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Ambroa-Conde A, Casares de Cal MA, Gómez-Tato A, Robinson O, Mosquera-Miguel A, de la Puente M, Ruiz-Ramírez J, Phillips C, Lareu MV, Freire-Aradas A. Inference of tobacco and alcohol consumption habits from DNA methylation analysis of blood. Forensic Sci Int Genet 2024; 70:103022. [PMID: 38309257 DOI: 10.1016/j.fsigen.2024.103022] [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: 08/22/2023] [Revised: 12/22/2023] [Accepted: 01/25/2024] [Indexed: 02/05/2024]
Abstract
DNA methylation has become a biomarker of great interest in the forensic and clinical fields. In criminal investigations, the study of this epigenetic marker has allowed the development of DNA intelligence tools providing information that can be useful for investigators, such as age prediction. Following a similar trend, when the origin of a sample in a criminal scenario is unknown, the inference of an individual's lifestyle such as tobacco use and alcohol consumption could provide relevant information to help in the identification of DNA donors at the crime scene. At the same time, in the clinical domain, prediction of these trends of consumption could allow the identification of people at risk or better identification of the causes of different pathologies. In the present study, DNA methylation data from the UK AIRWAVE study was used to build two binomial logistic models for the inference of smoking and drinking status. A total of 348 individuals (116 non-smokers, 116 former smokers and 116 smokers) plus a total of 237 individuals (79 non-drinkers, 79 moderate drinkers and 79 drinkers) were used for development of tobacco and alcohol consumption prediction models, respectively. The tobacco prediction model was composed of two CpGs (cg05575921 in AHRR and cg01940273) and the alcohol prediction model three CpGs (cg06690548 in SLC7A11, cg0886875 and cg21294714 in MIR4435-2HG), providing correct classifications of 86.49% and 74.26%, respectively. Validation of the models was performed using leave-one-out cross-validation. Additionally, two independent testing sets were also assessed for tobacco and alcohol consumption. Considering that the consumption of these substances could underlie accelerated epigenetic ageing patterns, the effect of these lifestyles on the prediction of age was evaluated. To do that, a quantile regression model based on previous studies was generated, and the potential effect of tobacco and alcohol consumption with the epigenetic age was assessed. The Wilcoxon test was used to evaluate the residuals generated by the model and no significant differences were observed between the categories analyzed.
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Affiliation(s)
- A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M A Casares de Cal
- CITMAga (Center for Mathematical Research and Technology of Galicia), University of Santiago de Compostela, Spain
| | - A Gómez-Tato
- CITMAga (Center for Mathematical Research and Technology of Galicia), University of Santiago de Compostela, Spain
| | - O Robinson
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - J Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain.
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2
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Rabotnick MH, Ehlinger J, Haidari A, Goodrich JM. Prenatal exposures to endocrine disrupting chemicals: The role of multi-omics in understanding toxicity. Mol Cell Endocrinol 2023; 578:112046. [PMID: 37598796 PMCID: PMC10592024 DOI: 10.1016/j.mce.2023.112046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are a diverse group of toxicants detected in populations globally. Prenatal EDC exposures impact birth and childhood outcomes. EDCs work through persistent changes at the molecular, cellular, and organ level. Molecular and biochemical signals or 'omics' can be measured at various functional levels - including the epigenome, transcriptome, proteome, metabolome, and the microbiome. In this narrative review, we introduce each omics and give examples of associations with prenatal EDC exposures. There is substantial research on epigenomic modifications in offspring exposed to EDCs during gestation, and a growing number of studies evaluating the transcriptome, proteome, metabolome, or microbiome in response to these exposures. Multi-omics, integrating data across omics layers, may improve understanding of disrupted function pathways related to early life exposures. We highlight several data integration methods to consider in multi-omics studies. Information from multi-omics can improve understanding of the biological processes and mechanisms underlying prenatal EDC toxicity.
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Affiliation(s)
- Margaret H Rabotnick
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Jessa Ehlinger
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Ariana Haidari
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
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3
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Yu W, Drzymalla E, Gyorfy MF, Khoury MJ, Sun YV, Gwinn M. Navigating epigenetic epidemiology publications. EPIGENETICS COMMUNICATIONS 2023; 3:8. [PMID: 38414576 PMCID: PMC10895989 DOI: 10.1186/s43682-023-00023-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/25/2023] [Indexed: 02/29/2024]
Affiliation(s)
- Wei Yu
- Office of Genomics and Precision Public Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Emily Drzymalla
- Office of Genomics and Precision Public Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Muin J Khoury
- Office of Genomics and Precision Public Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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4
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Conole ELS, Vaher K, Cabez MB, Sullivan G, Stevenson AJ, Hall J, Murphy L, Thrippleton MJ, Quigley AJ, Bastin ME, Miron VE, Whalley HC, Marioni RE, Boardman JP, Cox SR. Immuno-epigenetic signature derived in saliva associates with the encephalopathy of prematurity and perinatal inflammatory disorders. Brain Behav Immun 2023; 110:322-338. [PMID: 36948324 DOI: 10.1016/j.bbi.2023.03.011] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/12/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Preterm birth is closely associated with a phenotype that includes brain dysmaturation and neurocognitive impairment, commonly termed Encephalopathy of Prematurity (EoP), of which systemic inflammation is considered a key driver. DNA methylation (DNAm) signatures of inflammation from peripheral blood associate with poor brain imaging outcomes in adult cohorts. However, the robustness of DNAm inflammatory scores in infancy, their relation to comorbidities of preterm birth characterised by inflammation, neonatal neuroimaging metrics of EoP, and saliva cross-tissue applicability are unknown. METHODS Using salivary DNAm from 258 neonates (n = 155 preterm, gestational age at birth 23.28 - 34.84 weeks, n = 103 term, gestational age at birth 37.00 - 42.14 weeks), we investigated the impact of a DNAm surrogate for C-reactive protein (DNAm CRP) on brain structure and other clinically defined inflammatory exposures. We assessed i) if DNAm CRP estimates varied between preterm infants at term equivalent age and term infants, ii) how DNAm CRP related to different types of inflammatory exposure (maternal, fetal and postnatal) and iii) whether elevated DNAm CRP associated with poorer measures of neonatal brain volume and white matter connectivity. RESULTS Higher DNAm CRP was linked to preterm status (-0.0107 ± 0.0008, compared with -0.0118 ± 0.0006 among term infants; p < 0.001), as well as perinatal inflammatory diseases, including histologic chorioamnionitis, sepsis, bronchopulmonary dysplasia, and necrotising enterocolitis (OR range |2.00 | to |4.71|, p < 0.01). Preterm infants with higher DNAm CRP scores had lower brain volume in deep grey matter, white matter, and hippocampi and amygdalae (β range |0.185| to |0.218|). No such associations were observed for term infants. Association magnitudes were largest for measures of white matter microstructure among preterms, where elevated epigenetic inflammation associated with poorer global measures of white matter integrity (β range |0.206| to |0.371|), independent of other confounding exposures. CONCLUSIONS Inflammatory-related DNAm captures the allostatic load of inflammatory burden in preterm infants. Such DNAm measures complement biological and clinical metrics when investigating the determinants of neurodevelopmental differences.
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Affiliation(s)
- Eleanor L S Conole
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
| | - Kadi Vaher
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Manuel Blesa Cabez
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Gemma Sullivan
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jill Hall
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Michael J Thrippleton
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Alan J Quigley
- Imaging Department, Royal Hospital for Children and Young People, Edinburgh, EH16 4TJ, UK
| | - Mark E Bastin
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Veronique E Miron
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Heather C Whalley
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - James P Boardman
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; MRC Centre for Reproductive Health, Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Simon R Cox
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK.
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Kefayati F, Karimi Babaahmadi A, Mousavi T, Hodjat M, Abdollahi M. Epigenotoxicity: a danger to the future life. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2023; 58:382-411. [PMID: 36942370 DOI: 10.1080/10934529.2023.2190713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Environmental toxicants can regulate gene expression in the absence of DNA mutations via epigenetic mechanisms such as DNA methylation, histone modifications, and non-coding RNAs' (ncRNAs). Here, all three epigenetic modifications for seven important categories of diseases and the impact of eleven main environmental factors on epigenetic modifications were discussed. Epigenetic-related mechanisms are among the factors that could explain the root cause of a wide range of common diseases. Its overall impression on the development of diseases can help us diagnose and treat diseases, and besides, predict transgenerational and intergenerational effects. This comprehensive article attempted to address the relationship between environmental factors and epigenetic modifications that cause diseases in different categories. The studies main gap is that the precise role of environmentally-induced epigenetic alterations in the etiology of the disorders is unknown; thus, still more well-designed researches need to be accomplished to fill this gap. The present review aimed to first summarize the adverse effect of certain chemicals on the epigenome that may involve in the onset of particular disease based on in vitro and in vivo models. Subsequently, the possible adverse epigenetic changes that can lead to many human diseases were discussed.
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Affiliation(s)
- Farzaneh Kefayati
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Karimi Babaahmadi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Taraneh Mousavi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahshid Hodjat
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Abdollahi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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6
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Castagné R, Ménard S, Delpierre C. The epigenome as a biological candidate to incorporate the social environment over the life course and generations. Epigenomics 2023; 15:5-10. [PMID: 36916280 DOI: 10.2217/epi-2022-0457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Affiliation(s)
- Raphaële Castagné
- Center for Epidemiology & Research in POPulation Health (CERPOP), UMR 1295, Université Toulouse III Paul Sabatier, INSERM, 31000, Toulouse, France
| | - Sandrine Ménard
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, 31024, France
| | - Cyrille Delpierre
- Center for Epidemiology & Research in POPulation Health (CERPOP), UMR 1295, Université Toulouse III Paul Sabatier, INSERM, 31000, Toulouse, France
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7
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Elkin ER, Higgins C, Aung MT, Bakulski KM. Metals Exposures and DNA Methylation: Current Evidence and Future Directions. Curr Environ Health Rep 2022; 9:673-696. [PMID: 36282474 PMCID: PMC10082670 DOI: 10.1007/s40572-022-00382-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF THE REVIEW Exposure to essential and non-essential metals is widespread. Metals exposure is linked to epigenetic, particularly DNA methylation, differences. The strength of evidence with respect to the metal exposure type, timing, and level, as well as the DNA methylation association magnitude, and reproducibility are not clear. Focusing on the most recent 3 years, we reviewed the human epidemiologic evidence (n = 26 studies) and the toxicologic animal model evidence (n = 18 studies) for associations between metals exposure and DNA methylation. RECENT FINDINGS In humans, the greatest number of studies focused on lead exposure, followed by studies examining cadmium and arsenic. Approximately half of studies considered metals exposure during the in utero period and measured DNA methylation with the genome-wide Illumina arrays in newborn blood or placenta. Few studies performed formal replication testing or meta-analyses. Toxicology studies of metals and epigenetics had diversity in model systems (mice, rats, drosophila, tilapia, and zebrafish were represented), high heterogeneity of tissues used for DNA methylation measure (liver, testis, ovary, heart, blood, brain, muscle, lung, kidney, whole embryo), and a variety of technologies used for DNA methylation assessment (global, gene specific, genome-wide). The most common metals tested in toxicologic studies were lead and cadmium. Together, the recent studies reviewed provide the strongest evidence for DNA methylation signatures with prenatal metals exposures. There is also mounting epidemiologic evidence supporting lead, arsenic, and cadmium exposures with DNA methylation signatures in adults. The field of metals and DNA methylation is strengthened by the inclusion of both epidemiology and toxicology approaches, and further advancements can be made by coordinating efforts or integrating analyses across studies. Future advances in understanding the molecular basis of sequence specific epigenetic responses to metals exposures, methods for handling exposure mixtures in a genome-wide analytic framework, and pipelines to facilitate collaborative testing will continue to advance the field.
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Affiliation(s)
- Elana R Elkin
- Department of Environmental Health School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Cesar Higgins
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Max T Aung
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
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8
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Wang N, Jin S. Meta-Analysis for Epigenome-Wide Association Studies. Methods Mol Biol 2022; 2432:101-111. [PMID: 35505210 DOI: 10.1007/978-1-0716-1994-0_8] [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: 06/14/2023]
Abstract
With the rapid development of methylation profiling technology, many datasets are generated to quantify genome-wide methylation patterns. Given the heavy burden of multiple testing of hundreds of thousands of DNA methylation markers, individual studies often have limited sample sizes and power. The EWAS meta-analysis is an approach that combines results from multiple studies on the same scientific question. It helps to improve statistical power by combining information from individual studies and reduce the chances of false positives. This chapter introduces commonly used meta-analysis methods and analytical tools with application to EWAS data.
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Affiliation(s)
- Nan Wang
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang, China.
| | - Shuilin Jin
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang, China.
