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Patil V, Perez-Carpena P, Lopez-Escamez JA. A systematic review on the contribution of DNA methylation to hearing loss. Clin Epigenetics 2024; 16:88. [PMID: 38970134 PMCID: PMC11227199 DOI: 10.1186/s13148-024-01697-9] [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: 02/09/2024] [Accepted: 06/17/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND DNA methylation may have a regulatory role in monogenic sensorineural hearing loss and complex, polygenic phenotypic forms of hearing loss, including age-related hearing impairment or Meniere disease. The purpose of this systematic review is to critically assess the evidence supporting a functional role of DNA methylation in phenotypes associated with hearing loss. RESULTS The search strategy yielded a total of 661 articles. After quality assessment, 25 records were selected (12 human DNA methylation studies, 5 experimental animal studies and 8 studies reporting mutations in the DNMT1 gene). Although some methylation studies reported significant differences in CpG methylation in diverse gene promoters associated with complex hearing loss phenotypes (ARHI, otosclerosis, MD), only one study included a replication cohort that supported a regulatory role for CpG methylation in the genes TCF25 and POLE in ARHI. Conversely, several studies have independently confirmed pathogenic mutations within exon 21 of the DNMT1 gene, which encodes the DNA (cytosine-5)-methyltransferase 1 enzyme. This methylation enzyme is strongly associated with a rare disease defined by autosomal dominant cerebellar ataxia, deafness and narcolepsy (ADCA-DN). Of note, rare variants in DNMT1 and DNMT3A genes have also been reported in noise-induced hearing loss. CONCLUSIONS Evidence supporting a functional role for DNA methylation in hearing loss is limited to few genes in complex disorders such as ARHI. Mutations in the DNMT1 gene are associated with ADCA-DN, suggesting the CpG methylation in hearing loss genes deserves further attention in hearing research.
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Affiliation(s)
- Vibha Patil
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine and Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Rm 611024, Level 11 Kolling Institute | 10 Westbourne St, St Leonards, Sydney, NSW, 2064, Australia.
| | - Patricia Perez-Carpena
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, Ibs.Granada, Universidad de Granada, Granada, Spain
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Program, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
- Department of Otolaryngology, Hospital Universitario San Cecilio, Instituto de Investigacion Biosanitaria, ibs.GRANADA, Granada, Spain
| | - Jose A Lopez-Escamez
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine and Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Rm 611024, Level 11 Kolling Institute | 10 Westbourne St, St Leonards, Sydney, NSW, 2064, Australia
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, Ibs.Granada, Universidad de Granada, Granada, Spain
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Program, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
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2
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Khodasevich D, Holland N, Harley KG, Eskenazi B, Barcellos LF, Cardenas A. Prenatal exposure to environmental phenols and phthalates and altered patterns of DNA methylation in childhood. ENVIRONMENT INTERNATIONAL 2024; 190:108862. [PMID: 38972116 DOI: 10.1016/j.envint.2024.108862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 06/13/2024] [Accepted: 06/28/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION Epigenetic marks are key biomarkers linking the prenatal environment to health and development. However, DNA methylation associations and persistence of marks for prenatal exposure to multiple Endocrine Disrupting Chemicals (EDCs) in human populations have not been examined in great detail. METHODS We measured Bisphenol-A (BPA), triclosan, benzophenone-3 (BP3), methyl-paraben, propyl-paraben, and butyl-paraben, as well as 11 phthalate metabolites, in two pregnancy urine samples, at approximately 13 and 26 weeks of gestation in participants of the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) study (N = 309). DNA methylation of cord blood at birth and child peripheral blood at ages 9 and 14 years was measured with 450K and EPIC arrays. Robust linear regression was used to identify differentially methylated probes (DMPs), and comb-p was used to identify differentially methylated regions (DMRs) in association with pregnancy-averaged EDC concentrations. Quantile g-computation was used to assess associations of the whole phenol/phthalate mixture with DMPs and DMRs. RESULTS Prenatal BPA exposure was associated with 1 CpG among males and Parabens were associated with 10 CpGs among females at Bonferroni-level significance in cord blood. Other suggestive DMPs (unadjusted p-value < 1 × 10-6) and several DMRs associated with the individual phenols and whole mixture were also identified. A total of 10 CpG sites at least suggestively associated with BPA, Triclosan, BP3, Parabens, and the whole mixture in cord blood were found to persist into adolescence in peripheral blood. CONCLUSIONS We found sex-specific associations between prenatal phenol exposure and DNA methylation, particularly with BPA in males and Parabens in females. Additionally, we found several DMPs that maintained significant associations with prenatal EDC exposures at age 9 and age 14 years.
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Affiliation(s)
- Dennis Khodasevich
- Division of Environmental Health Sciences, Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Nina Holland
- Center for Environmental Research and Community Health (CERCH), Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Kim G Harley
- Center for Environmental Research and Community Health (CERCH), Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Community Health (CERCH), Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Lisa F Barcellos
- Division of Epidemiology, Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Patel D, McElroy JP, Weng DY, Sahar K, Reisinger SA, Freudenheim JL, Wewers MD, Shields PG, Song MA. Sex-related DNA methylation is associated with inflammation and gene expression in the lungs of healthy individuals. Sci Rep 2024; 14:14280. [PMID: 38902313 PMCID: PMC11190195 DOI: 10.1038/s41598-024-65027-y] [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: 03/07/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024] Open
Abstract
Lung cancer exhibits sex-biased molecular characteristics and epidemiological trends, suggesting a need for sex-specific approaches to understanding its etiology and treatment. DNA methylation alterations play critical roles in lung carcinogenesis and may serve as valuable biomarkers for precision medicine strategies. We employed the Infinium MethylationEPIC array to identify autosomal sex-related differentially methylated CpG sites (DM-CpGs) in lung epithelium of healthy individuals (32 females and 37 males) while controlling for age, BMI, and tobacco use. We correlated DM-CpGs with gene expression in lung epithelium and immune responses in bronchoalveolar lavage. We validated these DM-CpGs in lung tumors and adjacent normal tissue from The Cancer Genome Atlas (TCGA). Among 522 identified DM-CpGs, 61% were hypermethylated in females, predominantly located in promoter regions. These DM genes were implicated in cell-to-cell signaling, cellular function, transport, and lipid metabolism. Correlation analysis revealed sex-specific patterns between DM-CpGs and gene expression. Additionally, several DM-CpGs were correlated significantly with cytokines (IL-1β, IL-4, IL-12p70, and IFN-γ), macrophage, and lymphocyte counts. Also, some DM-CpGs were observed in TCGA lung adenocarcinoma, squamous cell carcinoma, and adjacent normal tissues. Our findings highlight sex-specific DNA methylation patterns in healthy lung epithelium and their associations with lung gene expression and lung immune biomarkers. These findings underscore the potential role of lung sex-related CpGs as epigenetic predispositions influencing sex disparities in lung cancer risk and outcomes, warranting further investigation for personalized lung cancer management strategies.
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Affiliation(s)
- Devki Patel
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Joseph P McElroy
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Daniel Y Weng
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Kamel Sahar
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Sarah A Reisinger
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Mark D Wewers
- Pulmonary and Critical Care Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Peter G Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA.
- Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
| | - Min-Ae Song
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA.
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4
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Guerithault N, Stinson EJ, Cabeza De Baca T, Looker HC, Votruba SB, Piaggi P, Gluck ME, Krakoff J, Chang DC. Sex-specific associations between birthweight and objectively measured energy intake in healthy indigenous American adults. Appetite 2024; 197:107334. [PMID: 38569442 DOI: 10.1016/j.appet.2024.107334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 01/29/2024] [Accepted: 03/30/2024] [Indexed: 04/05/2024]
Affiliation(s)
- Nicolas Guerithault
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Emma J Stinson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Tomás Cabeza De Baca
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Helen C Looker
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Susanne B Votruba
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Paolo Piaggi
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Marci E Gluck
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Jonathan Krakoff
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Douglas C Chang
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA.
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5
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Creasey N, Beijers R, O'Donnell KJ, de Weerth C, Tollenaar MS. Maternal sensitivity and child internalizing and externalizing behavior: a mediating role for glucocorticoid receptor gene ( NR3C1) methylation? Dev Psychopathol 2024; 36:967-978. [PMID: 36896668 DOI: 10.1017/s0954579423000226] [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] [Indexed: 03/11/2023]
Abstract
The early caregiving environment can have lasting effects on child mental health. Animal models suggest that glucocorticoid receptor gene (NR3C1) DNA methylation plays a mediating role in linking more responsive caregiving to improved behavioral outcomes by its impact on the stress regulatory system. In this longitudinal study, we examined whether children's NR3C1 methylation levels mediate an effect of maternal sensitivity in infancy on levels of child internalizing and externalizing behavior in a community sample. Maternal sensitivity of 145 mothers was rated at infant age 5 weeks, 12 months, and 30 months by observing mother-infant interactions. Buccal DNA methylation was assessed in the same children at age 6 years and maternal-reported internalizing and externalizing behavior was assessed at age 6 and 10 years. Higher sensitivity at age 5 weeks significantly predicted lower DNA methylation levels at two NR3C1 CpG loci, although methylation levels at these loci did not mediate an effect of maternal sensitivity on levels of child internalizing and externalizing behavior. Overall, the study provides evidence that maternal sensitivity in early infancy is associated with DNA methylation levels at loci involved in stress regulation, but the significance of this finding for child mental health remains unclear.
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Affiliation(s)
- Nicole Creasey
- Preventive Youth Care, Research Institute of Child Development and Education, University of Amsterdam, the Netherlands
| | - Roseriet Beijers
- Department of Social Development, Behavioral Science Institute, Radboud University, the Netherlands, and Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, the Netherlands
| | - Kieran J O'Donnell
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Hospital Research Centre, McGill University, QC, Canada; Canadian Institute for Advanced Research, Child and Brain Development Program, Canada; and Yale Child Study Center & Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, USA
| | - Carolina de Weerth
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, the Netherlands
| | - Marieke S Tollenaar
- Institute of Psychology and Leiden Institute for Brain and Cognition, Leiden University, the Netherlands
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6
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Czamara D, Dieckmann L, Lahti-Pulkkinen M, Cruceanu C, Henrich W, Plagemann A, Räikkönen K, Braun T, Binder EB, Lahti J, Entringer S. Sex differences in DNA methylation across gestation: a large scale, cross-cohort, multi-tissue analysis. Cell Mol Life Sci 2024; 81:177. [PMID: 38600394 PMCID: PMC11006734 DOI: 10.1007/s00018-024-05208-0] [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: 10/09/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024]
Abstract
Biological sex is a key variable influencing many physiological systems. Disease prevalence as well as treatment success can be modified by sex. Differences emerge already early in life and include pregnancy complications and adverse birth outcomes. The placenta is a critical organ for fetal development and shows sex-based differences in the expression of hormones and cytokines. Epigenetic regulation, such as DNA methylation (DNAm), may underlie the previously reported placental sexual dimorphism. We associated placental DNAm with fetal sex in three cohorts. Individual cohort results were meta-analyzed with random-effects modelling. CpG-sites differentially methylated with sex were further investigated regarding pathway enrichment, overlap with methylation quantitative trait loci (meQTLs), and hits from phenome-wide association studies (PheWAS). We evaluated the consistency of findings across tissues (CVS, i.e. chorionic villus sampling from early placenta, and cord blood) as well as with gene expression. We identified 10,320 epigenome-wide significant sex-differentially methylated probes (DMPs) spread throughout the epigenome of the placenta at birth. Most DMPs presented with lower DNAm levels in females. DMPs mapped to genes upregulated in brain, were enriched for neurodevelopmental pathways and significantly overlapped with meQTLs and PheWAS hits. Effect sizes were moderately correlated between CVS and placenta at birth, but only weakly correlated between birth placenta and cord blood. Sex differential gene expression in birth placenta was less pronounced and implicated genetic regions only marginally overlapped with those associated with differential DNAm. Our study provides an integrative perspective on sex-differential DNAm in perinatal tissues underscoring the possible link between placenta and brain.
