faculty of Medicine, University of Southampton, UK
| | - Keith M. Godfrey
- Human Development and Health, Faculty of Medicine, University of Southampton, UK
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Negusse T. Kitaba
- Human Development and Health, Faculty of Medicine, University of Southampton, UK
| | - Karen A. Lillycrop
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
| | - Kathryn V. Dalrymple
- Department of Women and Children’s Health, School of Life Course Sciences, King’s College London
| | - Agata Sobczyńska-Malefora
- Nutristasis Unit, Viapath, St. Thomas’ Hospital, London, UK
- Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Rebecca C. Painter
- Department of Obstetrics and Gynaecology, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Lucilla Poston
- Department of Women and Children’s Health, School of Life Course Sciences, King’s College London
| | - Sara L. White
- Department of Women and Children’s Health, School of Life Course Sciences, King’s College London
| | - Angela C. Flynn
- Department of Women and Children’s Health, School of Life Course Sciences, King’s College London
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