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9
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Bakulski KM, Dou JF, Feinberg JI, Aung MT, Ladd-Acosta C, Volk HE, Newschaffer CJ, Croen LA, Hertz-Picciotto I, Levy SE, Landa R, Feinberg AP, Fallin MD. Autism-Associated DNA Methylation at Birth From Multiple Tissues Is Enriched for Autism Genes in the Early Autism Risk Longitudinal Investigation. Front Mol Neurosci 2021; 14:775390. [PMID: 34899183 PMCID: PMC8655859 DOI: 10.3389/fnmol.2021.775390] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/28/2021] [Indexed: 12/30/2022] Open
Abstract
Background: Pregnancy measures of DNA methylation, an epigenetic mark, may be associated with autism spectrum disorder (ASD) development in children. Few ASD studies have considered prospective designs with DNA methylation measured in multiple tissues and tested overlap with ASD genetic risk loci. Objectives: To estimate associations between DNA methylation in maternal blood, cord blood, and placenta and later diagnosis of ASD, and to evaluate enrichment of ASD-associated DNA methylation for known ASD-associated genes. Methods: In the Early Autism Risk Longitudinal Investigation (EARLI), an ASD-enriched risk birth cohort, genome-scale maternal blood (early n = 140 and late n = 75 pregnancy), infant cord blood (n = 133), and placenta (maternal n = 106 and fetal n = 107 compartments) DNA methylation was assessed on the Illumina 450k HumanMethylation array and compared to ASD diagnosis at 36 months of age. Differences in site-specific and global methylation were tested with ASD, as well as enrichment of single site associations for ASD risk genes (n = 881) from the Simons Foundation Autism Research Initiative (SFARI) database. Results: No individual DNA methylation site was associated with ASD at genome-wide significance, however, individual DNA methylation sites nominally associated with ASD (P < 0.05) in each tissue were highly enriched for SFARI genes (cord blood P = 7.9 × 10-29, maternal blood early pregnancy P = 6.1 × 10-27, maternal blood late pregnancy P = 2.8 × 10-16, maternal placenta P = 5.6 × 10-15, fetal placenta P = 1.3 × 10-20). DNA methylation sites nominally associated with ASD across all five tissues overlapped at 144 (29.5%) SFARI genes. Conclusion: DNA methylation sites nominally associated with later ASD diagnosis in multiple tissues were enriched for ASD risk genes. Our multi-tissue study demonstrates the utility of examining DNA methylation prior to ASD diagnosis.
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Affiliation(s)
- Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Jason I Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Max T Aung
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Heather E Volk
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States
| | - Craig J Newschaffer
- College of Health and Human Development, Penn State University, State College, PA, United States
| | - Lisa A Croen
- Kaiser Permanente Division of Research, Oakland, CA, United States
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California, Davis, Davis, CA, United States
| | - Susan E Levy
- Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Rebecca Landa
- Kennedy Krieger Institute Center for Autism and Related Disorders, Baltimore, MD, United States
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States.,Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Margaret D Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States
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10
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Polverino A, Sorrentino P, Pesoli M, Mandolesi L. Nutrition and cognition across the lifetime: an overview on epigenetic mechanisms. AIMS Neurosci 2021; 8:448-476. [PMID: 34877399 PMCID: PMC8611190 DOI: 10.3934/neuroscience.2021024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/12/2021] [Indexed: 12/28/2022] Open
Abstract
The functioning of our brain depends on both genes and their interactions with environmental factors. The close link between genetics and environmental factors produces structural and functional cerebral changes early on in life. Understanding the weight of environmental factors in modulating neuroplasticity phenomena and cognitive functioning is relevant for potential interventions. Among these, nutrition plays a key role. In fact, the link between gut and brain (the gut-brain axis) is very close and begins in utero, since the Central Nervous System (CNS) and the Enteric Nervous System (ENS) originate from the same germ layer during the embryogenesis. Here, we investigate the epigenetic mechanisms induced by some nutrients on the cognitive functioning, which affect the cellular and molecular processes governing our cognitive functions. Furthermore, epigenetic phenomena can be positively affected by specific healthy nutrients from diet, with the possibility of preventing or modulating cognitive impairments. Specifically, we described the effects of several nutrients on diet-dependent epigenetic processes, in particular DNA methylation and histones post-translational modifications, and their potential role as therapeutic target, to describe how some forms of cognitive decline could be prevented or modulated from the early stages of life.
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Affiliation(s)
- Arianna Polverino
- Institute of Diagnosis and Treatment Hermitage Capodimonte, Naples, Italy.,Department of Motor and Wellness Sciences, University of Naples "Parthenope", Naples, Italy
| | - Pierpaolo Sorrentino
- Institut de Neurosciences des Systèmes, Aix-Marseille University, Marseille, France.,Institute of Applied Sciences and Intelligent Systems, National Research Council, Pozzuoli, Italy
| | - Matteo Pesoli
- Department of Motor and Wellness Sciences, University of Naples "Parthenope", Naples, Italy
| | - Laura Mandolesi
- Department of Humanities Studies, University of Naples Federico II, Naples, Italy
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11
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Liu K, Jiang J, Lin Y, Liu W, Zhu X, Zhang Y, Jiang H, Yu K, Liu X, Zhou M, Yuan Y, Long P, Wang Q, Zhang X, He M, Chen W, Guo H, Wu T. Exposure to polycyclic aromatic hydrocarbons, DNA methylation and heart rate variability among non-current smokers. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 288:117777. [PMID: 34265559 DOI: 10.1016/j.envpol.2021.117777] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/28/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) exposure is associated with heart rate variability (HRV) reduction, a widely used marker of cardiovascular autonomic dysfunction. The role of DNA methylation in the relationship between PAHs exposure and decreased HRV is largely unknown. This study aims to explore epigenome-wide DNA methylation changes associated with PAHs exposure and further evaluate their associations with HRV alternations among non-current smokers. We measured 10 mono-hydroxylated PAHs (OH-PAHs) in urine and DNA methylation levels in blood leukocytes among participants from three panels of Chinese non-current smokers (152 in WHZH, 99 in SY, and 53 in COW). We conducted linear regression analyses between DNA methylation and OH-PAHs metabolites with adjustment for age, gender, body mass index, drinking, blood cell counts, and surrogate variables in each panel separately, and combined the results by using inverse-variance weighted fixed-effect meta-analysis to obtain estimates of effect size. The median value of total OH-PAHs ranged from 0.92 × 10-2 in SY panel (62.6% men) to 13.82 × 10-2 μmol/mmol creatinine in COW panel (43.4% men). The results showed that methylation levels of cg18223625 (COL20A1) and cg07805771 (SLC16A1) were significantly or marginally significantly associated with urinary 2-hydroxynaphthalene [β(SE) = 0.431(0.074) and 0.354(0.068), FDR = 0.016 and 0.056, respectively], while methylation level of cg09235308 (PLEC1) was positively associated with urinary total OH-PAHs [β(SE) = 0.478(0.079), FDR = 0.004]. Hypermethylations of cg18223625, cg07805771, and cg09235308 were inversely associated with HRV indices among the WHZH and COW non-current smokers. However, we did not observe significant epigenome-wide associations for the other 9 urinary OH-PAHs. These findings provide new evidence that PAHs exposure is linked to differential DNA methylation, which may help better understand the influences of PAHs exposure on HRV alternations.
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Affiliation(s)
- Kang Liu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jing Jiang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuhui Lin
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Liu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoyan Zhu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Suzhou Center for Disease Prevention and Control, Suzhou, 215004, China
| | - Yizhi Zhang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Haijing Jiang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Kuai Yu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xuezhen Liu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Min Zhou
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yu Yuan
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Pinpin Long
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qiuhong Wang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Meian He
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Weihong Chen
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Huan Guo
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Tangchun Wu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
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12
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Magwai T, Shangase KB, Oginga FO, Chiliza B, Mpofana T, Xulu KR. DNA Methylation and Schizophrenia: Current Literature and Future Perspective. Cells 2021; 10:2890. [PMID: 34831111 PMCID: PMC8616184 DOI: 10.3390/cells10112890] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Schizophrenia is a neuropsychiatric disorder characterized by dissociation of thoughts, idea, identity, and emotions. It has no central pathophysiological mechanism and precise diagnostic markers. Despite its high heritability, there are also environmental factors implicated in the development of schizophrenia. Epigenetic factors are thought to mediate the effects of environmental factors in the development of the disorder. Epigenetic modifications like DNA methylation are a risk factor for schizophrenia. Targeted gene approach studies attempted to find candidate gene methylation, but the results are contradictory. Genome-wide methylation studies are insufficient in literature and the available data do not cover different populations like the African populations. The current genome-wide studies have limitations related to the sample and methods used. Studies are required to control for these limitations. Integration of DNA methylation, gene expression, and their effects are important in the understanding of the development of schizophrenia and search for biomarkers. There are currently no precise and functional biomarkers for the disorder. Several epigenetic markers have been reported to be common in functional and peripheral tissue. This makes the peripheral tissue epigenetic changes a surrogate of functional tissue, suggesting common epigenetic alteration can be used as biomarkers of schizophrenia in peripheral tissue.
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Affiliation(s)
- Thabo Magwai
- Department of Physiology, School of Laboratory Medicine and Medical Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa; (K.B.S.); (F.O.O.); (T.M.)
- National Health Laboratory Service, Department of Chemical Pathology, University of Kwa-Zulu Natal, Durban 4085, South Africa
| | - Khanyiso Bright Shangase
- Department of Physiology, School of Laboratory Medicine and Medical Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa; (K.B.S.); (F.O.O.); (T.M.)
| | - Fredrick Otieno Oginga
- Department of Physiology, School of Laboratory Medicine and Medical Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa; (K.B.S.); (F.O.O.); (T.M.)
| | - Bonginkosi Chiliza
- Department of Psychiatry, Nelson R Mandela School of Medicine, University of Kwa-Zulu Natal, Durban 4001, South Africa;
| | - Thabisile Mpofana
- Department of Physiology, School of Laboratory Medicine and Medical Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa; (K.B.S.); (F.O.O.); (T.M.)
| | - Khethelo Richman Xulu
- Department of Physiology, School of Laboratory Medicine and Medical Sciences, University of Kwa-Zulu Natal, Durban 4001, South Africa; (K.B.S.); (F.O.O.); (T.M.)
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13
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Prenatal Particulate Matter Exposure Is Associated with Saliva DNA Methylation at Age 15: Applying Cumulative DNA Methylation Scores as an Exposure Biomarker. TOXICS 2021; 9:toxics9100262. [PMID: 34678958 PMCID: PMC8538839 DOI: 10.3390/toxics9100262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022]
Abstract
Exposure in utero to particulate matter (PM2.5 and PM10) is associated with maladaptive health outcomes. Although exposure to prenatal PM2.5 and PM10 has cord blood DNA methylation signatures at birth, signature persistence into childhood and saliva cross-tissue applicability has not been tested. In the Fragile Families and Child Wellbeing Study, a United States 20-city birth cohort, average residential PM2.5 and PM10 during the three months prior to birth was estimated using air quality monitors with inverse distance weighting. Saliva DNA methylation at ages 9 (n = 749) and 15 (n = 793) was measured using the Illumina HumanMethylation 450 k BeadArray. Cumulative DNA methylation scores for particulate matter were estimated by weighting participant DNA methylation at each site by independent meta-analysis effect estimates and standardizing the sums. Using a mixed-effects regression analysis, we tested the associations between cumulative DNA methylation scores at ages 9 and 15 and PM exposure during pregnancy, adjusted for child sex, age, race/ethnicity, maternal income-to-needs ratio, nonmartial birth status, and saliva cell-type proportions. Our study sample was 50.5% male, 56.3% non-Hispanic Black, and 19.8% Hispanic, with a median income-to-needs ratio of 1.4. Mean exposure levels for PM2.5 were 27.9 μg/m3/day (standard deviation: 7.0; 23.7% of observations exceeded safety standards) and for PM10 were 15.0 μg/m3/day (standard deviation: 3.1). An interquartile range increase in PM2.5 exposure (10.73 μg/m3/day) was associated with a −0.0287 standard deviation lower cumulative DNA methylation score for PM2.5 (95% CI: −0.0732, 0.0158, p = 0.20) across all participants. An interquartile range increase in PM10 exposure (3.20 μg/m3/day) was associated with a −0.1472 standard deviation lower cumulative DNA methylation score for PM10 (95% CI: −0.3038, 0.0095, p = 0.06) across all participants. The PM10 findings were driven by the age 15 subset where an interquartile range increase in PM10 exposure was associated with a −0.024 standard deviation lower cumulative DNA methylation score for PM10 (95% CI: −0.043, −0.005, p = 0.012). Findings were robust to adjustment for PM exposure at ages 1 and 3. In utero PM10-associated DNA methylation differences were identified at age 15 in saliva. Benchmarking the timing and cell-type generalizability is critical for epigenetic exposure biomarker assessment.
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14
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Vaiserman A, Lushchak O. DNA methylation changes induced by prenatal toxic metal exposure: An overview of epidemiological evidence. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab007. [PMID: 34631153 PMCID: PMC8493661 DOI: 10.1093/eep/dvab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/06/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Accumulating evidence suggests that exposure to unfavorable conditions early in life can substantially contribute to the risk of chronic disorders later in life ('developmental programming' phenomenon). The mechanistic basis for this phenomenon remains poorly understood so far, although epigenetic mechanisms such as DNA methylation, histone modifications and microRNA-mediated gene regulation apparently play a crucial role. The key role of epigenetic modifications triggered by unfavorable environmental cues during sensitive developmental periods in linking adverse early-life events to later-life health outcomes is evident from a large body of studies, including methylome-wide association studies and research of candidate genes. Toxic metals (TMs), such as heavy metals, including lead, chromium, cadmium, arsenic, mercury, etc., are among environmental contaminants currently most significantly impacting human health status. Since TMs can cross the placental barrier and accumulate in fetal tissues, exposure to high doses of these xenobiotics early in development is considered to be among important factors contributing to the developmental programming of adult-life diseases in modern societies. In this mini-review, we summarize epidemiological findings indicating that prenatal TM exposure can induce epigenetic dysregulation, thereby potentially affecting adult health outcomes.