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Affiliation(s)
- Darina Czamara
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany.
| | - Linda Dieckmann
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Marius Lahti-Pulkkinen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Cristiana Cruceanu
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Wolfgang Henrich
- Department of Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Andreas Plagemann
- Department of Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
- Department of Experimental Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Obstetrics and Gynecology, HUS Helsinki University Hospital, Helsinki, Finland
| | - Thorsten Braun
- Department of Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
- Department of Experimental Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Elisabeth B Binder
- Department Genes and Environment, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, Atlanta, GA, USA
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sonja Entringer
- Institute of Medical Psychology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany.
- Department of Pediatrics, Health and Disease Research Program, School of Medicine, University of California, Irvine, CA, USA.
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7
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Webster AP, Ecker S, Moghul I, Liu X, Dhami P, Marzi S, Paul DS, Kuxhausen M, Lee SJ, Spellman SR, Wang T, Feber A, Rakyan V, Peggs KS, Beck S. Donor whole blood DNA methylation is not a strong predictor of acute graft versus host disease in unrelated donor allogeneic haematopoietic cell transplantation. Front Genet 2024; 15:1242636. [PMID: 38633407 PMCID: PMC11021570 DOI: 10.3389/fgene.2024.1242636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 03/04/2024] [Indexed: 04/19/2024] Open
Abstract
Allogeneic hematopoietic cell transplantation (HCT) is used to treat many blood-based disorders and malignancies, however it can also result in serious adverse events, such as the development of acute graft-versus-host disease (aGVHD). This study aimed to develop a donor-specific epigenetic classifier to reduce incidence of aGVHD by improving donor selection. Genome-wide DNA methylation was assessed in a discovery cohort of 288 HCT donors selected based on recipient aGVHD outcome; this cohort consisted of 144 cases with aGVHD grades III-IV and 144 controls with no aGVHD. We applied a machine learning algorithm to identify CpG sites predictive of aGVHD. Receiver operating characteristic (ROC) curve analysis of these sites resulted in a classifier with an encouraging area under the ROC curve (AUC) of 0.91. To test this classifier, we used an independent validation cohort (n = 288) selected using the same criteria as the discovery cohort. Attempts to validate the classifier failed with the AUC falling to 0.51. These results indicate that donor DNA methylation may not be a suitable predictor of aGVHD in an HCT setting involving unrelated donors, despite the initial promising results in the discovery cohort. Our work highlights the importance of independent validation of machine learning classifiers, particularly when developing classifiers intended for clinical use.
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Affiliation(s)
- Amy P. Webster
- UCL Cancer Institute, University College London, London, United Kindom
- The University of Exeter Medical School, University of Exeter, Exeter, United Kindom
| | - Simone Ecker
- UCL Cancer Institute, University College London, London, United Kindom
| | - Ismail Moghul
- UCL Cancer Institute, University College London, London, United Kindom
| | - Xiaohong Liu
- UCL Cancer Institute, University College London, London, United Kindom
| | - Pawan Dhami
- UCL Cancer Institute, University College London, London, United Kindom
- NIHR Biomedical Research Centre, Guy’s Hospital London, London, United Kindom
| | - Sarah Marzi
- Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kindom
| | - Dirk S. Paul
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kindom
| | - Michelle Kuxhausen
- Center for International Blood and Marrow Transplant Research, NMDP, Minneapolis, United Kindom
| | - Stephanie J. Lee
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, United Kindom
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, United Kindom
| | - Stephen R. Spellman
- Center for International Blood and Marrow Transplant Research, NMDP, Minneapolis, United Kindom
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, United Kindom
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, United Kindom
| | - Andrew Feber
- UCL Cancer Institute, University College London, London, United Kindom
- The Institute of Cancer Research, London, United Kindom
| | - Vardhman Rakyan
- Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kindom
| | - Karl S. Peggs
- UCL Cancer Institute, University College London, London, United Kindom
- Department of Haematology, University College London, London, United Kindom
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, United Kindom
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8
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Tesfaye M, Spindola LM, Stavrum AK, Shadrin A, Melle I, Andreassen OA, Le Hellard S. Sex effects on DNA methylation affect discovery in epigenome-wide association study of schizophrenia. Mol Psychiatry 2024:10.1038/s41380-024-02513-9. [PMID: 38503926 DOI: 10.1038/s41380-024-02513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/21/2024]
Abstract
Sex differences in the epidemiology and clinical characteristics of schizophrenia are well-known; however, the molecular mechanisms underlying these differences remain unclear. Further, the potential advantages of sex-stratified meta-analyses of epigenome-wide association studies (EWAS) of schizophrenia have not been investigated. Here, we performed sex-stratified EWAS meta-analyses to investigate whether sex stratification improves discovery, and to identify differentially methylated regions (DMRs) in schizophrenia. Peripheral blood-derived DNA methylation data from 1519 cases of schizophrenia (male n = 989, female n = 530) and 1723 controls (male n = 997, female n = 726) from three publicly available datasets, and the TOP cohort were meta-analyzed to compare sex-specific, sex-stratified, and sex-adjusted EWAS. The predictive power of each model was assessed by polymethylation score (PMS). The number of schizophrenia-associated differentially methylated positions identified was higher for the sex-stratified model than for the sex-adjusted one. We identified 20 schizophrenia-associated DMRs in the sex-stratified analysis. PMS from sex-stratified analysis outperformed that from sex-adjusted analysis in predicting schizophrenia. Notably, PMSs from the sex-stratified and female-only analyses, but not those from sex-adjusted or the male-only analyses, significantly predicted schizophrenia in males. The findings suggest that sex-stratified EWAS meta-analyses improve the identification of schizophrenia-associated epigenetic changes and highlight an interaction between sex and schizophrenia status on DNA methylation. Sex-specific DNA methylation may have potential implications for precision psychiatry and the development of stratified treatments for schizophrenia.
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Grants
- 273291, 273446, 326813, 223273 Norges Forskningsråd (Research Council of Norway)
- 273291, 273446, 326813, 223273 Norges Forskningsråd (Research Council of Norway)
- 273291, 273446, 326813, 223273 Norges Forskningsråd (Research Council of Norway)
- 273291, 273446, 326813, 223273 Norges Forskningsråd (Research Council of Norway)
- 273291, 273446, 326813, 223273 Norges Forskningsråd (Research Council of Norway)
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Affiliation(s)
- Markos Tesfaye
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Leticia M Spindola
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
- Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Bergen Center for Brain Plasticity, Haukeland University Hospital, Bergen, Norway
| | - Anne-Kristin Stavrum
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
- Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Alexey Shadrin
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Ingrid Melle
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Stephanie Le Hellard
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
- Bergen Center for Brain Plasticity, Haukeland University Hospital, Bergen, Norway.
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9
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Reiner A, Bakulski KM, Fisher JD, Dou JF, Schneper L, Mitchell C, Notterman DA, Zawistowski M, Ware EB. Sex-specific DNA methylation in saliva from the multi-ethnic Future of Families and Child Wellbeing Study. Epigenetics 2023; 18:2222244. [PMID: 37300819 PMCID: PMC10259311 DOI: 10.1080/15592294.2023.2222244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/11/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
The prevalence and severity of many diseases differs by sex, potentially due to sex-specific patterns in DNA methylation. Autosomal sex-specific differences in DNA methylation have been observed in cord blood and placental tissue but are not well studied in saliva or in diverse populations. We sought to characterize sex-specific DNA methylation on autosomal chromosomes in saliva samples from children in the Future of Families and Child Wellbeing Study, a multi-ethnic prospective birth cohort containing an oversampling of Black, Hispanic and low-income families. DNA methylation from saliva samples was analysed on 796 children (50.6% male) at both ages 9 and 15 with DNA methylation measured using the Illumina HumanMethylation 450k array. An epigenome-wide association analysis of the age 9 samples identified 8,430 sex-differentiated autosomal DNA methylation sites (P < 2.4 × 10-7), of which 76.2% had higher DNA methylation in female children. The strongest sex-difference was in the cg26921482 probe, in the AMDHD2 gene, with 30.6% higher DNA methylation in female compared to male children (P < 1 × 10-300). Treating the age 15 samples as an internal replication set, we observed highly consistent results between the ages 9 and 15 measurements, indicating stable and replicable sex-differentiation. Further, we directly compared our results to previously published DNA methylation sex differences in both cord blood and saliva and again found strong consistency. Our findings support widespread and robust sex-differential DNA methylation across age, human tissues, and populations. These findings help inform our understanding of potential biological processes contributing to sex differences in human physiology and disease.
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Affiliation(s)
- Allison Reiner
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonah D Fisher
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Colter Mitchell
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel A Notterman
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Erin B Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
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10
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Protti G, Rubbi L, Gören T, Sabirli R, Civlan S, Kurt Ö, Türkçüer İ, Köseler A, Pellegrini M. The methylome of buccal epithelial cells is influenced by age, sex, and physiological properties. Physiol Genomics 2023; 55:618-633. [PMID: 37781740 DOI: 10.1152/physiolgenomics.00063.2023] [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: 06/22/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023] Open
Abstract
Epigenetic modifications, particularly DNA methylation, have emerged as regulators of gene expression and are implicated in various biological processes and disease states. Understanding the factors influencing the epigenome is essential for unraveling its complexity. In this study, we aimed to identify how the methylome of buccal epithelial cells, a noninvasive and easily accessible tissue, is associated with demographic and health-related variables commonly used in clinical settings, such as age, sex, blood immune composition, hemoglobin levels, and others. We developed a model to assess the association of multiple factors with the human methylome and identify the genomic loci significantly impacted by each trait. We demonstrated that DNA methylation variation is accurately modeled by several factors. We confirmed the well-known impact of age and sex and unveiled novel clinical factors associated with DNA methylation, such as blood neutrophils, hemoglobin, red blood cell distribution width, high-density lipoprotein cholesterol, and urea. Genomic regions significantly associated with these traits were enriched in relevant transcription factors, drugs, and diseases. Among our findings, we showed that neutrophil-impacted loci were involved in neutrophil functionality and maturation. Similarly, hemoglobin-influenced sites were associated with several diseases, including aplastic anemia, and the genomic loci affected by urea were related to congenital anomalies of the kidney and urinary tract. Our findings contribute to a better understanding of the human methylome plasticity and provide insights into novel factors shaping DNA methylation patterns, highlighting their potential clinical implications as biomarkers and the importance of considering these physiological traits in future medical epigenomic investigations.NEW & NOTEWORTHY We have developed a quantitative model to assess how the human methylome is associated with several factors and to identify the genomic loci significantly impacted by each trait. We reported novel health-related factors driving DNA methylation patterns and new site-specific regulations that further elucidate methylome dynamics. Our study contributes to a better understanding of the plasticity of the human methylome and unveils novel physiological traits with a potential role in future medical epigenomic investigations.
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Affiliation(s)
- Giulia Protti
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
| | - Tarik Gören
- Emergency Department, Pamukkale University Medical Faculty, Denizli, Turkey
| | - Ramazan Sabirli
- Emergency Department, Bakircay University Faculty of Medicine Cigli Training and Research Hospital, Izmir, Turkey
| | - Serkan Civlan
- Department of Neurosurgery, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Özgür Kurt
- Department of Microbiology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - İbrahim Türkçüer
- Emergency Department, Pamukkale University Medical Faculty, Denizli, Turkey
| | - Aylin Köseler
- Department of Biophysics, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
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11
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Zhou J, Xia Y, Li M, Chen Y, Dai J, Liu C, Chen C. A higher dysregulation burden of brain DNA methylation in female patients implicated in the sex bias of Schizophrenia. Mol Psychiatry 2023; 28:4842-4852. [PMID: 37696874 PMCID: PMC10925554 DOI: 10.1038/s41380-023-02243-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/13/2023]
Abstract
Sex differences are pervasive in schizophrenia (SCZ), but the extent and magnitude of DNA methylation (DNAm) changes underlying these differences remain uncharacterized. In this study, sex-stratified differential DNAm analysis was performed in postmortem brain samples from 117 SCZ and 137 controls, partitioned into discovery and replication datasets. Three differentially methylated positions (DMPs) were identified (adj.p < 0.05) in females and 29 DMPs in males without overlap between them. Over 81% of these sex-stratified DMPs were directionally consistent between sexes but with different effect sizes. Females experienced larger magnitude of DNAm changes and more DMPs (based on data of equal sample size) than males, contributing to a higher dysregulation burden of DNAm in females SCZ. Additionally, despite similar proportions of female-related DMPs (fDMPs, 8%) being under genetic control compared with males (10%), significant enrichment of DMP-related single nucleotide polymorphisms (SNPs) in signals of genome-wide association studies was identified only in fDMPs. One DMP in each sex connected the SNPs and gene expression of CALHM1 in females and CCDC149 in males. PPI subnetworks revealed that both female- and male-related differential DNAm interacted with synapse-related dysregulation. Immune-related pathways were unique for females and neuron-related pathways were associated with males. This study reveals remarkable quantitative differences in DNAm-related sexual dimorphism in SCZ and that females have a higher dysregulation burden of SCZ-associated DNAm than males.
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Affiliation(s)
- Jiaqi Zhou
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yan Xia
- Department of Medicine, Harvard Medical School, Boston, MA, 02114, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02114, USA.
- Analytic and Translational Genetics unit, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Miao Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
| | - Yu Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02114, USA
| | - Jiacheng Dai
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and the Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan, 410078, China.
- National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China.
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12
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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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13
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Shayota BJ. Downstream Assays for Variant Resolution: Epigenetics, RNA Sequnncing, and Metabolomics. Pediatr Clin North Am 2023; 70:929-936. [PMID: 37704351 DOI: 10.1016/j.pcl.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
As the availability of advanced molecular testing like whole exome and genome sequencing expands, it comes with the added complication of interpreting inconclusive results, including determining the relevance of variants of uncertain significance or failing to find a variant in an otherwise suspected specific genetic disorder. This complication necessitates the use of alternative testing methods to gather more information in support of, or against, a particular genetic diagnosis. Therefore, new genome-wide approaches, including DNA epigenetic testing, RNA sequencing, and metabolomics, are increasingly being used to increase the diagnostic yield when used in conjunction with more conventional genetic tests.
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Affiliation(s)
- Brian J Shayota
- University of Utah, 295 Chipeta Way, Salt Lake City, UT 84108, USA; Primary Children's Hospital, Salt Lake City, UT, USA.
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14
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Sommer AJ, Okonkwo J, Monteiro J, Bind MAC. A permutation-based approach using a rank-based statistic to identify sex differences in epigenetics. Sci Rep 2023; 13:14838. [PMID: 37684282 PMCID: PMC10491832 DOI: 10.1038/s41598-023-41360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Epigenetic sex differences and their resulting implications for human health have been studied for about a decade. The objective of this paper is to use permutation-based inference and a new ranked-based test statistic to identify sex-based epigenetic differences in the human DNA methylome. In particular, we examine whether we could identify separations between the female and male distributions of DNA methylation across hundred of thousands CpG sites in two independent cohorts, the Swedish Adoption Twin study and the Lamarck study. Based on Fisherian p-values, we set a threshold for methylation differences "worth further scrutiny". At this threshold, we were able to confirm previously-found CpG sites that stratify with respect to sex. These CpG sites with sex differences in DNA methylation should be further investigated for their possible contribution to various physiological and pathological functions in the human body. We followed-up our statistical analyses with a literature review in order to inform the proposed disease implications for the loci we uncovered.
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Affiliation(s)
- Alice J Sommer
- Institute for Medical Information Processing, Biometry, and Epidemiology, Faculty of Medicine, Ludwig-Maximilians-University München, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jude Okonkwo
- Columbia Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jonathan Monteiro
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA
| | - Marie-Abèle C Bind
- Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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15
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Santos HP, Enggasser AE, Clark J, Roell K, Zhabotynsky V, Gower WA, Yanni D, Yang NG, Washburn L, Gogcu S, Marsit CJ, Kuban K, O'Shea TM, Fry RC. Sexually dimorphic methylation patterns characterize the placenta and blood from extremely preterm newborns. BMC Biol 2023; 21:173. [PMID: 37608375 PMCID: PMC10464100 DOI: 10.1186/s12915-023-01662-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 07/12/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Health outcomes among children born prematurely are known to be sexually dimorphic, with male infants often more affected, yet the mechanism behind this observation is not clear. CpG methylation levels in the placenta and blood also differ by sex and are associated with adverse health outcomes. We contrasted CpG methylation levels in the placenta and neonatal blood (n = 358) from the Extremely Low Gestational Age Newborn (ELGAN) cohort based on the EPIC array, which assays over 850,000 CpG sites across the epigenome. Sex-specific epigenome-wide association analyses were conducted for the placenta and neonatal blood samples independently, and the results were compared to determine tissue-specific differences between the methylation patterns in males and females. All models were adjusted for cell type heterogeneity. Enrichment pathway analysis was performed to identify the biological functions of genes related to the sexually dimorphic CpG sites. RESULTS Approximately 11,500 CpG sites were differentially methylated in relation to sex. Of these, 5949 were placenta-specific and 5361 were blood-specific, with only 233 CpG sites overlapping in both tissues. For placenta-specific CpG sites, 90% were hypermethylated in males. For blood-specific CpG sites, 95% were hypermethylated in females. In the placenta, keratinocyte differentiation biological pathways were enriched among the differentially methylated genes. No enrichment pathways were observed for blood. CONCLUSIONS Distinct methylation patterns were observed between male and female children born extremely premature, and keratinocyte differentiation pathways were enriched in the placenta. These findings provide new insights into the epigenetic mechanisms underlying sexually dimorphic health outcomes among extremely premature infants.
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Affiliation(s)
- Hudson P Santos
- School of Nursing and Health Studies, University of Miami, Coral Gables, FL, USA.
| | - Adam E Enggasser
- Gillings School of Global Public Health, Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeliyah Clark
- Gillings School of Global Public Health, Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kyle Roell
- Gillings School of Global Public Health, Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vasyl Zhabotynsky
- Gillings School of Global Public Health, Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William Adam Gower
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Diana Yanni
- Department of Neonatology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Nou Gao Yang
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Lisa Washburn
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Semsa Gogcu
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Karl Kuban
- Division of Pediatric Neurology, Department of Pediatrics, School of Medicine, Boston. University, Boston, MA, USA
| | - T Michael O'Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C Fry
- Gillings School of Global Public Health, Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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16
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Khodasevich D, Holland N, Hubbard A, Harley K, Deardorff J, Eskenazi B, Cardenas A. Associations between prenatal phthalate exposure and childhood epigenetic age acceleration. ENVIRONMENTAL RESEARCH 2023; 231:116067. [PMID: 37149020 PMCID: PMC10330458 DOI: 10.1016/j.envres.2023.116067] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/06/2023] [Accepted: 05/04/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND Phthalates, a group of pervasive endocrine-disrupting chemicals found in plastics and personal care products, have been associated with a wide range of developmental and health outcomes. However, their impact on biomarkers of aging has not been characterized. We tested associations between prenatal exposure to 11 phthalate metabolites on epigenetic aging in children at birth, 7, 9, and 14 years of age. We hypothesized that prenatal phthalate exposure will be associated with epigenetic age acceleration measures at birth and in early childhood, with patterns dependent on sex and timing of DNAm measurement. METHODS Among 385 mother-child pairs from the CHAMACOS cohort, we measured DNAm at birth, 7, 9, and 14 years of age, and utilized adjusted linear regression to assess the association between prenatal phthalate exposure and Bohlin's Gestational Age Acceleration (GAA) at birth and Intrinsic Epigenetic Age Acceleration (IEAA) throughout childhood. Additionally, quantile g-computation was utilized to assess the effect of the phthalate mixture on GAA at birth and IEAA throughout childhood. RESULTS We found a negative association between prenatal di (2-ethylhexyl) phthalate (DEHP) exposure and IEAA among males at age 7 (-0.62 years; 95% CI:-1.06 to -0.18), and a marginal negative association between the whole phthalate mixture and GAA among males at birth (-1.54 days, 95% CI: -2.79 to -0.28), while most other associations were nonsignificant. CONCLUSIONS Our results suggest that prenatal exposure to certain phthalates is associated with epigenetic aging in children. Additionally, our findings suggest that the influence of prenatal exposures on epigenetic age may only manifest during specific periods of child development, and studies relying on DNAm measurements solely from cord blood or single time points may overlook potential relationships.
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Affiliation(s)
- Dennis Khodasevich
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA; Center for Computational Biology, 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, Berkeley, CA, USA
| | - Alan Hubbard
- Division of Biostatistics, 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, Berkeley, CA, USA
| | - Julianna Deardorff
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California, Berkeley, Berkeley, CA, USA; Division of Community 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, Berkeley, CA, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA.
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17
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Nakamura A, Broséus L, Tost J, Vaiman D, Martins S, Keyes K, Bonello K, Fekom M, Strandberg-Larsen K, Sutter-Dallay AL, Heude B, Melchior M, Lepeule J. Epigenome-Wide Associations of Placental DNA Methylation and Behavioral and Emotional Difficulties in Children at 3 Years of Age. Int J Mol Sci 2023; 24:11772. [PMID: 37511531 PMCID: PMC10380531 DOI: 10.3390/ijms241411772] [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: 05/12/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The placenta is a key organ for fetal and brain development. Its epigenome can be regarded as a biochemical record of the prenatal environment and a potential mechanism of its association with the future health of the fetus. We investigated associations between placental DNA methylation levels and child behavioral and emotional difficulties, assessed at 3 years of age using the Strengths and Difficulties Questionnaire (SDQ) in 441 mother-child dyads from the EDEN cohort. Hypothesis-driven and exploratory analyses (on differentially methylated probes (EWAS) and regions (DMR)) were adjusted for confounders, technical factors, and cell composition estimates, corrected for multiple comparisons, and stratified by child sex. Hypothesis-driven analyses showed an association of cg26703534 (AHRR) with emotional symptoms, and exploratory analyses identified two probes, cg09126090 (intergenic region) and cg10305789 (PPP1R16B), as negatively associated with peer relationship problems, as well as 33 DMRs, mostly positively associated with at least one of the SDQ subscales. Among girls, most associations were seen with emotional difficulties, whereas in boys, DMRs were as much associated with emotional than behavioral difficulties. This study provides the first evidence of associations between placental DNA methylation and child behavioral and emotional difficulties. Our results suggest sex-specific associations and might provide new insights into the mechanisms of neurodevelopment.
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Affiliation(s)
- Aurélie Nakamura
- Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences (IAB), University Grenoble Alpes, INSERM, 38700 La Tronche, France;
| | - Lucile Broséus
- Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences (IAB), University Grenoble Alpes, INSERM, 38700 La Tronche, France;
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA—Institut de Biologie François Jacob, University Paris Saclay, 91057 Evry, France;
| | - Daniel Vaiman
- From Gametes to Birth, Institut Cochin, U1016 INSERM, UMR 8104 CNRS, Paris Cité University, 75014 Paris, France;
| | - Silvia Martins
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA; (S.M.); (K.K.)
| | - Katherine Keyes
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA; (S.M.); (K.K.)
| | - Kim Bonello
- Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP), Equipe de Recherche en Epidémiologie Sociale (ERES), Sorbonne Université, INSERM, 75571 Paris, France; (K.B.); (M.F.); (M.M.)