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Affiliation(s)
- Alexander Vaiserman
- Laboratory of Epigenetics, D.F. Chebotarev Institute of Gerontology, NAMS, 67 Vyshgorodska str., Kyiv 04114, Ukraine
| | - Oleh Lushchak
- *Correspondence address. Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenka str., Ivano-Frankivsk 76018, Ukraine. Tel/Fax: +38 0342 71 46 83; E-mail:
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15
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Breton CV, Landon R, Kahn LG, Enlow MB, Peterson AK, Bastain T, Braun J, Comstock SS, Duarte CS, Hipwell A, Ji H, LaSalle JM, Miller RL, Musci R, Posner J, Schmidt R, Suglia SF, Tung I, Weisenberger D, Zhu Y, Fry R. Exploring the evidence for epigenetic regulation of environmental influences on child health across generations. Commun Biol 2021; 4:769. [PMID: 34158610 PMCID: PMC8219763 DOI: 10.1038/s42003-021-02316-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 06/03/2021] [Indexed: 02/08/2023] Open
Abstract
Environmental exposures, psychosocial stressors and nutrition are all potentially important influences that may impact health outcomes directly or via interactions with the genome or epigenome over generations. While there have been clear successes in large-scale human genetic studies in recent decades, there is still a substantial amount of missing heritability to be elucidated for complex childhood disorders. Mounting evidence, primarily in animals, suggests environmental exposures may generate or perpetuate altered health outcomes across one or more generations. One putative mechanism for these environmental health effects is via altered epigenetic regulation. This review highlights the current epidemiologic literature and supporting animal studies that describe intergenerational and transgenerational health effects of environmental exposures. Both maternal and paternal exposures and transmission patterns are considered, with attention paid to the attendant ethical, legal and social implications.
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Affiliation(s)
- Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Remy Landon
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Linda G Kahn
- Department of Pediatrics, NYU Grossman School of Medicine, New York, NY, USA
| | - Michelle Bosquet Enlow
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alicia K Peterson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Theresa Bastain
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joseph Braun
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
| | - Sarah S Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, USA
| | - Cristiane S Duarte
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center and New York State Psychiatric Institute, New York, NY, USA
| | - Alison Hipwell
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hong Ji
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, California National Primate Research Center, University of California, Davis, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, Davis, CA, USA
| | | | - Rashelle Musci
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jonathan Posner
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center and New York State Psychiatric Institute, New York, NY, USA
| | - Rebecca Schmidt
- Department of Public Health Sciences, UC Davis School of Medicine, Davis, CA, USA
| | | | - Irene Tung
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yeyi Zhu
- Division of Research, Kaiser Permanente Northern California and Department of Epidemiology and Biostatistics, University of California, San Francisco, Oakland, CA, USA
| | - Rebecca Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, UNC Chapel Hill, Chapel Hill, NC, USA
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16
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Sternbach S, West N, Singhal NK, Clements R, Basu S, Tripathi A, Dutta R, Freeman EJ, McDonough J. The BHMT-betaine methylation pathway epigenetically modulates oligodendrocyte maturation. PLoS One 2021; 16:e0250486. [PMID: 33975330 PMCID: PMC8112889 DOI: 10.1371/journal.pone.0250486] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/08/2021] [Indexed: 11/18/2022] Open
Abstract
Research into the epigenome is of growing importance as a loss of epigenetic control has been implicated in the development of neurodegenerative diseases. Previous studies have implicated aberrant DNA and histone methylation in multiple sclerosis (MS) disease pathogenesis. We have previously reported that the methyl donor betaine is depleted in MS and is linked to changes in histone H3 trimethylation (H3K4me3) in neurons. We have also shown that betaine increases histone methyltransferase activity by activating chromatin bound betaine homocysteine S-methyltransferase (BHMT). Here, we investigated the role of the BHMT-betaine methylation pathway in oligodendrocytes. Immunocytochemistry in the human MO3.13 cell line, primary rat oligodendrocytes, and tissue from MS postmortem brain confirmed the presence of the BHMT enzyme in the nucleus in oligodendrocytes. BHMT expression is increased 2-fold following oxidative insult, and qRT-PCR demonstrated that betaine can promote an increase in expression of oligodendrocyte maturation genes SOX10 and NKX-2.2 under oxidative conditions. Chromatin fractionation provided evidence of a direct interaction of BHMT on chromatin and co-IP analysis indicates an interaction between BHMT and DNMT3a. Our data show that both histone and DNA methyltransferase activity are increased following betaine administration. Betaine effects were shown to be dependent on BHMT expression following siRNA knockdown of BHMT. This is the first report of BHMT expression in oligodendrocytes and suggests that betaine acts through BHMT to modulate histone and DNA methyltransferase activity on chromatin. These data suggest that methyl donor availability can impact epigenetic changes and maturation in oligodendrocytes.
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Affiliation(s)
- Sarah Sternbach
- School of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
| | - Nicole West
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, United States of America
| | - Naveen K. Singhal
- Department of Biological Sciences, Kent State University, Kent, Ohio, United States of America
| | - Robert Clements
- School of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
- Department of Biological Sciences, Kent State University, Kent, Ohio, United States of America
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, United States of America
| | - Ajai Tripathi
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Ranjan Dutta
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Ernest J. Freeman
- School of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
- Department of Biological Sciences, Kent State University, Kent, Ohio, United States of America
| | - Jennifer McDonough
- School of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
- Department of Biological Sciences, Kent State University, Kent, Ohio, United States of America
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17
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Tukker AM, Royal CD, Bowman AB, McAllister KA. The Impact of Environmental Factors on Monogenic Mendelian Diseases. Toxicol Sci 2021; 181:3-12. [PMID: 33677604 PMCID: PMC8599782 DOI: 10.1093/toxsci/kfab022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Environmental factors and gene-environment interactions modify the variable expressivity, progression, severity, and onset of some classic (monogenic) Mendelian-inherited genetic diseases. Cystic fibrosis, Huntington disease, Parkinson's disease, and sickle cell disease are examples of well-known Mendelian disorders that are influenced by exogenous exposures. Environmental factors may act by direct or indirect mechanisms to modify disease severity, timing, and presentation, including through epigenomic influences, protein misfolding, miRNA alterations, transporter activity, and mitochondrial effects. Because pathological features of early-onset Mendelian diseases can mimic later onset complex diseases, we propose that studies of environmental exposure vulnerabilities using monogenic model systems of rare Mendelian diseases have high potential to provide insight into complex disease phenotypes arising from multi-genetic/multi-toxicant interactions. Mendelian disorders can be modeled by homologous mutations in animal model systems with strong recapitulation of human disease etiology and natural history, providing an important advantage for study of these diseases. Monogenic high penetrant mutations are ideal for toxicant challenge studies with a wide variety of environmental stressors, because background genetic variability may be less able to alter the relatively strong phenotype driving disease-causing mutations. These models promote mechanistic understandings of gene-environment interactions and biological pathways relevant to both Mendelian and related sporadic complex disease outcomes by creating a sensitized background for relevant environmental risk factors. Additionally, rare disease communities are motivated research participants, creating the potential of strong research allies among rare Mendelian disease advocacy groups and disease registries and providing a variety of translational opportunities that are under-utilized in genetic or environmental health science.
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Affiliation(s)
- Anke M Tukker
- School of Health Sciences, Purdue University, West Lafayette, Indiana 47907-2051
| | - Charmaine D Royal
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health and Center on Genomics, Race, Identity, Difference, Duke University, Durham, North Carolina 27708
| | - Aaron B Bowman
- School of Health Sciences, Purdue University, West Lafayette, Indiana 47907-2051
| | - Kimberly A McAllister
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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18
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Aung MT, M Bakulski K, Feinberg JI, F Dou J, D Meeker J, Mukherjee B, Loch-Caruso R, Ladd-Acosta C, Volk HE, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Fallin MD. Maternal blood metal concentrations and whole blood DNA methylation during pregnancy in the Early Autism Risk Longitudinal Investigation (EARLI). Epigenetics 2021; 17:253-268. [PMID: 33794742 DOI: 10.1080/15592294.2021.1897059] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The maternal epigenome may be responsive to prenatal metals exposures. We tested whether metals are associated with concurrent differential maternal whole blood DNA methylation. In the Early Autism Risk Longitudinal Investigation cohort, we measured first or second trimester maternal blood metals concentrations (cadmium, lead, mercury, manganese, and selenium) using inductively coupled plasma mass spectrometry. DNA methylation in maternal whole blood was measured on the Illumina 450 K array. A subset sample of 97 women had both measures available for analysis, all of whom did not report smoking during pregnancy. Linear regression was used to test for site-specific associations between individual metals and DNA methylation, adjusting for cell type composition and confounding variables. Discovery gene ontology analysis was conducted on the top 1,000 sites associated with each metal. We observed hypermethylation at 11 DNA methylation sites associated with lead (FDR False Discovery Rate q-value <0.1), near the genes CYP24A1, ASCL2, FAT1, SNX31, NKX6-2, LRC4C, BMP7, HOXC11, PCDH7, ZSCAN18, and VIPR2. Lead-associated sites were enriched (FDR q-value <0.1) for the pathways cell adhesion, nervous system development, and calcium ion binding. Manganese was associated with hypermethylation at four DNA methylation sites (FDR q-value <0.1), one of which was near the gene ARID2. Manganese-associated sites were enriched for cellular metabolism pathways (FDR q-value<0.1). Effect estimates for DNA methylation sites associated (p < 0.05) with cadmium, lead, and manganese were highly correlated (Pearson ρ > 0.86). DNA methylation sites associated with lead and manganese may be potential biomarkers of exposure or implicate downstream gene pathways.
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Affiliation(s)
- Max T Aung
- Department of Biostatistics, University of Michigan, Ann Arbor, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Jason I Feinberg
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins University, Baltimore, USA.,Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA.,Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, USA
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - John D Meeker
- Department of Environmental Health, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Bhramar Mukherjee
- Department of Biostatistics, University of Michigan, Ann Arbor, USA.,Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Rita Loch-Caruso
- Department of Environmental Health, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins University, Baltimore, USA.,Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA
| | - Heather E Volk
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins University, Baltimore, USA.,Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA
| | - Lisa A Croen
- Division of Research, Kaiser Permanente, Oakland, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, USA
| | - Craig J Newschaffer
- Department of Biobehavioral Health, College of Health and Human Development, Penn State University, USA
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins University, Baltimore, USA.,Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA
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19
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Mohammadnejad A, Soerensen M, Baumbach J, Mengel‐From J, Li W, Lund J, Li S, Christiansen L, Christensen K, Hjelmborg JVB, Tan Q. Novel DNA methylation marker discovery by assumption-free genome-wide association analysis of cognitive function in twins. Aging Cell 2021; 20:e13293. [PMID: 33528912 PMCID: PMC7884045 DOI: 10.1111/acel.13293] [Citation(s) in RCA: 6] [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: 06/08/2020] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 01/23/2023] Open
Abstract
Privileged by rapid increase in available epigenomic data, epigenome-wide association studies (EWAS) are to make a profound contribution to understand the molecular mechanism of DNA methylation in cognitive aging. Current statistical methods used in EWAS are dominated by models based on multiple assumptions, for example, linear relationship between molecular profiles and phenotype, normal distribution for the methylation data and phenotype. In this study, we applied an assumption-free method, the generalized correlation coefficient (GCC), and compare it to linear models, namely the linear mixed model and kinship model. We use DNA methylation associated with a cognitive score in 400 and 206 twins as discovery and replication samples respectively. DNA methylation associated with cognitive function using GCC, linear mixed model, and kinship model, identified 65 CpGs (p < 1e-04) from discovery sample displaying both nonlinear and linear correlations. Replication analysis successfully replicated 9 of these top CpGs. When combining results of GCC and linear models to cover diverse patterns of relationships, we identified genes like KLHDC4, PAPSS2, and MRPS18B as well as pathways including focal adhesion, axon guidance, and some neurological signaling. Genomic region-based analysis found 15 methylated regions harboring 11 genes, with three verified in gene expression analysis, also the 11 genes were related to top functional clusters including neurohypophyseal hormone and maternal aggressive behaviors. The GCC approach detects valuable methylation sites missed by traditional linear models. A combination of methylation markers from GCC and linear models enriched biological pathways sensible in neurological function that could implicate cognitive performance and cognitive aging.
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Affiliation(s)
- Afsaneh Mohammadnejad
- Unit of Epidemiology, Biostatistics and BiodemographyDepartment of Public HealthUniversity of Southern DenmarkOdenseDenmark
| | - Mette Soerensen
- Unit of Epidemiology, Biostatistics and BiodemographyDepartment of Public HealthUniversity of Southern DenmarkOdenseDenmark
- Unit of Human GeneticsDepartment of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
- Department of Clinical Biochemistry and PharmacologyOdense University HospitalOdenseDenmark
| | - Jan Baumbach
- Computational BiomedicineDepartment of Mathematics and Computer ScienceUniversity of Southern DenmarkOdenseDenmark
- Chair of Experimental BioinformaticsTUM School of Life SciencesTechnical University of MunichMunichGermany
| | - Jonas Mengel‐From
- Unit of Epidemiology, Biostatistics and BiodemographyDepartment of Public HealthUniversity of Southern DenmarkOdenseDenmark
- Unit of Human GeneticsDepartment of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | - Weilong Li
- Unit of Epidemiology, Biostatistics and BiodemographyDepartment of Public HealthUniversity of Southern DenmarkOdenseDenmark
- Population Research UnitFaculty of Social SciencesUniversity of HelsinkiHelsinkiFinland
| | - Jesper Lund
- Unit of Epidemiology, Biostatistics and BiodemographyDepartment of Public HealthUniversity of Southern DenmarkOdenseDenmark
- Digital Health & Machine Learning Research GroupHasso Plattner Institute for Digital EngineeringPotsdamGermany
| | - Shuxia Li
- Unit of Epidemiology, Biostatistics and BiodemographyDepartment of Public HealthUniversity of Southern DenmarkOdenseDenmark
| | - Lene Christiansen
- Unit of Epidemiology, Biostatistics and BiodemographyDepartment of Public HealthUniversity of Southern DenmarkOdenseDenmark
- Department of Clinical ImmunologyCopenhagen University HospitalRigshospitaletCopenhagen ØDenmark
| | - Kaare Christensen
- Unit of Epidemiology, Biostatistics and BiodemographyDepartment of Public HealthUniversity of Southern DenmarkOdenseDenmark
- Unit of Human GeneticsDepartment of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | - Jacob V. B. Hjelmborg
- Unit of Epidemiology, Biostatistics and BiodemographyDepartment of Public HealthUniversity of Southern DenmarkOdenseDenmark
| | - Qihua Tan
- Unit of Epidemiology, Biostatistics and BiodemographyDepartment of Public HealthUniversity of Southern DenmarkOdenseDenmark
- Unit of Human GeneticsDepartment of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
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20
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Mancilla VJ, Peeri NC, Silzer T, Basha R, Felini M, Jones HP, Phillips N, Tao MH, Thyagarajan S, Vishwanatha JK. Understanding the Interplay Between Health Disparities and Epigenomics. Front Genet 2020; 11:903. [PMID: 32973872 PMCID: PMC7468461 DOI: 10.3389/fgene.2020.00903] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/21/2020] [Indexed: 12/13/2022] Open
Abstract
Social epigenomics has emerged as an integrative field of research focused on identification of socio-environmental factors, their influence on human biology through epigenomic modifications, and how they contribute to current health disparities. Several health disparities studies have been published using genetic-based approaches; however, increasing accessibility and affordability of molecular technologies have allowed for an in-depth investigation of the influence of external factors on epigenetic modifications (e.g., DNA methylation, micro-RNA expression). Currently, research is focused on epigenetic changes in response to environment, as well as targeted epigenetic therapies and environmental/social strategies for potentially minimizing certain health disparities. Here, we will review recent findings in this field pertaining to conditions and diseases over life span encompassing prenatal to adult stages.