- Department of General Practice, School of Medicine, Sorbonne University, 75013 Paris, France
| | - Mathilde Fekom
- Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP), Equipe de Recherche en Epidémiologie Sociale (ERES), Sorbonne Université, INSERM, 75571 Paris, France; (K.B.); (M.F.); (M.M.)
| | - Katrine Strandberg-Larsen
- Section of Epidemiology, Department of Public Health, University of Copenhagen, 1165 Copenhagen, Denmark;
| | - Anne-Laure Sutter-Dallay
- Bordeaux Population Health, Bordeaux University, INSERM, UMR 1219, 33076 Bordeaux, France;
- University Department of Child and Adolescent Psychiatry, Charles Perrens Hospital, 33000 Bordeaux, France
| | - Barbara Heude
- Center for Research in Epidemiology and Statistics (CRESS), Université Paris Cité and Université Sorbonne Paris Nord, INSERM, INRAE, 75004 Paris, France;
| | - Maria Melchior
- Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP), Equipe de Recherche en Epidémiologie Sociale (ERES), Sorbonne Université, INSERM, 75571 Paris, France; (K.B.); (M.F.); (M.M.)
| | - Johanna Lepeule
- Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences (IAB), University Grenoble Alpes, INSERM, 38700 La Tronche, France;
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18
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Tarracchini C, Alessandri G, Fontana F, Rizzo SM, Lugli GA, Bianchi MG, Mancabelli L, Longhi G, Argentini C, Vergna LM, Anzalone R, Viappiani A, Turroni F, Taurino G, Chiu M, Arboleya S, Gueimonde M, Bussolati O, van Sinderen D, Milani C, Ventura M. Genetic strategies for sex-biased persistence of gut microbes across human life. Nat Commun 2023; 14:4220. [PMID: 37452041 PMCID: PMC10349097 DOI: 10.1038/s41467-023-39931-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023] Open
Abstract
Although compositional variation in the gut microbiome during human development has been extensively investigated, strain-resolved dynamic changes remain to be fully uncovered. In the current study, shotgun metagenomic sequencing data of 12,415 fecal microbiomes from healthy individuals are employed for strain-level tracking of gut microbiota members to elucidate its evolving biodiversity across the human life span. This detailed longitudinal meta-analysis reveals host sex-related persistence of strains belonging to common, maternally-inherited species, such as Bifidobacterium bifidum and Bifidobacterium longum subsp. longum. Comparative genome analyses, coupled with experiments including intimate interaction between microbes and human intestinal cells, show that specific bacterial glycosyl hydrolases related to host-glycan metabolism may contribute to more efficient colonization in females compared to males. These findings point to an intriguing ancient sex-specific host-microbe coevolution driving the selective persistence in women of key microbial taxa that may be vertically passed on to the next generation.
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Affiliation(s)
- Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Massimiliano Giovanni Bianchi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Laura Maria Vergna
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Martina Chiu
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Silvia Arboleya
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, CSIC, 33300, Villaviciosa, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, CSIC, 33300, Villaviciosa, Spain
| | - Ovidio Bussolati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, T12YT20, Cork, Ireland
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy.
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy.
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19
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Li KY, Tam CHT, Liu H, Day S, Lim CKP, So WY, Huang C, Jiang G, Shi M, Lee HM, Lan HY, Szeto CC, Hanson RL, Nelson RG, Susztak K, Chan JCN, Yip KY, Ma RCW. DNA methylation markers for kidney function and progression of diabetic kidney disease. Nat Commun 2023; 14:2543. [PMID: 37188670 PMCID: PMC10185566 DOI: 10.1038/s41467-023-37837-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
Epigenetic markers are potential biomarkers for diabetes and related complications. Using a prospective cohort from the Hong Kong Diabetes Register, we perform two independent epigenome-wide association studies to identify methylation markers associated with baseline estimated glomerular filtration rate (eGFR) and subsequent decline in kidney function (eGFR slope), respectively, in 1,271 type 2 diabetes subjects. Here we show 40 (30 previously unidentified) and eight (all previously unidentified) CpG sites individually reach epigenome-wide significance for baseline eGFR and eGFR slope, respectively. We also develop a multisite analysis method, which selects 64 and 37 CpG sites for baseline eGFR and eGFR slope, respectively. These models are validated in an independent cohort of Native Americans with type 2 diabetes. Our identified CpG sites are near genes enriched for functional roles in kidney diseases, and some show association with renal damage. This study highlights the potential of methylation markers in risk stratification of kidney disease among type 2 diabetes individuals.
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Affiliation(s)
- Kelly Yichen Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Claudia Ha Ting Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Hongbo Liu
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Samantha Day
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies and Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Cadmon King Poo Lim
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Chuiguo Huang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Guozhi Jiang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Mai Shi
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Heung Man Lee
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Hui-Yao Lan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Cheuk-Chun Szeto
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Robert G Nelson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
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20
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van Oers K, van den Heuvel K, Sepers B. The Epigenetics of Animal Personality. Neurosci Biobehav Rev 2023; 150:105194. [PMID: 37094740 DOI: 10.1016/j.neubiorev.2023.105194] [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: 10/29/2022] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023]
Abstract
Animal personality, consistent individual differences in behaviour, is an important concept for understanding how individuals vary in how they cope with environmental challenges. In order to understand the evolutionary significance of animal personality, it is crucial to understand the underlying regulatory mechanisms. Epigenetic marks such as DNA methylation are hypothesised to play a major role in explaining variation in phenotypic changes in response to environmental alterations. Several characteristics of DNA methylation also align well with the concept of animal personality. In this review paper, we summarise the current literature on the role that molecular epigenetic mechanisms may have in explaining personality variation. We elaborate on the potential for epigenetic mechanisms to explain behavioural variation, behavioural development and temporal consistency in behaviour. We then suggest future routes for this emerging field and point to potential pitfalls that may be encountered. We conclude that a more inclusive approach is needed for studying the epigenetics of animal personality and that epigenetic mechanisms cannot be studied without considering the genetic background.
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Affiliation(s)
- Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands.
| | - Krista van den Heuvel
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Bernice Sepers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands
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21
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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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22
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Hu J, Xu X, Li J, Jiang Y, Hong X, Rexrode KM, Wang G, Hu FB, Zhang H, Karmaus WJ, Wang X, Liang L. Sex differences in the intergenerational link between maternal and neonatal whole blood DNA methylation: a genome-wide analysis in 2 birth cohorts. Clin Epigenetics 2023; 15:51. [PMID: 36966332 PMCID: PMC10040137 DOI: 10.1186/s13148-023-01442-8] [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: 03/02/2022] [Accepted: 02/06/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND The mother-child inheritance of DNA methylation (DNAm) variations could contribute to the inheritance of disease susceptibility across generations. However, no study has investigated patterns of mother-child associations in DNAm at the genome-wide scale. It remains unknown whether there are sex differences in mother-child DNAm associations. RESULTS Using genome-wide DNAm profiling data (721,331 DNAm sites, including 704,552 on autosomes and 16,779 on the X chromosome) of 396 mother-newborn pairs (54.5% male) from the Boston Birth Cohort, we found significant sex differences in mother-newborn correlations in genome-wide DNAm patterns (Spearman's rho = 0.91-0.98; p = 4.0 × 10-8), with female newborns having stronger correlations. Sex differences in correlations were attenuated but remained significant after excluding X-chromosomal DNAm sites (Spearman's rho = 0.91-0.98; p = 0.035). Moreover, 89,267 DNAm sites (12.4% of all analyzed, including 88,051 [12.5% of analyzed] autosomal and 1,216 [7.2% of analyzed] X-chromosomal sites) showed significant mother-newborn associations in methylation levels, and the top autosomal DNAm sites had high heritability than the genome-wide background (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.92). Additionally, significant interactions between newborn sex and methylation levels were observed for 11 X-chromosomal and 4 autosomal DNAm sites that were mapped to genes that have been associated with sex-specific disease/traits or early development (e.g., EFHC2, NXY, ADCYAP1R1, and BMP4). Finally, 18,769 DNAm sites (14,482 [77.2%] on the X chromosome) showed mother-newborn differences in methylation levels that were significantly associated with newborn sex, and the top autosomal DNAm sites had relatively small heritability (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.23). These DNAm sites were mapped to 2,532 autosomal genes and 978 X-chromosomal genes with significant enrichment in pathways involved in neurodegenerative and psychological diseases, development, neurophysiological process, immune response, and sex-specific cancers. Replication analysis in the Isle of Wight birth cohort yielded consistent results. CONCLUSION In two independent birth cohorts, we demonstrated strong mother-newborn correlations in whole blood DNAm on both autosomes and ChrX, and such correlations vary substantially by sex. Future studies are needed to examine to what extent our findings contribute to developmental origins of pediatric and adult diseases with well-observed sex differences.
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Affiliation(s)
- Jie Hu
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Xin Xu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Jun Li
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiumei Hong
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kathryn M Rexrode
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Guoying Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried J Karmaus
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiaobin Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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23
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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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24
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Martin EM, Grimm SA, Xu Z, Taylor JA, Wade PA. Beadchip technology to detect DNA methylation in mouse faithfully recapitulates whole-genome bisulfite sequencing. Epigenomics 2023; 15:115-129. [PMID: 37020391 PMCID: PMC10131490 DOI: 10.2217/epi-2023-0034] [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: 02/01/2023] [Accepted: 03/15/2023] [Indexed: 04/07/2023] Open
Abstract
Aim: To facilitate wide-scale implementation of Illumina Mouse Methylation BeadChip (MMB) technology, array-based measurement of cytosine methylation was compared with the gold-standard assessment of DNA methylation by whole-genome bisulfite sequencing (WGBS). Methods: DNA methylation across two mouse strains (C57B6 and C3H) and both sexes was assessed using the MMB and compared with previously existing deep-coverage WGBS of mice of the same strain and sex. Results & conclusion: The findings demonstrated that 93.3-99.2% of sites had similar measurements of methylation across technologies and that differentially methylated cytosines and regions identified by each technology overlap and enrich for similar biological functions, suggesting that the MMB faithfully recapitulates the findings of WGBS.
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Affiliation(s)
- Elizabeth M Martin
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Sara A Grimm
- Integrative Bioinformatics, Biostatistics & Computational Biology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Jack A Taylor
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
- Epidemiology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Paul A Wade
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
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25
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Chen C, Zhou J, Xia Y, Li M, Chen Y, Dai J, Liu C. A Higher Dysregulation Burden of Brain DNA Methylation in Female Patients Implicated in the Sex Bias of Schizophrenia. RESEARCH SQUARE 2023:rs.3.rs-2496133. [PMID: 36778507 PMCID: PMC9915764 DOI: 10.21203/rs.3.rs-2496133/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Sex differences are pervasive in schizophrenia (SCZ), but the extent and magnitude of DNA methylation (DNAm) changes underlying these differences remain uncharacterized. In this study, sex-stratified differential DNAm analysis was performed in postmortem brain samples from 117 SCZ and 137 controls, partitioned into discovery and replication datasets. Three differentially methylated positions (DMPs) were identified (adj. p < 0.05) in females and 29 DMPs in males without overlap between them. Over 81% of these sex-stratified DMPs were directionally consistent between sexes but with different effect sizes. Down-sampling analysis revealed more DMPs in females than in males when the sample sizes matched. Females had higher DNAm levels in healthy individuals and larger magnitude of DNAm changes in patients than males. Despite similar proportions of female-related DMPs (fDMPs, 8%) being under genetic control compared with males (10%), significant enrichment of DMP-related SNPs in signals of genome-wide association studies was identified only in fDMPs. One DMP in each sex connected the SNPs and gene expression of CALHM1 in females and CCDC149 in males. PPI subnetworks revealed that both female- and male-related differential DNAm interacted with synapse-related dysregulation. Immune-related pathways were unique for females and neuron-related pathways were associated with males. This study reveals remarkable quantitative differences in DNAm-related sexual dimorphism in SCZ and that females have a higher dysregulation burden of SCZ-associated DNAm than males.
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Comtois-Cabana M, Barr E, Provençal N, Ouellet-Morin I. Association between child maltreatment and depressive symptoms in emerging adulthood: The mediating and moderating roles of DNA methylation. PLoS One 2023; 18:e0280203. [PMID: 36634080 PMCID: PMC9836296 DOI: 10.1371/journal.pone.0280203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Prospective studies suggest that child maltreatment substantially increases the risk for depression in adulthood. However, the mechanisms underlying this association require further elucidation. In recent years, DNA methylation has emerged as a potential mechanism by which maltreatment experiences (a) could partly explain the emergence or aggravation of depressive symptoms (i.e., mediation) and/or (b) could increase (or decrease) the risk for depressive symptoms (i.e., moderation). The present study tested whether the methylation levels of nine candidate genes mediated and/or moderated the association between maltreatment experiences in childhood and depressive symptoms in emerging adulthood. The sample comprised 156 men aged between 18 and 35 years. Maltreatment experiences and depressive symptoms were assessed retrospectively using self-reported questionnaires. Methylation levels of nine candidate genes (COMT, FKBP5, IL6, IL10, MAOA, NR3C1, OXTR, SLC6A3 and SLC6A4), previously reported to be sensitive to early-life stress, were quantified from saliva samples. Maltreatment experiences in childhood were significantly associated with depressive symptoms in emerging adulthood. Both maltreatment experiences and depressive symptoms were associated with the methylation levels of two genomic sites, which cumulatively, but not individually, explained 16% of the association between maltreatment experiences in childhood and depressive symptoms in emerging adulthood. Moreover, maltreatment experiences in childhood interacted with the methylation levels of fourteen genomic sites, which cumulatively, but not individually, modulated the level of depressive symptoms in young male adults who were maltreated as children. However, none of these effects survived multiple testing correction. These findings bring attention to the cumulative effects of DNA methylation measured in several candidate genes on the risk of reporting depressive symptoms following maltreatment experiences in childhood. Nonetheless, future studies need to clarify the robustness of these putative cumulative effects in larger samples and longitudinal cohorts.
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Affiliation(s)
- Maude Comtois-Cabana
- Department of Psychology, University of Montreal, Montreal, Quebec, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Emily Barr
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Nadine Provençal
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Isabelle Ouellet-Morin
- School of Criminology, University of Montreal, Montreal, Quebec, Canada
- Research Center of the Montreal Mental Health University Institute, Montreal, Quebec, Canada
- * E-mail:
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King DE, Sparling AC, Lloyd D, Satusky MJ, Martinez M, Grenier C, Bergemann CM, Maguire R, Hoyo C, Meyer JN, Murphy SK. Sex-specific DNA methylation and associations with in utero tobacco smoke exposure at nuclear-encoded mitochondrial genes. Epigenetics 2022; 17:1573-1589. [PMID: 35238269 PMCID: PMC9620986 DOI: 10.1080/15592294.2022.2043591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Sex-linked differences in mitochondrial ATP production, enzyme activities, and reactive oxygen species generation have been reported in multiple tissue and cell types. While the effects of reproductive hormones underlie many of these differences, regulation of sexually dimorphic mitochondrial function has not been fully characterized. We hypothesized that sex-specific DNA methylation contributes to sex-specific expression of nuclear genes that influence mitochondrial function. Herein, we analysed DNA methylation data specifically focused on nuclear-encoded mitochondrial genes in 191 males and 190 females. We found 596 differentially methylated sites (DMSs) (FDR p < 0.05), corresponding to 324 genes, with at least a 1% difference in methylation between sexes. To investigate the potential functional significance, we utilized gene expression microarray data. Of the 324 genes containing DMSs, 17 showed differences in gene expression by sex. Particularly striking was that ATP5G2, encoding subunit C of ATP synthase, contains seven DMSs and exhibits a sex difference in expression (p = 0.04). Finally, we also found that alterations in DNA methylation associated with in utero tobacco smoke exposure were sex-specific in these nuclear-encoded mitochondrial genes. Interestingly, the level of sex differences in DNA methylation at nuclear-encoded mitochondrial genes and the level of methylation changes associated with smoke exposure were less prominent than that of other genes. This suggests more conservative regulation of DNA methylation at these nuclear-encoded mitochondrial genes as compared to others. Overall, our findings suggest that sex-specific DNA methylation may help establish sex differences in expression and function and that sex-specific alterations in DNA methylation in response to exposures could contribute to sex-variable toxicological responses.
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Affiliation(s)
- Dillon E. King
- Nicholas School of the Environment, Duke University, Durham, NC, USA,Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Anna Clare Sparling
- Nicholas School of the Environment, Duke University, Durham, NC, USA,Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Dillon Lloyd
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Matthew Joseph Satusky
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mackenzie Martinez
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Carole Grenier
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | | | - Rachel Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Joel Newman Meyer
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Susan K. Murphy
- Nicholas School of the Environment, Duke University, Durham, NC, USA,Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA,CONTACT Susan K. Murphy 701 W. Main Street, Suite 510, Durham, NC27701, USA Department of Obstetrics and Gynecology, Duke University Medical Center
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Childhood Trauma and Epigenetics: State of the Science and Future. Curr Environ Health Rep 2022; 9:661-672. [PMID: 36242743 DOI: 10.1007/s40572-022-00381-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW There is a great deal of interest regarding the biological embedding of childhood trauma and social exposures through epigenetic mechanisms, including DNA methylation (DNAm), but a comprehensive understanding has been hindered by issues of limited reproducibility between studies. This review presents a summary of the literature on childhood trauma and DNAm, highlights issues in the field, and proposes some potential solutions. RECENT FINDINGS Investigations of the associations between DNAm and childhood trauma are commonly performed using candidate gene approaches, specifically involving genes related to neurological and stress pathways. Childhood trauma is defined in a wide range of ways in several societal contexts. However, although variations in DNAm are frequently found in stress-related genes, unsupervised epigenome-wide association studies (EWAS) have shown limited reproducibility both between studies and in relating these changes to exposures. The reproducibility of childhood trauma DNAm studies, and the field of social epigenetics in general, may be improved by increasing sample sizes, standardizing variables, making use of effect size thresholds, collecting longitudinal and intervention samples, appropriately accounting for known confounding factors, and applying causal analysis wherever possible, such as "two-step epigenetic Mendelian randomization."
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Carlsen EØ, Lee Y, Magnus P, Jugessur A, Page CM, Nustad HE, Håberg SE, Lie RT, Magnus MC. An examination of mediation by DNA methylation on birthweight differences induced by assisted reproductive technologies. Clin Epigenetics 2022; 14:151. [PMID: 36443807 PMCID: PMC9703677 DOI: 10.1186/s13148-022-01381-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Children born after assisted reproductive technologies (ART) differ in birthweight from those naturally conceived. It has been hypothesized that this might be explained by epigenetic mechanisms. We examined whether cord blood DNA methylation mediated the birthweight difference between 890 newborns conceived by ART (764 by fresh embryo transfer and 126 frozen thawed embryo transfer) and 983 naturally conceived newborns from the Norwegian Mother, Father, and Child Cohort Study (MoBa). DNA methylation was measured by the Illumina Infinium MethylationEPIC array. We conducted mediation analyses to assess whether differentially methylated CpGs mediated the differences in birthweight observed between: (1) fresh embryo transfer and natural conception and (2) frozen and fresh embryo transfer. RESULTS We observed a difference in birthweight between fresh embryo transfer and naturally conceived offspring of - 120 g. 44% (95% confidence interval [CI] 26% to 81%) of this difference in birthweight between fresh embryo transfer and naturally conceived offspring was explained by differences in methylation levels at four CpGs near LOXL1, CDH20, and DRC1. DNA methylation differences at two CpGs near PTGS1 and RASGRP4 jointly mediated 22% (95% CI 8.1% to 50.3%) of the birthweight differences between fresh and frozen embryo transfer. CONCLUSION Our findings suggest that DNA methylation is an important mechanism in explaining birthweight differences according to the mode of conception. Further research should examine how gene regulation at these loci influences fetal growth.
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Affiliation(s)
- Ellen Ø. Carlsen
- grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway ,grid.5510.10000 0004 1936 8921Department of Community Medicine, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Yunsung Lee
- grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Magnus
- grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway ,grid.7914.b0000 0004 1936 7443Department of Global Public Health and Primary Care, University of Bergen, Bergen, 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, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Haakon E. Nustad
- grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway ,Deepinsight, Oslo, Norway
| | - Siri E. Håberg
- grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Rolv T. Lie
- grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway ,grid.7914.b0000 0004 1936 7443Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Maria C. Magnus
- grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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The immune factors driving DNA methylation variation in human blood. Nat Commun 2022; 13:5895. [PMID: 36202838 PMCID: PMC9537159 DOI: 10.1038/s41467-022-33511-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/21/2022] [Indexed: 11/08/2022] Open
Abstract
Epigenetic changes are required for normal development, yet the nature and respective contribution of factors that drive epigenetic variation in humans remain to be fully characterized. Here, we assessed how the blood DNA methylome of 884 adults is affected by DNA sequence variation, age, sex and 139 factors relating to life habits and immunity. Furthermore, we investigated whether these effects are mediated or not by changes in cellular composition, measured by deep immunophenotyping. We show that DNA methylation differs substantially between naïve and memory T cells, supporting the need for adjustment on these cell-types. By doing so, we find that latent cytomegalovirus infection drives DNA methylation variation and provide further support that the increased dispersion of DNA methylation with aging is due to epigenetic drift. Finally, our results indicate that cellular composition and DNA sequence variation are the strongest predictors of DNA methylation, highlighting critical factors for medical epigenomics studies.
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Barbu MC, Harris M, Shen X, Aleks S, Green C, Amador C, Walker R, Morris S, Adams M, Sandu A, McNeil C, Waiter G, Evans K, Campbell A, Wardlaw J, Steele D, Murray A, Porteous D, McIntosh A, Whalley H. Epigenome-wide association study of global cortical volumes in generation Scotland: Scottish family health study. Epigenetics 2022; 17:1143-1158. [PMID: 34738878 PMCID: PMC9542280 DOI: 10.1080/15592294.2021.1997404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 01/22/2023] Open
Abstract
A complex interplay of genetic and environmental risk factors influence global brain structural alterations associated with brain health and disease. Epigenome-wide association studies (EWAS) of global brain imaging phenotypes have the potential to reveal the mechanisms of brain health and disease and can lead to better predictive analytics through the development of risk scores.We perform an EWAS of global brain volumes in Generation Scotland using peripherally measured whole blood DNA methylation (DNAm) from two assessments, (i) at baseline recruitment, ~6 years prior to MRI assessment (N = 672) and (ii) concurrent with MRI assessment (N=565). Four CpGs at baseline were associated with global cerebral white matter, total grey matter, and whole-brain volume (Bonferroni p≤7.41×10-8, βrange = -1.46x10-6 to 9.59 × 10-7). These CpGs were annotated to genes implicated in brain-related traits, including psychiatric disorders, development, and ageing. We did not find significant associations in the meta-analysis of the EWAS of the two sets concurrent with imaging at the corrected level.These findings reveal global brain structural changes associated with DNAm measured ~6 years previously, indicating a potential role of early DNAm modifications in brain structure. Although concurrent DNAm was not associated with global brain structure, the nominally significant findings identified here present a rationale for future investigation of associations between DNA methylation and structural brain phenotypes in larger population-based samples.