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Affiliation(s)
- Viviana J. Mancilla
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Noah C. Peeri
- Department of Biostatistics and Epidemiology, School of Public Health, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Talisa Silzer
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Riyaz Basha
- Department of Pediatrics, Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX, United States
- Texas Center for Health Disparities, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Martha Felini
- Department of Pediatrics, Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX, United States
- Texas Center for Health Disparities, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Harlan P. Jones
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, United States
- Texas Center for Health Disparities, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Nicole Phillips
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, United States
- Texas Center for Health Disparities, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Meng-Hua Tao
- Department of Biostatistics and Epidemiology, School of Public Health, University of North Texas Health Science Center, Fort Worth, TX, United States
- Texas Center for Health Disparities, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Srikantha Thyagarajan
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, United States
- Texas Center for Health Disparities, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Jamboor K. Vishwanatha
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, United States
- Texas Center for Health Disparities, University of North Texas Health Science Center, Fort Worth, TX, United States
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21
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Go RCP, Corley MJ, Ross GW, Petrovitch H, Masaki KH, Maunakea AK, He Q, Tiirikainen MI. Genome-wide epigenetic analyses in Japanese immigrant plantation workers with Parkinson's disease and exposure to organochlorines reveal possible involvement of glial genes and pathways involved in neurotoxicity. BMC Neurosci 2020; 21:31. [PMID: 32650713 PMCID: PMC7350633 DOI: 10.1186/s12868-020-00582-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 07/07/2020] [Indexed: 12/29/2022] Open
Abstract
Background Parkinson’s disease (PD) is a disease of the central nervous system that progressively affects the motor system. Epidemiological studies have provided evidence that exposure to agriculture-related occupations or agrichemicals elevate a person’s risk for PD. Here, we sought to examine the possible epigenetic changes associated with working on a plantation on Oahu, HI and/or exposure to organochlorines (OGC) in PD cases. Results We measured genome-wide DNA methylation using the Illumina Infinium HumanMethylation450K BeadChip array in matched peripheral blood and postmortem brain biospecimens in PD cases (n = 20) assessed for years of plantation work and presence of organochlorines in brain tissue. The comparison of 10+ to 0 years of plantation work exposure detected 7 and 123 differentially methylated loci (DML) in brain and blood DNA, respectively (p < 0.0001). The comparison of cases with 4+ to 0–2 detectable levels of OGCs, identified 8 and 18 DML in brain and blood DNA, respectively (p < 0.0001). Pathway analyses revealed links to key neurotoxic and neuropathologic pathways related to impaired immune and proinflammatory responses as well as impaired clearance of damaged proteins, as found in the predominantly glial cell population in these environmental exposure-related PD cases. Conclusions These results suggest that distinct DNA methylation biomarker profiles related to environmental exposures in PD cases with previous exposure can be found in both brain and blood.
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Affiliation(s)
- Rodney C P Go
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Kuakini Health Systems, 347 N Kuakini St, Honolulu, HI, 96817, USA.,Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL, 35294, USA
| | - Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i at Manoa, 650 Ilalo St, Honolulu, HI, 96813, USA
| | - G Webster Ross
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Veterans Affairs Pacific Islands Health Care System, 459 Patterson Rd, Honolulu, HI, 96819, USA.,Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii at Manoa, 650 Ilalo St, Honolulu, HI, 96817, USA
| | - Helen Petrovitch
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Veterans Affairs Pacific Islands Health Care System, 459 Patterson Rd, Honolulu, HI, 96819, USA.,Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii at Manoa, 650 Ilalo St, Honolulu, HI, 96817, USA
| | - Kamal H Masaki
- Kuakini Health Systems, 347 N Kuakini St, Honolulu, HI, 96817, USA.,Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii at Manoa, 650 Ilalo St, Honolulu, HI, 96817, USA
| | - Alika K Maunakea
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i at Manoa, 650 Ilalo St, Honolulu, HI, 96813, USA
| | - Qimei He
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Kuakini Health Systems, 347 N Kuakini St, Honolulu, HI, 96817, USA.,Veterans Affairs Pacific Islands Health Care System, 459 Patterson Rd, Honolulu, HI, 96819, USA
| | - Maarit I Tiirikainen
- University of Hawaii Cancer Center, University of Hawaii at Manoa, 701 Ilalo St, Honolulu, HI, 96813, USA.
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22
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Hollander JA, Cory-Slechta DA, Jacka FN, Szabo ST, Guilarte TR, Bilbo SD, Mattingly CJ, Moy SS, Haroon E, Hornig M, Levin ED, Pletnikov MV, Zehr JL, McAllister KA, Dzierlenga AL, Garton AE, Lawler CP, Ladd-Acosta C. Beyond the looking glass: recent advances in understanding the impact of environmental exposures on neuropsychiatric disease. Neuropsychopharmacology 2020; 45:1086-1096. [PMID: 32109936 PMCID: PMC7234981 DOI: 10.1038/s41386-020-0648-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/17/2020] [Indexed: 12/22/2022]
Abstract
The etiologic pathways leading to neuropsychiatric diseases remain poorly defined. As genomic technologies have advanced over the past several decades, considerable progress has been made linking neuropsychiatric disorders to genetic underpinnings. Interest and consideration of nongenetic risk factors (e.g., lead exposure and schizophrenia) have, in contrast, lagged behind heritable frameworks of explanation. Thus, the association of neuropsychiatric illness to environmental chemical exposure, and their potential interactions with genetic susceptibility, are largely unexplored. In this review, we describe emerging approaches for considering the impact of chemical risk factors acting alone and in concert with genetic risk, and point to the potential role of epigenetics in mediating exposure effects on transcription of genes implicated in mental disorders. We highlight recent examples of research in nongenetic risk factors in psychiatric disorders that point to potential shared biological mechanisms-synaptic dysfunction, immune alterations, and gut-brain interactions. We outline new tools and resources that can be harnessed for the study of environmental factors in psychiatric disorders. These tools, combined with emerging experimental evidence, suggest that there is a need to broadly incorporate environmental exposures in psychiatric research, with the ultimate goal of identifying modifiable risk factors and informing new treatment strategies for neuropsychiatric disease.
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Affiliation(s)
- Jonathan A Hollander
- Genes, Environment and Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA.
| | - Deborah A Cory-Slechta
- Department of Environmental Medicine, Box EHSC, University of Rochester Medical Center, Rochester, NY, USA
| | - Felice N Jacka
- Food & Mood Centre, IMPACT SRC, School of Medicine, Deakin University, Geelong, VIC, Australia
- iMPACT (the Institute for Mental and Physical Health and Clinical Translation), Food & Mood Centre, Deakin University, Geelong, VIC, Australia
- Centre for Adolescent Health, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Black Dog Institute, Sydney, NSW, Australia
- James Cook University, Townsville, QLD, Australia
| | - Steven T Szabo
- Duke University Medical Center, Durham, NC, USA
- Durham Veterans Affairs Medical Center, Durham, NC, USA
| | - Tomás R Guilarte
- Department of Environmental Health Sciences Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Staci D Bilbo
- Department of Psychology & Neuroscience, Duke University, Durham, NC, USA
| | - Carolyn J Mattingly
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Sheryl S Moy
- Department of Psychiatry and Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ebrahim Haroon
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Mady Hornig
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Edward D Levin
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Mikhail V Pletnikov
- Departments of Psychiatry, Neuroscience, Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julia L Zehr
- Developmental Mechanisms and Trajectories of Psychopathology Branch, National Institute of Mental Health, NIH, Rockville, MD, USA
| | - Kimberly A McAllister
- Genes, Environment and Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Anika L Dzierlenga
- Genes, Environment and Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Amanda E Garton
- Genes, Environment and Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Cindy P Lawler
- Genes, Environment and Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology and Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins University, Baltimore, MD, USA
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23
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Yin W, Wang X, Li Y, Wang B, Song M, Hulbert A, Chen C, Yu F. Promoter hypermethylation of cysteine dioxygenase type 1 in patients with non-small cell lung cancer. Oncol Lett 2020; 20:967-973. [PMID: 32566027 DOI: 10.3892/ol.2020.11592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 02/28/2020] [Indexed: 12/19/2022] Open
Abstract
In the present study, promoter hypermethylation of cysteine dioxygenase type 1 (CDO1) was evaluated in non-small cell lung cancer (NSCLC) tissues to assess the value of CDO1 as a novel biomarker to improve the diagnosis of NSCLC. Tumor tissue samples and corresponding normal lung tissue samples from 42 patients with NSCLC were obtained at the Department of Thoracic Surgery, The Second Xiangya Hospital (Changsha, China). Conventional methylation-specific PCR (cMSP) and methylation-on-beads followed by quantitative methylation-specific PCR (MOB-qMSP) were used to analyze the tumor and normal lung tissue samples. Using these two methods, promoter DNA hypermethylation of the CDO1 gene was detected in 59.4 and 71.0% of tumor tissues of patients with NSCLC and in 9.4 and 0% of normal lung tissue, respectively. Compared with the rate of methylation in the well-differentiated NSCLC tissues (15.4 and 55.6%, respectively), the rate of CDO1 gene promoter methylation was higher in the poorly differentiated tissues (89.5 and 92.3%, respectively). Overall, it was demonstrated that the MOB-qMSP method had a higher positive detection rate for CDO1 hypermethylation compared with the cMSP method. In conclusion, CDO1 gene promoter hypermethylation was more frequently observed in NSCLC tissues compared with in normal lung tissues, and a high methylation frequency of the CDO1 gene in biopsy specimens of NSCLC was associated with the degree of differentiation.
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Affiliation(s)
- Wei Yin
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Yunping Li
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Bin Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Mingzhe Song
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Alicia Hulbert
- Department of Surgery, University of Illinois at Chicago School of Medicine, Chicago, IL 60607, USA
| | - Chen Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
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24
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Wu HC, Cohn BA, Cirillo PM, Santella RM, Terry MB. DDT exposure during pregnancy and DNA methylation alterations in female offspring in the Child Health and Development Study. Reprod Toxicol 2020; 92:138-147. [PMID: 30822522 PMCID: PMC6710160 DOI: 10.1016/j.reprotox.2019.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/07/2019] [Accepted: 02/25/2019] [Indexed: 12/14/2022]
Abstract
Studies measuring dichlorodiphenyltrichloroethane (DDT) exposure during key windows of susceptibility including the intrauterine period suggest that DDT exposure is associated with breast cancer risk. We hypothesized that prenatal DDT exposure is associated with DNA methylation. Using prospective data from 316 daughters in the Child Health and Development Study, we examined the association between prenatal exposure to DDTs and DNA methylation in blood collected in midlife (mean age: 49 years). To identify differentially methylated regions (DMRs) associated with markers of DDTs (p,p'-DDT and the primary metabolite of p,p'-DDT, p,p'-DDE, and o,p'-DDT, the primary constituents of technical DDT), we measured methylation in 30 genes important to breast cancer. We observed DDT DMRs in three genes, CCDC85A, CYP1A1 and ZFPM2, each of which has been previously implicated in pubertal development and breast cancer susceptibility. These findings suggest prenatal DDT exposure may have life-long consequence through alteration in genes relevant to breast cancer.
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Affiliation(s)
- Hui-Chen Wu
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NY
| | - Barbara A. Cohn
- Child Health and Development Studies, Public Health Institute, Berkeley, California
| | - Piera M. Cirillo
- Child Health and Development Studies, Public Health Institute, Berkeley, California
| | - Regina M. Santella
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NY
| | - Mary Beth Terry
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NY
- Imprints Center, Columbia University Medical Center, New York, NY
- Department of Epidemiology, Mailman School of Public Health of Columbia University, New York, NY
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25
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Kennedy E, Everson TM, Punshon T, Jackson BP, Hao K, Lambertini L, Chen J, Karagas MR, Marsit CJ. Copper associates with differential methylation in placentae from two US birth cohorts. Epigenetics 2020; 15:215-230. [PMID: 31462129 PMCID: PMC7028322 DOI: 10.1080/15592294.2019.1661211] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022] Open
Abstract
Copper is an essential trace nutrient and an enzymatic cofactor necessary for diverse physiological and biological processes. Copper metabolism is uniquely controlled in the placenta and changes to copper metabolism have been linked with adverse birth outcomes. We investigated associations between patterns of DNA methylation (DNAm; measured at >485 k CpG sites) and copper concentration measured from placentae in two independent mother-infant cohorts: the New Hampshire Birth Cohort Study (NHBCS, n = 306) and the Rhode Island Child Health Study (RICHS, n = 141). We identified nine copper-associated differentially methylated regions (DMRs; adjusted P < 0.05) and 15 suggestive CpGs (raw P < 1e-5). One of the most robust variably methylated CpGs associated with the expression of the antioxidant, GSTP1. Our most robust DMR negatively associates with the expression of the zinc-finger gene, ZNF197 (FDR = 4.5e-11). Genes co-expressed with ZNF197, a transcription factor, are enriched for genes that associate with birth weight in RICHS (OR = 2.9, P = 2.6e-6, N = 194), genes that are near a ZNF197 consensus binding motif (OR = 1.34, P = 0.01, N = 194), and for those classified in GO biological processes growth hormone secretion (P = 3.4e-4), multicellular organism growth (P = 3.8e-4), and molecular functions related to lipid biosynthesis (P = 1.9e-4). Further, putative transcriptional targets for ZNF197 include genes involved in copper metabolism and placentation. Our results suggest that copper metabolism is tied to DNAm in the placenta and that copper-associated patterns in DNAm may mediate normal placentation and foetal development.