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Affiliation(s)
- Miruna Carmen Barbu
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Mat Harris
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Xueyi Shen
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Stolicyn Aleks
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Claire Green
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Carmen Amador
- Mrc Human Genetics Unit, Institute of Genetics and Cancer, the University of Edinburgh, UK
| | - Rosie Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Stewart Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Mark Adams
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Anca Sandu
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - Christopher McNeil
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - Gordon Waiter
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - Kathryn Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Archie Campbell
- Mrc Human Genetics Unit, Institute of Genetics and Cancer, the University of Edinburgh, UK
| | - Joanna Wardlaw
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Douglas Steele
- Imaging Science and Technology, School of Medicine, University of Dundee, DundeeUK
| | - Alison Murray
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - David Porteous
- Mrc Human Genetics Unit, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, UK
| | - Andrew McIntosh
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, UK
| | - Heather Whalley
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
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Bondhus L, Wei A, Arboleda VA. DMRscaler: a scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features. BMC Bioinformatics 2022; 23:364. [PMID: 36064314 PMCID: PMC9447346 DOI: 10.1186/s12859-022-04899-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 08/22/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Pathogenic mutations in genes that control chromatin function have been implicated in rare genetic syndromes. These chromatin modifiers exhibit extraordinary diversity in the scale of the epigenetic changes they affect, from single basepair modifications by DNMT1 to whole genome structural changes by PRM1/2. Patterns of DNA methylation are related to a diverse set of epigenetic features across this full range of epigenetic scale, making DNA methylation valuable for mapping regions of general epigenetic dysregulation. However, existing methods are unable to accurately identify regions of differential methylation across this full range of epigenetic scale directly from DNA methylation data. RESULTS To address this, we developed DMRscaler, a novel method that uses an iterative windowing procedure to capture regions of differential DNA methylation (DMRs) ranging in size from single basepairs to whole chromosomes. We benchmarked DMRscaler against several DMR callers in simulated and natural data comparing XX and XY peripheral blood samples. DMRscaler was the only method that accurately called DMRs ranging in size from 100 bp to 1 Mb (pearson's r = 0.94) and up to 152 Mb on the X-chromosome. We then analyzed methylation data from rare-disease cohorts that harbor chromatin modifier gene mutations in NSD1, EZH2, and KAT6A where DMRscaler identified novel DMRs spanning gene clusters involved in development. CONCLUSION Taken together, our results show DMRscaler is uniquely able to capture the size of DMR features across the full range of epigenetic scale and identify novel, co-regulated regions that drive epigenetic dysregulation in human disease.
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Affiliation(s)
- Leroy Bondhus
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA
| | - Angela Wei
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Bioinformatics Interdepartmental PhD Program, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA
| | - Valerie A. Arboleda
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Bioinformatics Interdepartmental PhD Program, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Molecular Biology Institute, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095 USA
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Svoboda LK, Perera BPU, Morgan RK, Polemi KM, Pan J, Dolinoy DC. Toxicoepigenetics and Environmental Health: Challenges and Opportunities. Chem Res Toxicol 2022; 35:1293-1311. [PMID: 35876266 PMCID: PMC9812000 DOI: 10.1021/acs.chemrestox.1c00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The rapidly growing field of toxicoepigenetics seeks to understand how toxicant exposures interact with the epigenome to influence disease risk. Toxicoepigenetics is a promising field of environmental health research, as integrating epigenetics into the field of toxicology will enable a more thorough evaluation of toxicant-induced disease mechanisms as well as the elucidation of the role of the epigenome as a biomarker of exposure and disease and possible mediator of exposure effects. Likewise, toxicoepigenetics will enhance our knowledge of how environmental exposures, lifestyle factors, and diet interact to influence health. Ultimately, an understanding of how the environment impacts the epigenome to cause disease may inform risk assessment, permit noninvasive biomonitoring, and provide potential opportunities for therapeutic intervention. However, the translation of research from this exciting field into benefits for human and animal health presents several challenges and opportunities. Here, we describe four significant areas in which we see opportunity to transform the field and improve human health by reducing the disease burden caused by environmental exposures. These include (1) research into the mechanistic role for epigenetic change in environment-induced disease, (2) understanding key factors influencing vulnerability to the adverse effects of environmental exposures, (3) identifying appropriate biomarkers of environmental exposures and their associated diseases, and (4) determining whether the adverse effects of environment on the epigenome and human health are reversible through pharmacologic, dietary, or behavioral interventions. We then highlight several initiatives currently underway to address these challenges.
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Affiliation(s)
- Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Katelyn M Polemi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Junru Pan
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
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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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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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36
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Derakhshan M, Kessler NJ, Ishida M, Demetriou C, Brucato N, Moore G, Fall CHD, Chandak GR, Ricaut FX, Prentice A, Hellenthal G, Silver M. Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo. Nucleic Acids Res 2022; 50:6735-6752. [PMID: 35713545 PMCID: PMC9749461 DOI: 10.1093/nar/gkac503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/06/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
We analysed DNA methylation data from 30 datasets comprising 3474 individuals, 19 tissues and 8 ethnicities at CpGs covered by the Illumina450K array. We identified 4143 hypervariable CpGs ('hvCpGs') with methylation in the top 5% most variable sites across multiple tissues and ethnicities. hvCpG methylation was influenced but not determined by genetic variation, and was not linked to probe reliability, epigenetic drift, age, sex or cell heterogeneity effects. hvCpG methylation tended to covary across tissues derived from different germ-layers and hvCpGs were enriched for proximity to ERV1 and ERVK retrovirus elements. hvCpGs were also enriched for loci previously associated with periconceptional environment, parent-of-origin-specific methylation, and distinctive methylation signatures in monozygotic twins. Together, these properties position hvCpGs as strong candidates for studying how stochastic and/or environmentally influenced DNA methylation states which are established in the early embryo and maintained stably thereafter can influence life-long health and disease.
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Affiliation(s)
| | - Noah J Kessler
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, UK
| | - Miho Ishida
- UCL Great Ormond Street Institute of Child Health, UK
| | | | - Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | | | - Caroline H D Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton,
Southampton, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular
and Molecular Biology,Hyderabad, India
| | - Francois-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
| | - Garrett Hellenthal
- UCL Genetics Institute, University College London,
Gower Street, London WC1E 6BT, UK
| | - Matt J Silver
- London School of Hygiene and Tropical Medicine, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
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37
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Wang Y, Gorrie-Stone TJ, Grant OA, Andrayas AD, Zhai X, McDonald-Maier KD, Schalkwyk LC. InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias. Bioinformatics 2022; 38:3950-3957. [PMID: 35771651 PMCID: PMC9364386 DOI: 10.1093/bioinformatics/btac436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 05/31/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Data normalization is an essential step to reduce technical variation within and between arrays. Due to the different karyotypes and the effects of X chromosome inactivation, females and males exhibit distinct methylation patterns on sex chromosomes; thus, it poses a significant challenge to normalize sex chromosome data without introducing bias. Currently, existing methods do not provide unbiased solutions to normalize sex chromosome data, usually, they just process autosomal and sex chromosomes indiscriminately. RESULTS Here, we demonstrate that ignoring this sex difference will lead to introducing artificial sex bias, especially for thousands of autosomal CpGs. We present a novel two-step strategy (interpolatedXY) to address this issue, which is applicable to all quantile-based normalization methods. By this new strategy, the autosomal CpGs are first normalized independently by conventional methods, such as funnorm or dasen; then the corrected methylation values of sex chromosome-linked CpGs are estimated as the weighted average of their nearest neighbors on autosomes. The proposed two-step strategy can also be applied to other non-quantile-based normalization methods, as well as other array-based data types. Moreover, we propose a useful concept: the sex explained fraction of variance, to quantitatively measure the normalization effect. AVAILABILITY AND IMPLEMENTATION The proposed methods are available by calling the function 'adjustedDasen' or 'adjustedFunnorm' in the latest wateRmelon package (https://github.com/schalkwyk/wateRmelon), with methods compatible with all the major workflows, including minfi. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yucheng Wang
- School of Computer Science and Electronic Engineering, University of Essex, Colchester CO4 3SQ, UK
| | | | - Olivia A Grant
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Alexandria D Andrayas
- Institute for Social and Economic Research, University of Essex, Colchester CO4 3SQ, UK
| | | | - Klaus D McDonald-Maier
- School of Computer Science and Electronic Engineering, University of Essex, Colchester CO4 3SQ, UK
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Abstract
Sex is a key risk factor for many types of cardiovascular disease. It is imperative to understand the mechanisms underlying sex differences to devise optimal preventive and therapeutic approaches for all individuals. Both biological sex (determined by sex chromosomes and gonadal hormones) and gender (social and cultural behaviors associated with femininity or masculinity) influence differences between men and women in disease susceptibility and pathology. Here, we focus on the application of experimental mouse models that elucidate the influence of 2 components of biological sex-sex chromosome complement (XX or XY) and gonad type (ovaries or testes). These models have revealed that in addition to well-known effects of gonadal hormones, sex chromosome complement influences cardiovascular risk factors, such as plasma cholesterol levels and adiposity, as well as the development of atherosclerosis and pulmonary hypertension. One mechanism by which sex chromosome dosage influences cardiometabolic traits is through sex-biased expression of X chromosome genes that escape X inactivation. These include chromatin-modifying enzymes that regulate gene expression throughout the genome. The identification of factors that determine sex-biased gene expression and cardiometabolic traits will expand our mechanistic understanding of cardiovascular disease processes and provide insight into sex differences that remain throughout the lifespan as gonadal hormone levels alter with age.
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Affiliation(s)
- Karen Reue
- Department of Human Genetics, David Geffen School of Medicine at UCLA
- Department of Medicine, David Geffen School of Medicine at UCLA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
| | - Carrie B. Wiese
- Department of Human Genetics, David Geffen School of Medicine at UCLA
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39
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Andrews SV, Yang IJ, Froehlich K, Oskotsky T, Sirota M. Large-scale placenta DNA methylation integrated analysis reveals fetal sex-specific differentially methylated CpG sites and regions. Sci Rep 2022; 12:9396. [PMID: 35672357 PMCID: PMC9174475 DOI: 10.1038/s41598-022-13544-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/17/2022] [Indexed: 11/14/2022] Open
Abstract
Although male–female differences in placental structure and function have been observed, little is understood about their molecular underpinnings. Here, we present a mega-analysis of 14 publicly available placenta DNA methylation (DNAm) microarray datasets to identify individual CpGs and regions associated with fetal sex. In the discovery dataset of placentas from full term pregnancies (N = 532 samples), 5212 CpGs met genome-wide significance (p < 1E−8) and were enriched in pathways such as keratinization (FDR p-value = 7.37E−14), chemokine activity (FDR p-value = 1.56E−2), and eosinophil migration (FDR p-value = 1.83E−2). Nine differentially methylated regions were identified (fwerArea < 0.1) including a region in the promoter of ZNF300 that showed consistent differential DNAm in samples from earlier timepoints in pregnancy and appeared to be driven predominately by effects in the trophoblast cell type. We describe the largest study of fetal sex differences in placenta DNAm performed to date, revealing genes and pathways characterizing sex-specific placenta function and health outcomes later in life.
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Affiliation(s)
- Shan V Andrews
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Irene J Yang
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA.,Dougherty Valley High School, San Ramon, CA, USA
| | - Karolin Froehlich
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA. .,Department of Pediatrics, UCSF, San Francisco, CA, USA.
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA. .,Department of Pediatrics, UCSF, San Francisco, CA, USA.
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40
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Manu DM, Mwinyi J, Schiöth HB. Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health. Int J Mol Sci 2022; 23:ijms23105856. [PMID: 35628666 PMCID: PMC9147258 DOI: 10.3390/ijms23105856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 12/10/2022] Open
Abstract
The formative period of adolescence plays a crucial role in the development of skills and abilities for adulthood. Adolescents who are affected by mental health conditions are at risk of suicide and social and academic impairments. Gene–environment complementary contributions to the molecular mechanisms involved in psychiatric disorders have emphasized the need to analyze epigenetic marks such as DNA methylation (DNAm) and non-coding RNAs. However, the large and diverse bioinformatic and statistical methods, referring to the confounders of the statistical models, application of multiple-testing adjustment methods, questions regarding the correlation of DNAm across tissues, and sex-dependent differences in results, have raised challenges regarding the interpretation of the results. Based on the example of generalized anxiety disorder (GAD) and depressive disorder (MDD), we shed light on the current knowledge and usage of methodological tools in analyzing epigenetics. Statistical robustness is an essential prerequisite for a better understanding and interpretation of epigenetic modifications and helps to find novel targets for personalized therapeutics in psychiatric diseases.