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Affiliation(s)
- Elizabeth Kennedy
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Todd M. Everson
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Tracy Punshon
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Brian P. Jackson
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA
| | - Ke Hao
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luca Lambertini
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
- Children’s Environmental Health and Disease Prevention Research Center at Dartmouth, Dartmouth College, Lebanon, NH, USA
| | - Carmen J. Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Children’s Environmental Health and Disease Prevention Research Center at Dartmouth, Dartmouth College, Lebanon, NH, USA
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26
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Timms JA, Relton CL, Sharp GC, Rankin J, Strathdee G, McKay JA. Exploring a potential mechanistic role of DNA methylation in the relationship between in utero and post-natal environmental exposures and risk of childhood acute lymphoblastic leukaemia. Int J Cancer 2019; 145:2933-2943. [PMID: 30740682 PMCID: PMC6790139 DOI: 10.1002/ijc.32203] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 01/09/2019] [Accepted: 01/23/2019] [Indexed: 12/11/2022]
Abstract
The aetiology of childhood acute lymphoblastic leukaemia (ALL) is unclear. Genetic abnormalities have been identified in a number of ALL cases, although these alone are not sufficient for leukaemic transformation. Various in utero and post-natal environmental exposures have been suggested to alter risk of childhood ALL. DNA methylation patterns can be influenced by environmental exposures, and are reported to be altered in ALL, suggesting a potential mediating mechanism between environment and ALL disease risk. To investigate this, we used a 'meet in the middle' approach, investigating the overlap between exposure-associated and disease-associated methylation change. Genome-wide DNA methylation changes in response to possible ALL-risk exposures (i.e. breast feeding, infection history, day care attendance, maternal smoking, alcohol, caffeine, folic acid, iron and radiation exposure) were investigated in a sub-population of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort using an epigenome-wide association study (EWAS) approach (n = 861-927), and compared to a list of ALL disease-associated methylation changes compiled from published data. Hypergeometric probability tests suggested that the number of directionally concordant gene methylation changes observed in ALL disease and in response to the following exposures; maternal radiation exposure (p = 0.001), alcohol intake (p = 0.006); sugary caffeinated drink intake during pregnancy (p = 0.045); and infant day care attendance (p = 0.003), were not due to chance. Data presented suggests that DNA methylation may be one mediating mechanism in the multiple hit pathway needed for ALL disease manifestation.
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Affiliation(s)
- Jessica A Timms
- Institute of Health & Society, Newcastle University, Newcastle, United Kingdom
- Research Oncology, King's College London, Guy's Hospital, London
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Judith Rankin
- Research Oncology, King's College London, Guy's Hospital, London
| | - Gordon Strathdee
- Northern Institute for Cancer Research, Newcastle University, United Kingdom
| | - Jill A McKay
- Institute of Health & Society, Newcastle University, Newcastle, United Kingdom
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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27
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Cardenas A, Lutz SM, Everson TM, Perron P, Bouchard L, Hivert MF. Mediation by Placental DNA Methylation of the Association of Prenatal Maternal Smoking and Birth Weight. Am J Epidemiol 2019; 188:1878-1886. [PMID: 31497855 DOI: 10.1093/aje/kwz184] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 04/17/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023] Open
Abstract
Prenatal maternal smoking is a risk factor for lower birth weight. We performed epigenome-wide association analyses of placental DNA methylation (DNAm) at 720,077 cytosine-phosphate-guanine (CpG) sites and prenatal maternal smoking among 441 mother-infant pairs (2010-2014) and evaluated whether DNAm mediates the association between smoking and birth weight using mediation analysis. Mean birth weight was 3,443 (standard deviation, 423) g, and 38 mothers (8.6%) reported smoking at a mean of 9.4 weeks of gestation. Prenatal maternal smoking was associated with a 175-g lower birth weight (95% confidence interval (CI): -305.5, -44.8) and with differential DNAm of 71 CpGs in placenta, robust to latent-factor adjustment reflecting cell types (Bonferroni-adjusted P < 6.94 × 10-8). Of the 71 CpG sites, 7 mediated the association between prenatal smoking and birth weight (on MDS2, PBX1, CYP1A2, VPRBP, WBP1L, CD28, and CDK6 genes), and prenatal smoking × DNAm interactions on birth weight were observed for 5 CpG sites. The strongest mediator, cg22638236, was annotated to the PBX1 gene body involved in skeletal patterning and programming, with a mediated effect of 301-g lower birth weight (95% CI: -543, -86) among smokers but no mediated effect for nonsmokers (β = -38 g; 95% CI: -88, 9). Prenatal maternal smoking might interact with placental DNAm at specific loci, mediating the association with lower infant birth weight.
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Mørkve Knudsen GT, Rezwan FI, Johannessen A, Skulstad SM, Bertelsen RJ, Real FG, Krauss-Etschmann S, Patil V, Jarvis D, Arshad SH, Holloway JW, Svanes C. Epigenome-wide association of father's smoking with offspring DNA methylation: a hypothesis-generating study. ENVIRONMENTAL EPIGENETICS 2019; 5:dvz023. [PMID: 31827900 PMCID: PMC6896979 DOI: 10.1093/eep/dvz023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 08/22/2019] [Accepted: 11/04/2019] [Indexed: 05/23/2023]
Abstract
Epidemiological studies suggest that father's smoking might influence their future children's health, but few studies have addressed whether paternal line effects might be related to altered DNA methylation patterns in the offspring. To investigate a potential association between fathers' smoking exposures and offspring DNA methylation using epigenome-wide association studies. We used data from 195 males and females (11-54 years) participating in two population-based cohorts. DNA methylation was quantified in whole blood using Illumina Infinium MethylationEPIC Beadchip. Comb-p was used to analyse differentially methylated regions (DMRs). Robust multivariate linear models, adjusted for personal/maternal smoking and cell-type proportion, were used to analyse offspring differentially associated probes (DMPs) related to paternal smoking. In sensitivity analyses, we adjusted for socio-economic position and clustering by family. Adjustment for inflation was based on estimation of the empirical null distribution in BACON. Enrichment and pathway analyses were performed on genes annotated to cytosine-phosphate-guanine (CpG) sites using the gometh function in missMethyl. We identified six significant DMRs (Sidak-corrected P values: 0.0006-0.0173), associated with paternal smoking, annotated to genes involved in innate and adaptive immunity, fatty acid synthesis, development and function of neuronal systems and cellular processes. DMP analysis identified 33 CpGs [false discovery rate (FDR) < 0.05]. Following adjustment for genomic control (λ = 1.462), no DMPs remained epigenome-wide significant (FDR < 0.05). This hypothesis-generating study found that fathers' smoking was associated with differential methylation in their adolescent and adult offspring. Future studies are needed to explore the intriguing hypothesis that fathers' exposures might persistently modify their future offspring's epigenome.
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Affiliation(s)
- G T Mørkve Knudsen
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway
- Department of Occupational Medicine, Haukeland University Hospital, N-5021 Bergen, Norway
- Correspondence address. Haukanesvegen 260, N-5650 Tysse, Norway; Tel: +47 977 98 147; E-mail: and
| | - F I Rezwan
- Human Genetics and Genomic Medicine, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - A Johannessen
- Department of Occupational Medicine, Haukeland University Hospital, N-5021 Bergen, Norway
- Department of Global Public Health and Primary Care, Centre for International Health, University of Bergen, N-5018 Bergen, Norway
| | - S M Skulstad
- Department of Occupational Medicine, Haukeland University Hospital, N-5021 Bergen, Norway
| | - R J Bertelsen
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway
| | - F G Real
- Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway
| | - S Krauss-Etschmann
- Division of Experimental Asthma Research, Research Center Borstel, 23845 Borstel, Germany
- German Center for Lung Research (DZL) and Institute of Experimental Medicine, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - V Patil
- David Hide Asthma and Allergy Research Centre, St. Mary’s Hospital, Isle of Wight PO30 5TG, UK
| | - D Jarvis
- Faculty of Medicine, National Heart & Lung Institute, Imperial College, London SW3 6LY, UK
| | - S H Arshad
- Clinical and Experimental Sciences, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
- NIHR Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton SO16 6YD, UK
| | - J W Holloway
- Human Genetics and Genomic Medicine, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - C Svanes
- Department of Occupational Medicine, Haukeland University Hospital, N-5021 Bergen, Norway
- Department of Global Public Health and Primary Care, Centre for International Health, University of Bergen, N-5018 Bergen, Norway
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Smoking-Related DNA Methylation is Associated with DNA Methylation Phenotypic Age Acceleration: The Veterans Affairs Normative Aging Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16132356. [PMID: 31277270 PMCID: PMC6651499 DOI: 10.3390/ijerph16132356] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/29/2019] [Accepted: 07/01/2019] [Indexed: 12/17/2022]
Abstract
DNA methylation may play a critical role in aging and age-related diseases. DNA methylation phenotypic age (DNAmPhenoAge) is a new aging biomarker and predictor of chronic disease risk. While smoking is a strong risk factor for chronic diseases and influences methylation, its influence on DNAmPhenoAge is unknown. We investigated associations of self-reported and epigenetic smoking indicators with DNAmPhenoAge acceleration in a longitudinal aging study in eastern Massachusetts. DNA methylation was measured in whole blood samples from multiple visits for 692 male participants in the Veterans Affairs Normative Aging Study during 1999–2013. Acceleration was defined using residuals from linear regression of the DNAmPhenoAge on the chronological age. Cumulative smoking (pack-years) was significantly associated with DNAmPhenoAge acceleration, whereas self-reported smoking status was not. We observed significant validated associations between smoking-related loci and DNAmPhenoAge acceleration for 52 CpG sites, where 18 were hypomethylated and 34 were hypermethylated, mapped to 16 genes. The AHRR gene had the most loci (N = 8) among the 16 genes. We generated a smoking aging index based on these 52 loci, which showed positive significant associations with DNAmPhenoAge acceleration. These epigenetic biomarkers may help to predict age-related risks driven by smoking.
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Lekszas C, Nanda I, Vona B, Böck J, Ashrafzadeh F, Donyadideh N, Ebrahimzadeh F, Ahangari N, Maroofian R, Karimiani EG, Haaf T. Unbalanced segregation of a paternal t(9;11)(p24.3;p15.4) translocation causing familial Beckwith-Wiedemann syndrome: a case report. BMC Med Genomics 2019; 12:83. [PMID: 31174542 PMCID: PMC6555757 DOI: 10.1186/s12920-019-0539-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 05/28/2019] [Indexed: 01/29/2023] Open
Abstract
Background The vast majority of cases with Beckwith-Wiedemann syndrome (BWS) are caused by a molecular defect in the imprinted chromosome region 11p15.5. The underlying mechanisms include epimutations, uniparental disomy, copy number variations, and structural rearrangements. In addition, maternal loss-of-function mutations in CDKN1C are found. Despite growing knowledge on BWS pathogenesis, up to 20% of patients with BWS phenotype remain without molecular diagnosis. Case presentation Herein, we report an Iranian family with two females affected with BWS in different generations. Bisulfite pyrosequencing revealed hypermethylation of the H19/IGF2: intergenic differentially methylated region (IG DMR), also known as imprinting center 1 (IC1) and hypomethylation of the KCNQ1OT1: transcriptional start site (TSS) DMR (IC2). Array CGH demonstrated an 8 Mb duplication on chromosome 11p15.5p15.4 (205,827-8,150,933) and a 1 Mb deletion on chromosome 9p24.3 (209,020-1,288,114). Chromosome painting revealed that this duplication-deficiency in both patients is due to unbalanced segregation of a paternal reciprocal t(9;11)(p24.3;p15.4) translocation. Conclusions This is the first report of a paternally inherited unbalanced translocation between the chromosome 9 and 11 short arms underlying familial BWS. Copy number variations involving the 11p15.5 region are detected by the consensus diagnostic algorithm. However, in complex cases which do not only affect the BWS region itself, characterization of submicroscopic chromosome rearrangements can assist to estimate the recurrence risk and possible phenotypic outcomes.
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Affiliation(s)
- Caroline Lekszas
- Institute of Human Genetics, Julius Maximilians University Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Julia Böck
- Institute of Human Genetics, Julius Maximilians University Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Farah Ashrafzadeh
- Department of Pediatric Diseases, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nahid Donyadideh
- Department of Pediatric Diseases, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farnoosh Ebrahimzadeh
- Department of Internal Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Najmeh Ahangari
- Department of Modern Sciences and Technologies, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Maroofian
- Molecular and Clinical Sciences Institute, St. George's University of London, Cranmer Terrace, London, UK
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's University of London, Cranmer Terrace, London, UK
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany.