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41
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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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42
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Wang KZ, Chaudhary Z, Qian J, Adanty C, Graff-Guerrero A, Gerretsen P, Zai CC, De Luca V. Differential Methylation Analysis of Suicidal Ideation Severity in Schizophrenia with the Illumina MethylationEPIC Array. Healthcare (Basel) 2022; 10:809. [PMID: 35627945 PMCID: PMC9141768 DOI: 10.3390/healthcare10050809] [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: 04/05/2022] [Accepted: 04/22/2022] [Indexed: 02/04/2023] Open
Abstract
There is a multitude of factors that makes difficult to identify those at risk for suicide, especially among schizophrenia patients. Suicide cannot be explained by genetics alone, therefore epigenetic mechanisms including DNA methylation are thought to play a role. DNA methylation could be a valuable tool in helping predict those at-risk individuals. This cross-sectional study comprised 112 subjects diagnosed with schizophrenia spectrum disorders, and were grouped according to the current suicidal ideation severity. DNA methylation across the genome was measured with the Infinium® MethylationEPIC BeadChip. We utilized the dmpFinder and bumphunter functions within the Bioconductor minfi package to identify differentially methylated positions (DMPs) and differentially methylated regions (DMRs), respectively. Following quality control, we removed one sample from the analysis and reported the most significant DMPs and DMRs associated with suicidal ideation severity. All positions and regions identified in this analysis were only found to have suggestive levels of significance at the genome-wide level. The present study was one of the first to investigate genome-wide methylation and suicidal ideation severity. While there were many strengths of our study, including investigating both differentially methylated positions and regions, further larger-scale studies are necessary to replicate, support, and validate our findings presented here.
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Affiliation(s)
| | | | | | | | | | | | | | - Vincenzo De Luca
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada; (K.Z.W.); (Z.C.); (J.Q.); (C.A.); (A.G.-G.); (P.G.); (C.C.Z.)
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43
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de Krijger M, Hageman IL, Li Yim AYF, Verhoeff J, Garcia Vallejo JJ, van Hamersveld PHP, Levin E, Hakvoort TBM, Wildenberg ME, Henneman P, Ponsioen CY, de Jonge WJ. Epigenetic Signatures Discriminate Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis From Patients With Ulcerative Colitis. Front Immunol 2022; 13:840935. [PMID: 35371111 PMCID: PMC8965896 DOI: 10.3389/fimmu.2022.840935] [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] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Background Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease affecting the intra- and extrahepatic bile ducts, and is strongly associated with ulcerative colitis (UC). In this study, we explored the peripheral blood DNA methylome and its immune cell composition in patients with PSC-UC, UC, and healthy controls (HC) with the aim to develop a predictive assay in distinguishing patients with PSC-UC from those with UC alone. Methods The peripheral blood DNA methylome of male patients with PSC and concomitant UC, UC and HCs was profiled using the Illumina HumanMethylation Infinium EPIC BeadChip (850K) array. Differentially methylated CpG position (DMP) and region (DMR) analyses were performed alongside gradient boosting classification analyses to discern PSC-UC from UC patients. As observed differences in the DNA methylome could be the result of differences in cellular populations, we additionally employed mass cytometry (CyTOF) to characterize the immune cell compositions. Results Genome wide methylation analysis did not reveal large differences between PSC-UC and UC patients nor HCs. Nonetheless, using gradient boosting we were capable of discerning PSC-UC from UC with an area under the receiver operator curve (AUROC) of 0.80. Four CpG sites annotated to the NINJ2 gene were found to strongly contribute to the predictive performance. While CyTOF analyses corroborated the largely similar blood cell composition among patients with PSC-UC, UC and HC, a higher abundance of myeloid cells was observed in UC compared to PSC-UC patients. Conclusion DNA methylation enables discerning PSC-UC from UC patients, with a potential for biomarker development.
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Affiliation(s)
- Manon de Krijger
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Ishtu L Hageman
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Andrew Y F Li Yim
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Jan Verhoeff
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Molecular Cell Biology and Immunology, Amsterdam Infection & Immunity and Cancer Center Amsterdam, Amsterdam University Medical Centers, Free University of Amsterdam, Amsterdam, Netherlands
| | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection & Immunity and Cancer Center Amsterdam, Amsterdam University Medical Centers, Free University of Amsterdam, Amsterdam, Netherlands
| | - Patricia H P van Hamersveld
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Evgeni Levin
- Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Horaizon BV, Delft, Netherlands
| | - Theodorus B M Hakvoort
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Manon E Wildenberg
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Surgery, University Clinic of Bonn, Bonn, Germany
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44
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Staley JR, Windmeijer F, Suderman M, Lyon MS, Davey Smith G, Tilling K. A robust mean and variance test with application to high-dimensional phenotypes. Eur J Epidemiol 2022; 37:377-387. [PMID: 34651232 PMCID: PMC9187575 DOI: 10.1007/s10654-021-00805-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 09/06/2021] [Indexed: 12/01/2022]
Abstract
Most studies of continuous health-related outcomes examine differences in mean levels (location) of the outcome by exposure. However, identifying effects on the variability (scale) of an outcome, and combining tests of mean and variability (location-and-scale), could provide additional insights into biological mechanisms. A joint test could improve power for studies of high-dimensional phenotypes, such as epigenome-wide association studies of DNA methylation at CpG sites. One possible cause of heterogeneity of variance is a variable interacting with exposure in its effect on outcome, so a joint test of mean and variability could help in the identification of effect modifiers. Here, we review a scale test, based on the Brown-Forsythe test, for analysing variability of a continuous outcome with respect to both categorical and continuous exposures, and develop a novel joint location-and-scale score (JLSsc) test. These tests were compared to alternatives in simulations and used to test associations of mean and variability of DNA methylation with gender and gestational age using data from the Accessible Resource for Integrated Epigenomics Studies (ARIES). In simulations, the Brown-Forsythe and JLSsc tests retained correct type I error rates when the outcome was not normally distributed in contrast to the other approaches tested which all had inflated type I error rates. These tests also identified > 7500 CpG sites for which either mean or variability in cord blood methylation differed according to gender or gestational age. The Brown-Forsythe test and JLSsc are robust tests that can be used to detect associations not solely driven by a mean effect.
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Affiliation(s)
- James R Staley
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Frank Windmeijer
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- Department of Statistics and Nuffield College, University of Oxford, Oxford, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Matthew S Lyon
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, Oakfield House, Bristol, BS8 2BN, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Kate Tilling
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK.
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45
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Laajala E, Halla-Aho V, Grönroos T, Kalim UU, Vähä-Mäkilä M, Nurmio M, Kallionpää H, Lietzén N, Mykkänen J, Rasool O, Toppari J, Orešič M, Knip M, Lund R, Lahesmaa R, Lähdesmäki H. Permutation-based significance analysis reduces the type 1 error rate in bisulfite sequencing data analysis of human umbilical cord blood samples. Epigenetics 2022; 17:1608-1627. [PMID: 35246015 DOI: 10.1080/15592294.2022.2044127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
DNA methylation patterns are largely established in-utero and might mediate the impacts of in-utero conditions on later health outcomes. Associations between perinatal DNA methylation marks and pregnancy-related variables, such as maternal age and gestational weight gain, have been earlier studied with methylation microarrays, which typically cover less than 2% of human CpG sites. To detect such associations outside these regions, we chose the bisulphite sequencing approach. We collected and curated clinical data on 200 newborn infants; whose umbilical cord blood samples were analysed with the reduced representation bisulphite sequencing (RRBS) method. A generalized linear mixed-effects model was fit for each high coverage CpG site, followed by spatial and multiple testing adjustment of P values to identify differentially methylated cytosines (DMCs) and regions (DMRs) associated with clinical variables, such as maternal age, mode of delivery, and birth weight. Type 1 error rate was then evaluated with a permutation analysis. We discovered a strong inflation of spatially adjusted P values through the permutation analysis, which we then applied for empirical type 1 error control. The inflation of P values was caused by a common method for spatial adjustment and DMR detection, implemented in tools comb-p and RADMeth. Based on empirically estimated significance thresholds, very little differential methylation was associated with any of the studied clinical variables, other than sex. With this analysis workflow, the sex-associated differentially methylated regions were highly reproducible across studies, technologies, and statistical models.
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Affiliation(s)
- Essi Laajala
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland.,Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland.,Department of Computer Science, Aalto University, Espoo, Finland
| | - Viivi Halla-Aho
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Toni Grönroos
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland
| | - Mari Vähä-Mäkilä
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Mirja Nurmio
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Henna Kallionpää
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Niina Lietzén
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Juha Mykkänen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland.,Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland
| | - Jorma Toppari
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland.,Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland.,Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland.,School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Mikael Knip
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Riikka Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,InFLAMES Research Flagship Center, University of Turku, Turku Finland.,Institute of Biomedicine, University of Turku, Turku, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
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46
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Nustad HE, Steinsland I, Ollikainen M, Cazaly E, Kaprio J, Benjamini Y, Gervin K, Lyle R. Modeling dependency structures in 450k DNA methylation data. Bioinformatics 2022; 38:885-891. [PMID: 34788815 PMCID: PMC8796368 DOI: 10.1093/bioinformatics/btab774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/01/2021] [Accepted: 11/09/2021] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION DNA methylation has been shown to be spatially dependent across chromosomes. Previous studies have focused on the influence of genomic context on the dependency structure, while not considering differences in dependency structure between individuals. RESULTS We modeled spatial dependency with a flexible framework to quantify the dependency structure, focusing on inter-individual differences by exploring the association between dependency parameters and technical and biological variables. The model was applied to a subset of the Finnish Twin Cohort study (N = 1611 individuals). The estimates of the dependency parameters varied considerably across individuals, but were generally consistent across chromosomes within individuals. The variation in dependency parameters was associated with bisulfite conversion plate, zygosity, sex and age. The age differences presumably reflect accumulated environmental exposures and/or accumulated small methylation differences caused by stochastic mitotic events, establishing recognizable, individual patterns more strongly seen in older individuals. AVAILABILITY AND IMPLEMENTATION The twin dataset used in the current study are located in the Biobank of the National Institute for Health and Welfare, Finland. All the biobanked data are publicly available for use by qualified researchers following a standardized application procedure (https://thl.fi/en/web/thl-biobank/for-researchers). A R-script for fitting the dependency structure to publicly available DNA methylation data with the software used in this article is provided in supplementary data. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Haakon E Nustad
- Department of Medical Genetics and Norwegian Sequencing Centre, Oslo University Hospital, 0450 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
- Department of Pharmacy, PharmaTox Strategic Research Initiative, University of Oslo, 0371 Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Ingelin Steinsland
- Department of Mathematical Sciences, Norwegian University of Science and Technology, 7034 Trondheim, Norway
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland FIMM, Helsinki Institute of Life Science, University of Helsinki, FI-00014 Helsinki, Finland
| | - Emma Cazaly
- Institute for Molecular Medicine Finland FIMM, Helsinki Institute of Life Science, University of Helsinki, FI-00014 Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland FIMM, Helsinki Institute of Life Science, University of Helsinki, FI-00014 Helsinki, Finland
| | - Yuval Benjamini
- Department of Statistics and Data Science, The Hebrew University, Mount Scopus, Jerusalem 9190501, Israel
| | - Kristina Gervin
- Department of Pharmacy, PharmaTox Strategic Research Initiative, University of Oslo, 0371 Oslo, Norway
- Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital, 0450 Oslo, Norway
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, 0363 Oslo, Norway
| | - Robert Lyle
- Department of Medical Genetics and Norwegian Sequencing Centre, Oslo University Hospital, 0450 Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, 0213 Oslo, Norway
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47
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Jung M, Ahn YS, Chang SJ, Kim CB, Jeong KS, Koh SB, Gim JA. Variation in Genotype and DNA Methylation Patterns Based on Alcohol Use and CVD in the Korean Genome and Epidemiology Study (KoGES). Genes (Basel) 2022; 13:genes13020172. [PMID: 35205218 PMCID: PMC8871634 DOI: 10.3390/genes13020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/09/2022] [Accepted: 01/14/2022] [Indexed: 12/14/2022] Open
Abstract
Alcohol consumption can increase the risk of chronic diseases, such as myocardial infarction, coronary artery disease, hyperlipidemia, and hypertension. We aimed to assess the association between genotype, DNA methylation patterns, alcohol consumption, and chronic diseases in Korean population. We analyzed 8840 subjects for genotypes and 446 for DNA methylation among the 9351 subjects from the Korean Genome and Epidemiology Study (KoGES). We further divided both groups into two sub-groups according to the presence/absence of chronic diseases. We selected genes whose methylation varied significantly with alcohol consumption, and visualized genotype and DNA methylation patterns specific to each group. Genome-wide association study (GWAS) revealed single nucleotide polymorphisms (SNPs) rs2074356 and rs11066280 in HECT domain E3 ubiquitin protein ligase 4 (HECTD4) to be significantly associated with alcohol consumption in both the presence. The rs12229654 genotype also displayed significantly different patterns with alcohol consumption. Furthermore, we retrieved differentially methylated regions (DMRs) from four groups based on sex and chronic diseases and compared them by drinking status. In genotype analysis, cardiovascular diseases (CVDs) showed a higher proportion in drinker than in non-drinker, but not in DMR analysis. Additionally, we analyzed the enriched Gene Ontology terms and Kyoto Gene and Genome Encyclopedia (KEGG) pathways and visualized the network, heatmap, and upset plot. We show that the pattern of DNA methylation associated with CVD is strongly influenced by alcoholism. Overall, this study identified genetic and epigenetic variants influenced by alcohol consumption and chronic diseases.
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Affiliation(s)
- Myoungjee Jung
- Department of Preventive Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea; (M.J.); (S.-J.C.); (C.-B.K.)
| | - Yeon-Soon Ahn
- Department of Preventive Medicine and Genomic Cohort Institute, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea;
| | - Sei-Jin Chang
- Department of Preventive Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea; (M.J.); (S.-J.C.); (C.-B.K.)
| | - Chun-Bae Kim
- Department of Preventive Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea; (M.J.); (S.-J.C.); (C.-B.K.)
| | - Kyoung Sook Jeong
- Department of Occupational and Environmental Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea;
| | - Sang-Baek Koh
- Department of Preventive Medicine, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea; (M.J.); (S.-J.C.); (C.-B.K.)
- Institute of Genomic Cohort, Yonsei University Wonju College of Medicine, 20 Ilsan-ro, Wonju 26426, Korea
- Correspondence: (S.-B.K.); (J.-A.G.); Tel.: +82-33-741-0345 (S.-B.K.); +82-2-2626-2362 (J.-A.G.)
| | - Jeong-An Gim
- Medical Science Research Center, College of Medicine, Korea University, 8 Gamasan-ro 20-gil, Guro-gu, Seoul 08308, Korea
- Correspondence: (S.-B.K.); (J.-A.G.); Tel.: +82-33-741-0345 (S.-B.K.); +82-2-2626-2362 (J.-A.G.)
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48
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OUP accepted manuscript. Hum Reprod Update 2022; 28:629-655. [DOI: 10.1093/humupd/dmac010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Indexed: 11/13/2022] Open
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49
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McKennan C, Nicolae D. Estimating and accounting for unobserved covariates in high-dimensional correlated data. J Am Stat Assoc 2022; 117:225-236. [PMID: 35615339 PMCID: PMC9126075 DOI: 10.1080/01621459.2020.1769635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Many high dimensional and high-throughput biological datasets have complex sample correlation structures, which include longitudinal and multiple tissue data, as well as data with multiple treatment conditions or related individuals. These data, as well as nearly all high-throughput 'omic' data, are influenced by technical and biological factors unknown to the researcher, which, if unaccounted for, can severely obfuscate estimation of and inference on the effects of interest. We therefore developed CBCV and CorrConf: provably accurate and computationally efficient methods to choose the number of and estimate latent confounding factors present in high dimensional data with correlated or nonexchangeable residuals. We demonstrate each method's superior performance compared to other state of the art methods by analyzing simulated multi-tissue gene expression data and identifying sex-associated DNA methylation sites in a real, longitudinal twin study.
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Affiliation(s)
| | - Dan Nicolae
- Department of Statistics, University of Chicago
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50
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Solomon O, Huen K, Yousefi P, Küpers LK, González JR, Suderman M, Reese SE, Page CM, Gruzieva O, Rzehak P, Gao L, Bakulski KM, Novoloaca A, Allard C, Pappa I, Llambrich M, Vives M, Jima DD, Kvist T, Baccarelli A, White C, Rezwan FI, Sharp GC, Tindula G, Bergström A, Grote V, Dou JF, Isaevska E, Magnus MC, Corpeleijn E, Perron P, Jaddoe VWV, Nohr EA, Maitre L, Foraster M, Hoyo C, Håberg SE, Lahti J, DeMeo DL, Zhang H, Karmaus W, Kull I, Koletzko B, Feinberg JI, Gagliardi L, Bouchard L, Ramlau-Hansen CH, Tiemeier H, Santorelli G, Maguire RL, Czamara D, Litonjua AA, Langhendries JP, Plusquin M, Lepeule J, Binder EB, Verduci E, Dwyer T, Carracedo Á, Ferre N, Eskenazi B, Kogevinas M, Nawrot TS, Munthe-Kaas MC, Herceg Z, Relton C, Melén E, Gruszfeld D, Breton C, Fallin MD, Ghantous A, Nystad W, Heude B, Snieder H, Hivert MF, Felix JF, Sørensen TIA, Bustamante M, Murphy SK, Raikkönen K, Oken E, Holloway JW, Arshad SH, London SJ, Holland N. Meta-analysis of epigenome-wide association studies in newborns and children show widespread sex differences in blood DNA methylation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108415. [PMID: 35690418 PMCID: PMC9623595 DOI: 10.1016/j.mrrev.2022.108415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 02/27/2022] [Accepted: 03/08/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Among children, sex-specific differences in disease prevalence, age of onset, and susceptibility have been observed in health conditions including asthma, immune response, metabolic health, some pediatric and adult cancers, and psychiatric disorders. Epigenetic modifications such as DNA methylation may play a role in the sexual differences observed in diseases and other physiological traits. METHODS We performed a meta-analysis of the association of sex and cord blood DNA methylation at over 450,000 CpG sites in 8438 newborns from 17 cohorts participating in the Pregnancy And Childhood Epigenetics (PACE) Consortium. We also examined associations of child sex with DNA methylation in older children ages 5.5-10 years from 8 cohorts (n = 4268). RESULTS In newborn blood, sex was associated at Bonferroni level significance with differences in DNA methylation at 46,979 autosomal CpG sites (p < 1.3 × 10-7) after adjusting for white blood cell proportions and batch. Most of those sites had lower methylation levels in males than in females. Of the differentially methylated CpG sites identified in newborn blood, 68% (31,727) met look-up level significance (p < 1.1 × 10-6) in older children and had methylation differences in the same direction. CONCLUSIONS This is a large-scale meta-analysis examining sex differences in DNA methylation in newborns and older children. Expanding upon previous studies, we replicated previous findings and identified additional autosomal sites with sex-specific differences in DNA methylation. Differentially methylated sites were enriched in genes involved in cancer, psychiatric disorders, and cardiovascular phenotypes.
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Affiliation(s)
- Olivia Solomon
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA.
| | - Paul Yousefi
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Leanne K Küpers
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Juan R González
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Sarah E Reese
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Center for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Peter Rzehak
- Div. Metabolic and Nutritional Medicine, Dept. Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Kelly M Bakulski
- School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, QC, Canada
| | - Irene Pappa
- Department of Child and Adolescent Psychiatry/ Psychology, Erasmus Medical Center, Sophia Children's Hospital, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
| | - Maria Llambrich
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Marta Vives
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
| | - Tuomas Kvist
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
| | - Andrea Baccarelli
- Laboratory of Precision Environmental Biosciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Cory White
- Merck Exploratory Science Center, Merck Research Laboratories, Cambridge, MA 02141, USA
| | - Faisal I Rezwan
- Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3DB, United Kingdom; Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Gwen Tindula
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Center for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Veit Grote
- Div. Metabolic and Nutritional Medicine, Dept. Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - John F Dou
- School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Eva Corpeleijn
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, QC, Canada; Department of Medicine, Universite de Sherbrooke, QC, Canada
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
| | - Ellen A Nohr
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark; Centre of Women's, Family and Child Health, University of South-Eastern Norway, Kongsberg, Norway
| | - Lea Maitre
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Maria Foraster
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; PHAGEX Research Group, Blanquerna School of Health Science, Universitat Ramon Llull, Barcelona, Spain
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA; Department of Biological Sciences, North Carolina State University, NC, USA
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 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
| | - Inger Kull
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Berthold Koletzko
- Div. Metabolic and Nutritional Medicine, Dept. Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Jason I Feinberg
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Luigi Gagliardi
- Department of Woman and Child Health, Ospedale Versilia, Azienda USL Toscana Nord Ovest, Viareggio, Italy
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, QC, Canada; Department of Medical Biology, CIUSSS Saguenay-Lac-Saint-Jean, Chicoutimi Hospital, Saguenay, QC, Canada
| | | | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/ Psychology, Erasmus Medical Center, Sophia Children's Hospital, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; Department of Social and Behavioral Science, Harvard TH Chan School of Public Health, 677 Huntington Ave, Boston, MA, USA
| | - Gillian Santorelli
- Bradford Institute of Health Research, Bradford Royal Infirmary, Bradford BD9 6RJ, UK
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, NC, USA; Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27701, USA
| | - Darina Czamara
- Dept. Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Augusto A Litonjua
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Johanna Lepeule
- Univ. Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, 38000 Grenoble, France
| | - Elisabeth B Binder
- Dept. Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, USA
| | - Elvira Verduci
- Department of Pediatrics, Ospedale dei Bambini Vittore Buzzi, University of Milan, Milan, Italy; Department of Health Sciences, University of Milan, Milan, Italy
| | - Terence Dwyer
- Clinical Sciences, Heart Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Pediatrics, University of Melbourne, Melbourne, Australia; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Fundación Pública Galega de Merdicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), SERGAS, Santiago de Compostela, Spain; Centro de Investigación en Red de Enfermedades Raras (CIBERER) y Centro Nacional de Genotipado (CEGEN-PRB3), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Natalia Ferre
- Pediatric Nutrition and Human Development Research Unit, Universitat Rovira i Virgili, IISPV, Reus, Spain
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, CA, USA
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; IMIM (Hospital del Mar Medical Research Institute), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium; Department Public Health & Primary care, Leuven University, Belgium
| | - Monica C Munthe-Kaas
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Pediatric Oncology and Hematology, Oslo University Hospital, Norway
| | - Zdenko Herceg
- International Agency for Research on Cancer, Lyon, France
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Dariusz Gruszfeld
- Neonatal Department, Children's Memorial Health Institute, Warsaw, Poland
| | - Carrie Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - M D Fallin
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Akram Ghantous
- International Agency for Research on Cancer, Lyon, France
| | - Wenche Nystad
- Department of Chronic Diseases and Ageing, Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004 Paris, France
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Marie-France Hivert
- Department of Medicine, Universite de Sherbrooke, QC, Canada; Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA; Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
| | - Thorkild I A Sørensen
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark; The Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27701, USA
| | - Katri Raikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Syed 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
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Nina Holland
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
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