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Gruzieva O, Xu CJ, Yousefi P, Relton C, Merid SK, Breton CV, Gao L, Volk HE, Feinberg JI, Ladd-Acosta C, Bakulski K, Auffray C, Lemonnier N, Plusquin M, Ghantous A, Herceg Z, Nawrot TS, Pizzi C, Richiardi L, Rusconi F, Vineis P, Kogevinas M, Felix JF, Duijts L, den Dekker HT, Jaddoe VWV, Ruiz JL, Bustamante M, Antó JM, Sunyer J, Vrijheid M, Gutzkow KB, Grazuleviciene R, Hernandez-Ferrer C, Annesi-Maesano I, Lepeule J, Bousquet J, Bergström A, Kull I, Söderhäll C, Kere J, Gehring U, Brunekreef B, Just AC, Wright RJ, Peng C, Gold DR, Kloog I, DeMeo DL, Pershagen G, Koppelman GH, London SJ, Baccarelli AA, Melén E. Prenatal Particulate Air Pollution and DNA Methylation in Newborns: An Epigenome-Wide Meta-Analysis. ENVIRONMENTAL HEALTH PERSPECTIVES 2019; 127:57012. [PMID: 31148503 PMCID: PMC6792178 DOI: 10.1289/ehp4522] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Prenatal exposure to air pollution has been associated with childhood respiratory disease and other adverse outcomes. Epigenetics is a suggested link between exposures and health outcomes. OBJECTIVES We aimed to investigate associations between prenatal exposure to particulate matter (PM) with diameter [Formula: see text] ([Formula: see text]) or [Formula: see text] ([Formula: see text]) and DNA methylation in newborns and children. METHODS We meta-analyzed associations between exposure to [Formula: see text] ([Formula: see text]) and [Formula: see text] ([Formula: see text]) at maternal home addresses during pregnancy and newborn DNA methylation assessed by Illumina Infinium HumanMethylation450K BeadChip in nine European and American studies, with replication in 688 independent newborns and look-up analyses in 2,118 older children. We used two approaches, one focusing on single cytosine-phosphate-guanine (CpG) sites and another on differentially methylated regions (DMRs). We also related PM exposures to blood mRNA expression. RESULTS Six CpGs were significantly associated [false discovery rate (FDR) [Formula: see text]] with prenatal [Formula: see text] and 14 with [Formula: see text] exposure. Two of the [Formula: see text] CpGs mapped to FAM13A (cg00905156) and NOTCH4 (cg06849931) previously associated with lung function and asthma. Although these associations did not replicate in the smaller newborn sample, both CpGs were significant ([Formula: see text]) in 7- to 9-y-olds. For cg06849931, however, the direction of the association was inconsistent. Concurrent [Formula: see text] exposure was associated with a significantly higher NOTCH4 expression at age 16 y. We also identified several DMRs associated with either prenatal [Formula: see text] and or [Formula: see text] exposure, of which two [Formula: see text] DMRs, including H19 and MARCH11, replicated in newborns. CONCLUSIONS Several differentially methylated CpGs and DMRs associated with prenatal PM exposure were identified in newborns, with annotation to genes previously implicated in lung-related outcomes. https://doi.org/10.1289/EHP4522.
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Affiliation(s)
- Olena Gruzieva
- 1 Institute of Environmental Medicine, Karolinska Institutet , Stockholm, Sweden
- 2 Centre for Occupational and Environmental Medicine, Stockholm County Council , Stockholm, Sweden
| | - Cheng-Jian Xu
- 3 Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen , Netherlands
- 4 Department of Pediatric Pulmonology and Pediatric Allergology, University Medical Center Groningen, Beatrix Children's Hospital, University of Groningen , Netherlands
- 5 Department of Genetics, University Medical Center Groningen, University of Groningen , Netherlands
| | - Paul Yousefi
- 6 MRC Integrative Epidemiology Unit, University of Bristol , Bristol, UK
- 7 Population Health Sciences, Bristol Medical School, University of Bristol , Bristol, UK
| | - Caroline Relton
- 6 MRC Integrative Epidemiology Unit, University of Bristol , Bristol, UK
- 7 Population Health Sciences, Bristol Medical School, University of Bristol , Bristol, UK
| | - Simon Kebede Merid
- 1 Institute of Environmental Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Carrie V Breton
- 8 Department of Preventive Medicine, University of Southern California Los Angeles , Los Angeles, California, USA
| | - Lu Gao
- 8 Department of Preventive Medicine, University of Southern California Los Angeles , Los Angeles, California, USA
| | - Heather E Volk
- 9 Department of Mental Health, Johns Hopkins Bloomberg School of Public Health , Baltimore, Maryland, USA
- 10 Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health , Baltimore, Maryland, USA
| | - Jason I Feinberg
- 9 Department of Mental Health, Johns Hopkins Bloomberg School of Public Health , Baltimore, Maryland, USA
| | - Christine Ladd-Acosta
- 11 Department of Epidemiology, School of Public Health, University of Michigan , Ann Arbor, Michigan, USA
| | - Kelly Bakulski
- 11 Department of Epidemiology, School of Public Health, University of Michigan , Ann Arbor, Michigan, USA
| | - Charles Auffray
- 12 European Institute for Systems Biology and Medicine (EISBM), CNRS-ENS-UCBL, Université de Lyon , Lyon, France
| | - Nathanaël Lemonnier
- 12 European Institute for Systems Biology and Medicine (EISBM), CNRS-ENS-UCBL, Université de Lyon , Lyon, France
- 13 Institute for Advanced Biosciences, UGA-Institut national de la santé et de la recherché médicale (Inserm) , La Tronche, France
| | - Michelle Plusquin
- 14 Centre for Environmental Sciences, Hasselt University , Diepenbeek, Belgium
- 15 MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London , London, UK
| | - Akram Ghantous
- 16 Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Zdenko Herceg
- 16 Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Tim S Nawrot
- 14 Centre for Environmental Sciences, Hasselt University , Diepenbeek, Belgium
- 17 Department of Public Health & Primary Care, Leuven University , Leuven, Belgium
| | - Costanza Pizzi
- 18 Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO-Piemonte , Turin, Italy
| | - Lorenzo Richiardi
- 18 Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO-Piemonte , Turin, Italy
| | - Franca Rusconi
- 19 Unit of Epidemiology, Meyer Children's University Hospital , Florence, Italy
| | - Paolo Vineis
- 15 MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London , London, UK
| | - Manolis Kogevinas
- 20 Barcelona Institute for Global Health (ISGlobal) , Barcelona, Spain
- 22 CIBER Epidemiología y Salud Pública (CIBERESP) , Madrid, Spain
| | - Janine F Felix
- 23 Generation R Study Group, Erasmus MC (Medical Centre) , University Medical Center Rotterdam , Rotterdam, Netherlands
- 25 Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam , Rotterdam, Netherlands
| | - Liesbeth Duijts
- 23 Generation R Study Group, Erasmus MC (Medical Centre) , University Medical Center Rotterdam , Rotterdam, Netherlands
- 26 Department of Pediatrics, Divisions of Respiratory Medicine and Allergology, and Neonatology, Erasmus MC, University Medical Center , Rotterdam, Netherlands
| | - Herman T den Dekker
- 23 Generation R Study Group, Erasmus MC (Medical Centre) , University Medical Center Rotterdam , Rotterdam, Netherlands
- 25 Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam , Rotterdam, Netherlands
| | - Vincent W V Jaddoe
- 23 Generation R Study Group, Erasmus MC (Medical Centre) , University Medical Center Rotterdam , Rotterdam, Netherlands
- 25 Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam , Rotterdam, Netherlands
| | - José L Ruiz
- 27 Center for Genomic Regulation (CRG) , Barcelona, Spain
- 28 Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Spanish National Research Council (CSIC) , Armilla, Granada, Spain
| | - Mariona Bustamante
- 20 Barcelona Institute for Global Health (ISGlobal) , Barcelona, Spain
- 22 CIBER Epidemiología y Salud Pública (CIBERESP) , Madrid, Spain
- 27 Center for Genomic Regulation (CRG) , Barcelona, Spain
| | - Josep Maria Antó
- 20 Barcelona Institute for Global Health (ISGlobal) , Barcelona, Spain
- 22 CIBER Epidemiología y Salud Pública (CIBERESP) , Madrid, Spain
- 29 Hospital de Mar Medical Research Institute (IMIM) , Barcelona, Spain
| | - Jordi Sunyer
- 20 Barcelona Institute for Global Health (ISGlobal) , Barcelona, Spain
- 22 CIBER Epidemiología y Salud Pública (CIBERESP) , Madrid, Spain
- 29 Hospital de Mar Medical Research Institute (IMIM) , Barcelona, Spain
| | - Martine Vrijheid
- 20 Barcelona Institute for Global Health (ISGlobal) , Barcelona, Spain
- 22 CIBER Epidemiología y Salud Pública (CIBERESP) , Madrid, Spain
| | | | - Regina Grazuleviciene
- 31 Department of Environmental Sciences, Vytauto Didziojo Universitetas , Kaunas, Lithuania
| | - Carles Hernandez-Ferrer
- 20 Barcelona Institute for Global Health (ISGlobal) , Barcelona, Spain
- 32 Computational Health Informatics Program , Boston Children's Hospital , Boston, Massachusetts, USA
| | - Isabella Annesi-Maesano
- 33 Epidemiology of Allergic and Respiratory Diseases Department, IPLESP, Inserm and Sorbonne University Medical School Saint-Antoine , Paris, France
| | - Johanna Lepeule
- 34 Université Grenoble Alpes, Inserm, National Institute of Health & Medical Research, CNRS, IAB , Grenoble, France
| | - Jean Bousquet
- 35 Innovation Partnership on Active and Healthy Ageing Reference Site, MACVIA-France (Contre les Maladies Chroniques pour un Vieillissement Actif en France European) , Montpellier, France
- 36 U 1168, VIMA: Ageing and Chronic Diseases Epidemiological and Public Health Approaches, Inserm Villejuif, Université Versailles St-Quentin-en-Yvelines , Montigny le Bretonneux, France
| | - Anna Bergström
- 1 Institute of Environmental Medicine, Karolinska Institutet , Stockholm, Sweden
- 2 Centre for Occupational and Environmental Medicine, Stockholm County Council , Stockholm, Sweden
| | - Inger Kull
- 1 Institute of Environmental Medicine, Karolinska Institutet , Stockholm, Sweden
- 37 Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet , Stockholm, Sweden
- 38 Sachs Children's Hospital , Stockholm, Sweden
| | - Cilla Söderhäll
- 39 Department of Women's and Children's Health, Karolinska Institutet , Stockholm, Sweden
- 40 Department of Biosciences and Nutrition, Karolinska Institutet , Stockholm, Sweden
| | - Juha Kere
- 40 Department of Biosciences and Nutrition, Karolinska Institutet , Stockholm, Sweden
- 42 School of Basic and Medical Biosciences, King's College London, Guy's Hospital , London, UK
| | - Ulrike Gehring
- 44 Institute for Risk Assessment Sciences, Utrecht University , Utrecht, Netherlands
| | - Bert Brunekreef
- 44 Institute for Risk Assessment Sciences, Utrecht University , Utrecht, Netherlands
- 45 Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University , Utrecht, Netherlands
| | - Allan C Just
- 46 Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai , New York, USA
| | - Rosalind J Wright
- 47 Department of Pediatrics, Icahn School of Medicine at Mount Sinai , New York, USA
| | - Cheng Peng
- 48 Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts, USA
| | - Diane R Gold
- 48 Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts, USA
- 49 Department of Environmental Health, Harvard T.H. Chan School of Public Health , Boston, Massachusetts, USA
| | - Itai Kloog
- 50 Department of Geography and Environmental Development, Ben-Gurion University of the Negev , Beer Sheva, Israel
| | - Dawn L DeMeo
- 48 Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts, USA
| | - Göran Pershagen
- 1 Institute of Environmental Medicine, Karolinska Institutet , Stockholm, Sweden
- 2 Centre for Occupational and Environmental Medicine, Stockholm County Council , Stockholm, Sweden
| | - Gerard H Koppelman
- 3 Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen , Netherlands
- 4 Department of Pediatric Pulmonology and Pediatric Allergology, University Medical Center Groningen, Beatrix Children's Hospital, University of Groningen , Netherlands
| | - Stephanie J London
- 51 National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), U.S. Department of Health and Human Services , Research Triangle Park, North Carolina, USA
| | - Andrea A Baccarelli
- 52 Department of Environmental Health Sciences, Columbia University Mailman School of Public Health , New York, USA
| | - Erik Melén
- 1 Institute of Environmental Medicine, Karolinska Institutet , Stockholm, Sweden
- 38 Sachs Children's Hospital , Stockholm, Sweden
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Abstract
Purpose of review This review demonstrates the growing body of evidence connecting DNA methylation to prior exposure. It highlights the potential to use DNA methylation patterns as a feasible, stable, and accurate biomarker of past exposure, opening new opportunities for environmental and gene-environment interaction studies among existing banked samples. Recent findings We present the evidence for association between past exposure, including prenatal exposures, and DNA methylation measured at a later time in the life course. We demonstrate the potential utility of DNA methylation-based biomarkers of past exposure using results from multiple studies of smoking as an example. Multiple studies show the ability to accurately predict prenatal smoking exposure based on DNA methylation measured at birth, in childhood, and even adulthood. Separate sets of DNA methylation loci have been used to predict past personal smoking exposure (postnatal) as well. Further, it appears that these two types of exposures, prenatal and previous personal exposure, can be isolated from each other. There is also a suggestion that quantitative methylation scores may be useful for estimating dose. We highlight the remaining needs for rigor in methylation biomarker development including analytic challenges as well as the need for development across multiple developmental windows, multiple tissue types, and multiple ancestries. Summary If fully developed, DNA methylation-based biomarkers can dramatically shift our ability to carry out environmental and genetic-environmental epidemiology using existing biobanks, opening up unprecedented opportunities for environmental health.
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McCaulley ME. Autism spectrum disorder and mercury toxicity: use of genomic and epigenetic methods to solve the etiologic puzzle. Acta Neurobiol Exp (Wars) 2019. [DOI: 10.21307/ane-2019-010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Marioni RE, McRae AF, Bressler J, Colicino E, Hannon E, Li S, Prada D, Smith JA, Trevisi L, Tsai PC, Vojinovic D, Simino J, Levy D, Liu C, Mendelson M, Satizabal CL, Yang Q, Jhun MA, Kardia SLR, Zhao W, Bandinelli S, Ferrucci L, Hernandez DG, Singleton AB, Harris SE, Starr JM, Kiel DP, McLean RR, Just AC, Schwartz J, Spiro A, Vokonas P, Amin N, Ikram MA, Uitterlinden AG, van Meurs JBJ, Spector TD, Steves C, Baccarelli AA, Bell JT, van Duijn CM, Fornage M, Hsu YH, Mill J, Mosley TH, Seshadri S, Deary IJ. Meta-analysis of epigenome-wide association studies of cognitive abilities. Mol Psychiatry 2018; 23:2133-2144. [PMID: 29311653 PMCID: PMC6035894 DOI: 10.1038/s41380-017-0008-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/02/2017] [Accepted: 10/27/2017] [Indexed: 12/21/2022]
Abstract
Cognitive functions are important correlates of health outcomes across the life-course. Individual differences in cognitive functions are partly heritable. Epigenetic modifications, such as DNA methylation, are susceptible to both genetic and environmental factors and may provide insights into individual differences in cognitive functions. Epigenome-wide meta-analyses for blood-based DNA methylation levels at ~420,000 CpG sites were performed for seven measures of cognitive functioning using data from 11 cohorts. CpGs that passed a Bonferroni correction, adjusting for the number of CpGs and cognitive tests, were assessed for: longitudinal change; being under genetic control (methylation QTLs); and associations with brain health (structural MRI), brain methylation and Alzheimer's disease pathology. Across the seven measures of cognitive functioning (meta-analysis n range: 2557-6809), there were epigenome-wide significant (P < 1.7 × 10-8) associations for global cognitive function (cg21450381, P = 1.6 × 10-8), and phonemic verbal fluency (cg12507869, P = 2.5 × 10-9). The CpGs are located in an intergenic region on chromosome 12 and the INPP5A gene on chromosome 10, respectively. Both probes have moderate correlations (~0.4) with brain methylation in Brodmann area 20 (ventral temporal cortex). Neither probe showed evidence of longitudinal change in late-life or associations with white matter brain MRI measures in one cohort with these data. A methylation QTL analysis suggested that rs113565688 was a cis methylation QTL for cg12507869 (P = 5 × 10-5 and 4 × 10-13 in two lookup cohorts). We demonstrate a link between blood-based DNA methylation and measures of phonemic verbal fluency and global cognitive ability. Further research is warranted to understand the mechanisms linking genomic regulatory changes with cognitive function to health and disease.
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Affiliation(s)
- Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Elena Colicino
- Columbia University Mailman School of Public Health, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Shuo Li
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Diddier Prada
- Instituto Nacional de Cancerologia, Mexico City, Mexico
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | | | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeannette Simino
- Department of Data Science, School of Population Health, University of Mississippi Medical Center, Jackson, MS, USA
- MIND Center, University of Mississippi Medical Center, Jackson, MS, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Mendelson
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Boston University School of Medicine, Boston, MA, USA
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Claudia L Satizabal
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Min A Jhun
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - Luigi Ferrucci
- Clinical Research Branch, National Institute on Aging, Baltimore, MD, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Douglas P Kiel
- Harvard Medical School, Boston, MA, USA
- Hebrew SeniorLife Institute for Aging Research, Boston, MA, USA
| | - Robert R McLean
- Harvard Medical School, Boston, MA, USA
- Hebrew SeniorLife Institute for Aging Research, Boston, MA, USA
| | - Allan C Just
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joel Schwartz
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Avron Spiro
- Boston University Schools of Public Health and Medicine, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Pantel Vokonas
- Boston University Schools of Public Health and Medicine, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Departments of Radiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce B J van Meurs
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Myriam Fornage
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yi-Hsiang Hsu
- Harvard Medical School, Boston, MA, USA
- Hebrew SeniorLife Institute for Aging Research, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Mill
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas H Mosley
- MIND Center, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Medicine, Division of Geriatrics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute of Alzheimer and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
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de Oliveira AAF, de Oliveira TF, Dias MF, Medeiros MHG, Di Mascio P, Veras M, Lemos M, Marcourakis T, Saldiva PHN, Loureiro APM. Genotoxic and epigenotoxic effects in mice exposed to concentrated ambient fine particulate matter (PM 2.5) from São Paulo city, Brazil. Part Fibre Toxicol 2018; 15:40. [PMID: 30340610 PMCID: PMC6194750 DOI: 10.1186/s12989-018-0276-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/03/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The Metropolitan Area of São Paulo has a unique composition of atmospheric pollutants, and positive correlations between exposure and the risk of diseases and mortality have been observed. Here we assessed the effects of ambient fine particulate matter (PM2.5) on genotoxic and global DNA methylation and hydroxymethylation changes, as well as the activities of antioxidant enzymes, in tissues of AJ mice exposed whole body to ambient air enriched in PM2.5, which was concentrated in a chamber near an avenue of intense traffic in São Paulo City, Brazil. RESULTS Mice exposed to concentrated ambient PM2.5 (1 h daily, 3 months) were compared to in situ ambient air exposed mice as the study control. The concentrated PM2.5 exposed group presented increased levels of the oxidized nucleoside 8-oxo-7,8-dihydro-2'-deoxyguanosine in lung and kidney DNA and increased levels of the etheno adducts 1,N6-etheno-2'-deoxyadenosine and 1,N2-etheno-2'-deoxyguanosine in kidney and liver DNA, respectively. Apart from the genotoxic effects, the exposure to PM2.5 led to decreased levels of the epigenetic mark 5-hydroxymethylcytosine (5-hmC) in lung and liver DNA. Changes in lung, liver, and erythrocyte antioxidant enzyme activities were also observed. Decreased glutathione reductase and increased superoxide dismutase (SOD) activities were observed in the lungs, while the liver presented increased glutathione S-transferase and decreased SOD activities. An increase in SOD activity was also observed in erythrocytes. These changes are consistent with the induction of local and systemic oxidative stress. CONCLUSIONS Mice exposed daily to PM2.5 at a concentration that mimics 24-h exposure to the mean concentration found in ambient air presented, after 3 months, increased levels of DNA lesions related to the occurrence of oxidative stress in the lungs, liver, and kidney, in parallel to decreased global levels of 5-hmC in lung and liver DNA. Genetic and epigenetic alterations induced by pollutants may affect the genes committed to cell cycle control, apoptosis, and cell differentiation, increasing the chance of cancer development, which merits further investigation.
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Affiliation(s)
- Antonio Anax Falcão de Oliveira
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes 580, Bloco 13 B, São Paulo, CEP 05508-000 Brazil
| | - Tiago Franco de Oliveira
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes 580, Bloco 13 B, São Paulo, CEP 05508-000 Brazil
- Present address: Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Rua Sarmento Leite 245, Porto Alegre, Rio Grande do Sul CEP 90050-170 Brazil
| | - Michelle Francini Dias
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes 580, Bloco 13 B, São Paulo, CEP 05508-000 Brazil
| | - Marisa Helena Gennari Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, CEP 05508-000 Brazil
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, CEP 05508-000 Brazil
| | - Mariana Veras
- Laboratório de Poluição Atmosférica Experimental – LIM05, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Arnaldo 455, São Paulo, CEP 01246903 Brazil
| | - Miriam Lemos
- Laboratório de Poluição Atmosférica Experimental – LIM05, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Arnaldo 455, São Paulo, CEP 01246903 Brazil
| | - Tania Marcourakis
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes 580, Bloco 13 B, São Paulo, CEP 05508-000 Brazil
| | - Paulo Hilário Nascimento Saldiva
- Laboratório de Poluição Atmosférica Experimental – LIM05, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Arnaldo 455, São Paulo, CEP 01246903 Brazil
- Instituto de Estudos Avançados, Universidade de São Paulo, R. do Anfiteatro, 513, São Paulo, CEP 05508060 Brazil
| | - Ana Paula Melo Loureiro
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes 580, Bloco 13 B, São Paulo, CEP 05508-000 Brazil
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Huang Y, Hui Q, Walker DI, Uppal K, Goldberg J, Jones DP, Vaccarino V, Sun YV. Untargeted metabolomics reveals multiple metabolites influencing smoking-related DNA methylation. Epigenomics 2018; 10:379-393. [PMID: 29528243 PMCID: PMC5925442 DOI: 10.2217/epi-2017-0101] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 11/27/2017] [Indexed: 12/20/2022] Open
Abstract
AIM We conducted a joint metabolomic-epigenomic study to identify patterns of epigenetic associations with smoking-related metabolites. PATIENTS & METHODS We performed an untargeted metabolome-wide association study of smoking and epigenome-wide association studies of smoking-related metabolites among 180 male twins. We examined the patterns of epigenetic association linked to smoking-related metabolites using hierarchical clustering. RESULTS Among 12 annotated smoking-related metabolites identified from a metabolome-wide association study, we observed significant hypomethylation associated with increased level of N-acetylpyrrolidine, cotinine, 5-hydroxycotinine and nicotine and hypermethylation associated with increased level of 8-oxoguanine. Hierarchical clustering revealed common and unique epigenetic-metabolic associations related to smoking. CONCLUSION Our study suggested that a joint metabolome-epigenome approach can reveal additional details in molecular responses to the environmental exposure to understand disease risk.
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Affiliation(s)
- Yunfeng Huang
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA
| | - Douglas I Walker
- Department of Medicine, Division of Pulmonary, Allergy & Critical Care Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Karan Uppal
- Department of Medicine, Division of Pulmonary, Allergy & Critical Care Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jack Goldberg
- Vietnam Era Twin Registry, VA Epidemiologic Research & Information Center & Department of Epidemiology, University of Washington School of Public Health, Seattle, WA 98195, USA
| | - Dean P Jones
- Department of Medicine, Division of Pulmonary, Allergy & Critical Care Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Viola Vaccarino
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Hertz-Picciotto I, Schmidt RJ, Krakowiak P. Understanding environmental contributions to autism: Causal concepts and the state of science. Autism Res 2018; 11:554-586. [PMID: 29573218 DOI: 10.1002/aur.1938] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/12/2017] [Accepted: 10/19/2017] [Indexed: 11/06/2022]
Abstract
The complexity of neurodevelopment, the rapidity of early neurogenesis, and over 100 years of research identifying environmental influences on neurodevelopment serve as backdrop to understanding factors that influence risk and severity of autism spectrum disorder (ASD). This Keynote Lecture, delivered at the May 2016 annual meeting of the International Society for Autism Research, describes concepts of causation, outlines the trajectory of research on nongenetic factors beginning in the 1960s, and briefly reviews the current state of this science. Causal concepts are introduced, including root causes; pitfalls in interpreting time trends as clues to etiologic factors; susceptible time windows for exposure; and implications of a multi-factorial model of ASD. An historical background presents early research into the origins of ASD. The epidemiologic literature from the last fifteen years is briefly but critically reviewed for potential roles of, for example, air pollution, pesticides, plastics, prenatal vitamins, lifestyle and family factors, and maternal obstetric and metabolic conditions during her pregnancy. Three examples from the case-control CHildhood Autism Risks from Genes and the Environment Study are probed to illustrate methodological approaches to central challenges in observational studies: capturing environmental exposure; causal inference when a randomized controlled clinical trial is either unethical or infeasible; and the integration of genetic, epigenetic, and environmental influences on development. We conclude with reflections on future directions, including exposomics, new technologies, the microbiome, gene-by-environment interaction in the era of -omics, and epigenetics as the interface of those two. As the environment is malleable, this research advances the goal of a productive and fulfilling life for all children, teen-agers and adults. Autism Res 2018, 11: 554-586. © 2018 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY This Keynote Lecture, delivered at the 2016 meeting of the International Society for Autism Research, discusses evidence from human epidemiologic studies of prenatal factors contributing to autism, such as pesticides, maternal nutrition and her health. There is no single cause for autism. Examples highlight the features of a high-quality epidemiology study, and what comprises a compelling case for causation. Emergent research directions hold promise for identifying potential interventions to reduce disabilities, enhance giftedness, and improve lives of those with ASD.
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Affiliation(s)
- Irva Hertz-Picciotto
- Department of Public Health Sciences, MIND Institute (Medical Investigations of Neurodevelopmental Disorders), University of California, Davis, Davis, California
| | - Rebecca J Schmidt
- Department of Public Health Sciences, MIND Institute (Medical Investigations of Neurodevelopmental Disorders), University of California, Davis, Davis, California
| | - Paula Krakowiak
- Department of Public Health Sciences, MIND Institute (Medical Investigations of Neurodevelopmental Disorders), University of California, Davis, Davis, California
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Clarke MA, Joshu CE. Early Life Exposures and Adult Cancer Risk. Epidemiol Rev 2018; 39:11-27. [PMID: 28407101 DOI: 10.1093/epirev/mxx004] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/19/2017] [Indexed: 12/14/2022] Open
Abstract
Very little is known about the influence of early life exposures on adult cancer risk. The purpose of this narrative review was to summarize the epidemiologic evidence relating early life tobacco use, obesity, diet, and physical activity to adult cancer risk; describe relevant theoretical frameworks and methodological strategies for studying early life exposures; and discuss policies and research initiatives focused on early life. Our findings suggest that in utero exposures may indirectly influence cancer risk by modifying biological pathways associated with carcinogenesis; however, more research is needed to firmly establish these associations. Initiation of exposures during childhood and adolescence may impact cancer risk by increasing duration and lifetime exposure to carcinogens and/or by acting during critical developmental periods. To expand the evidence base, we encourage the use of life course frameworks, causal inference methods such as Mendelian randomization, and statistical approaches such as group-based trajectory modeling in future studies. Further, we emphasize the need for objective exposure biomarkers and valid surrogate endpoints to reduce misclassification. With the exception of tobacco use, there is insufficient evidence to support the development of new cancer prevention policies; however, we highlight existing policies that may reduce the burden of these modifiable risk factors in early life.
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Bae JM. Interpretation of the hygiene and microflora hypothesis for allergic diseases through epigenetic epidemiology. Epidemiol Health 2018; 40:e2018006. [PMID: 29587338 PMCID: PMC5968202 DOI: 10.4178/epih.e2018006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/10/2018] [Indexed: 01/08/2023] Open
Abstract
The hygiene hypothesis (HH) proposed by Strachan in 1989 was expanded to explain the inverse association between the occurrence of allergy disorders and the risk of infectious diseases and parasite infestation. The microflora hypothesis (MH) suggests that gut microbial dysbiosis in early life might trigger hypersensitivity disorders. The sharing concept of both HH and MH is gene-environment interaction, which is also a key concept in epigenetics. The amalgamation of epidemiology and epigenetics has created a scientific discipline termed epigenetic epidemiology. To accomplish an era of gene-environment-wide interaction studies, it is necessary to launch a national human epigenome project.
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Affiliation(s)
- Jong-Myon Bae
- Department of Preventive Medicine, Jeju National University School of Medicine, Jeju, Korea
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Abstract
Even though the importance of epigenetics was first recognized in light of its role in tissue development, an increasing amount of evidence has shown that it also plays an important role in the development and progression of many common diseases. We discuss some recent findings on one representative epigenetic modification, DNA methylation, in some common diseases. While many new risk factors have been identified through the population-based epigenetic epidemiologic studies on the role of epigenetics in common diseases, this relatively new field still faces many unique challenges. Here, we describe those promises and unique challenges of epigenetic epidemiological studies and propose some potential solutions.
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Affiliation(s)
| | - Yun Liu
- The Ministry of Education Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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Dou J, Schmidt RJ, Benke KS, Newschaffer C, Hertz-Picciotto I, Croen LA, Iosif AM, LaSalle JM, Fallin MD, Bakulski KM. Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation. Epigenetics 2018; 13:108-116. [PMID: 29451060 PMCID: PMC5836975 DOI: 10.1080/15592294.2017.1417710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/29/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022] Open
Abstract
Cord blood DNA methylation is associated with numerous health outcomes and environmental exposures. Whole cord blood DNA reflects all nucleated blood cell types, while centrifuging whole blood separates red blood cells, generating a white blood cell buffy coat. Both sample types are used in DNA methylation studies. Cell types have unique methylation patterns and processing can impact cell distributions, which may influence comparability. We evaluated differences in cell composition and DNA methylation between cord blood buffy coat and whole cord blood samples. Cord blood DNA methylation was measured with the Infinium EPIC BeadChip (Illumina) in eight individuals, each contributing buffy coat and whole blood samples. We analyzed principal components (PC) of methylation, performed hierarchical clustering, and computed correlations of mean-centered methylation between pairs. We conducted moderated t-tests on single sites and estimated cell composition. DNA methylation PCs were associated with individual (PPC1 = 1.4 × 10-9; PPC2 = 2.9 × 10-5; PPC3 = 3.8 × 10-5; PPC4 = 4.2 × 10-6; PPC5 = 9.9 × 10-13, PPC6 = 1.3 × 10-11) and not with sample type (PPC1-6>0.7). Samples hierarchically clustered by individual. Pearson correlations of mean-centered methylation between paired samples ranged from r = 0.66 to r = 0.87. No individual site significantly differed between buffy coat and whole cord blood when adjusting for multiple comparisons (five sites had unadjusted P<10-5). Estimated cell type proportions did not differ by sample type (P = 0.46), and estimated proportions were highly correlated between paired samples (r = 0.99). Differences in methylation and cell composition between buffy coat and whole cord blood are much lower than inter-individual variation, demonstrating that both sample preparation types can be analytically combined and compared.
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Affiliation(s)
- John Dou
- Department of Epidemiology, School of Public Health, University of Michigan
| | - Rebecca J. Schmidt
- Department of Public Health Sciences, University of California Davis
- University of California Davis, MIND Institute
| | - Kelly S. Benke
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University
| | - Craig Newschaffer
- Department of Epidemiology and Biostatistics, Dornsife School of Public Health, Drexel University
- A.J. Drexel Autism Institute, Drexel University
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, University of California Davis
- University of California Davis, MIND Institute
| | | | - Ana-Maria Iosif
- Department of Public Health Sciences, University of California Davis
- University of California Davis, MIND Institute
| | - Janine M. LaSalle
- University of California Davis, MIND Institute
- Department of Medical Microbiology and Immunology, Genome Center, University of California Davis
| | - M. Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins University
| | - Kelly M. Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan
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Felix JF, Joubert BR, Baccarelli AA, Sharp GC, Almqvist C, Annesi-Maesano I, Arshad H, Baïz N, Bakermans-Kranenburg MJ, Bakulski KM, Binder EB, Bouchard L, Breton CV, Brunekreef B, Brunst KJ, Burchard EG, Bustamante M, Chatzi L, Cheng Munthe-Kaas M, Corpeleijn E, Czamara D, Dabelea D, Davey Smith G, De Boever P, Duijts L, Dwyer T, Eng C, Eskenazi B, Everson TM, Falahi F, Fallin MD, Farchi S, Fernandez MF, Gao L, Gaunt TR, Ghantous A, Gillman MW, Gonseth S, Grote V, Gruzieva O, Håberg SE, Herceg Z, Hivert MF, Holland N, Holloway JW, Hoyo C, Hu D, Huang RC, Huen K, Järvelin MR, Jima DD, Just AC, Karagas MR, Karlsson R, Karmaus W, Kechris KJ, Kere J, Kogevinas M, Koletzko B, Koppelman GH, Küpers LK, Ladd-Acosta C, Lahti J, Lambrechts N, Langie SAS, Lie RT, Liu AH, Magnus MC, Magnus P, Maguire RL, Marsit CJ, McArdle W, Melén E, Melton P, Murphy SK, Nawrot TS, Nisticò L, Nohr EA, Nordlund B, Nystad W, Oh SS, Oken E, Page CM, Perron P, Pershagen G, Pizzi C, Plusquin M, Raikkonen K, Reese SE, Reischl E, Richiardi L, Ring S, Roy RP, Rzehak P, Schoeters G, Schwartz DA, Sebert S, Snieder H, Sørensen TIA, Starling AP, Sunyer J, Taylor JA, Tiemeier H, Ullemar V, Vafeiadi M, Van Ijzendoorn MH, Vonk JM, Vriens A, Vrijheid M, Wang P, Wiemels JL, Wilcox AJ, Wright RJ, Xu CJ, Xu Z, Yang IV, Yousefi P, Zhang H, Zhang W, Zhao S, Agha G, Relton CL, Jaddoe VWV, London SJ. Cohort Profile: Pregnancy And Childhood Epigenetics (PACE) Consortium. Int J Epidemiol 2018; 47:22-23u. [PMID: 29025028 PMCID: PMC5837319 DOI: 10.1093/ije/dyx190] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2017] [Indexed: 12/21/2022] Open
Affiliation(s)
- Janine F Felix
- Department of Epidemiology, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Generation R Study Group Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bonnie R Joubert
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Isabella Annesi-Maesano
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP UMRS 1136), Epidemiology of Allergic and Respiratory diseases department (EPAR), Medical School Saint-Antoine, Paris, France
| | - Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nour Baïz
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP UMRS 1136), Epidemiology of Allergic and Respiratory diseases department (EPAR), Medical School Saint-Antoine, Paris, France
| | | | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, USA
| | - Elisabeth B Binder
- Department Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Luigi Bouchard
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- ECOGENE-21 and Lipid Clinic, Chicoutimi Hospital, Saguenay, QC, Canada
| | - Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Bert Brunekreef
- Institute for Risk Assessment Sciences, Universiteit Utrecht, Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kelly J Brunst
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Mariona Bustamante
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Genomics and Disease Group, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Leda Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Monica Cheng Munthe-Kaas
- Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Norwegian Institute of Public Health, Oslo, Norway
| | - Eva Corpeleijn
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Darina Czamara
- Department Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Life Course Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Patrick De Boever
- Environmental Risk and Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Faculty of Sciences, Hasselt University, Diepenbeek, Belgium
| | - Liesbeth Duijts
- Department of Epidemiology, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Generation R Study Group Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Terence Dwyer
- The George Institute for Global Health, Nuffield Department of Obstetrics & Gynaecology, University of Oxford, Oxford, United Kingdom
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research on Children's Health, University of California, Berkeley, CA, USA
| | - Todd M Everson
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, USA
| | - Fahimeh Falahi
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA
| | - Sara Farchi
- Department of Epidemiology, Regional Health Service, Lazio Region, Rome, Italy
| | - Mariana F Fernandez
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, University of Granada, San Cecilio University Hospital, Granada, Spain
| | - Lu Gao
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Matthew W Gillman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Semira Gonseth
- University of California, Berkeley, School of Public Health, Berkeley, USA
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Nina Holland
- Center for Environmental Research on Children's Health, University of California, Berkeley, CA, USA
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, CA, USA
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Karen Huen
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, CA, USA
| | - Marjo-Riitta Järvelin
- Center For Lifecourse Health Research, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Allan C Just
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, USA
| | - Katerina J Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Manolis Kogevinas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Gerard H Koppelman
- University of Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, The Netherlands
| | - Leanne K Küpers
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA
| | - Jari Lahti
- Department of Psychology and Logopedics, Faulty of Medicine, University of Helsinki, Helsinki, Finland
- Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
| | - Nathalie Lambrechts
- Environmental Risk and Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Sabine AS Langie
- Environmental Risk and Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Faculty of Sciences, Hasselt University, Diepenbeek, Belgium
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Andrew H Liu
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Children's Hospital Colorado, Aurora, CO, USA
| | - Maria C Magnus
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- Department for Non-Communicable Diseases, Domain for Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Magnus
- Norwegian Institute of Public Health, Oslo, Norway
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, USA
| | - Wendy McArdle
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Sachs Children’s Hospital, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Phillip Melton
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health Sciences, Curtin University and Faculty of Medicine Dentistry & Health Sciences, The University of Western Australia, Perth, Australia
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- Department of Public Health & Primary Care, Leuven University, Leuven, Belgium
| | - Lorenza Nisticò
- National Center of Epidemiology, Surveillance and Health Promotion, Istituto Superiore di Sanità, Rome, Italy
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Björn Nordlund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
| | | | - Sam S Oh
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Patrice Perron
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Costanza Pizzi
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- MRC/PHE Centre for Environment and Health School of Public Health, Imperial College London, London, UK
| | - Katri Raikkonen
- Department of Psychology and Logopedics, Faulty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sarah E Reese
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, USA
| | - Eva Reischl
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum Muenchen, Munich, Germany
| | - Lorenzo Richiardi
- Department of Medical Sciences, University of Turin, Turin, Italy
- AOU Città della Salute e della Sceinza, CPO Piemonte, Turin, Italy
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Ritu P Roy
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), UCSF, San Francisco, CA, USA
- Computational Biology Core, UCSF, San Francisco, CA, USA
| | - Peter Rzehak
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Greet Schoeters
- Environmental Risk and Health Unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
- Department of Environmental Medicine, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - David A Schwartz
- Department of Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sylvain Sebert
- Center For Lifecourse Health Research, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Genomics of Complex Diseases, School of Public Health, Imperial College London, London, United Kingdom
| | - Harold Snieder
- Generation R Study Group Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Thorkild IA Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, and Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Epidemiology (formerly Institute of Preventive Medicine), Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Anne P Starling
- Department of Epidemiology, Colorado School of Public Health
- Life Course Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jordi Sunyer
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jack A Taylor
- National Institute of Environmental Health Sciences, Epidemiology Branch, Durham, NC, USA
| | - Henning Tiemeier
- Department of Epidemiology, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Marina Vafeiadi
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Marinus H Van Ijzendoorn
- Centre for Child and Family Studies, Leiden University, Leiden, The Netherlands
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, GRIAC Research Institute Groningen, the Netherlands
| | - Annette Vriens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Martine Vrijheid
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA
- Department of Neurosurgery, UCSF, San Francisco, CA, USA
| | - Allen J Wilcox
- National Institute of Environmental Health Sciences, Epidemiology Branch, Durham, NC, USA
| | - Rosalind J Wright
- Department of Pediatrics, Kravis Children's Hospital, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Zongli Xu
- National Institute of Environmental Health Sciences, Epidemiology Branch, Durham, NC, USA
| | - Ivana V Yang
- Department of Epidemiology, Colorado School of Public Health
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Paul Yousefi
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, CA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, USA
| | - Weiming Zhang
- Life Course Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Shanshan Zhao
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, USA
| | - Golareh Agha
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Vincent WV Jaddoe
- Department of Epidemiology, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Generation R Study Group Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, USA
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Everson TM, Punshon T, Jackson BP, Hao K, Lambertini L, Chen J, Karagas MR, Marsit CJ. Cadmium-Associated Differential Methylation throughout the Placental Genome: Epigenome-Wide Association Study of Two U.S. Birth Cohorts. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:017010. [PMID: 29373860 PMCID: PMC6014712 DOI: 10.1289/ehp2192] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cadmium (Cd) is a ubiquitous environmental toxicant that can accumulate in the placenta during pregnancy, where it may impair placental function and affect fetal development. OBJECTIVES We aimed to investigate Cd-associated variations in placental DNA methylation (DNAM) and associations with gene expression; we also aimed to identify novel pathways involved in Cd-associated reproductive toxicity. METHODS Using placental DNAM and Cd concentrations in the New Hampshire Birth Cohort Study (NHBCS, n=343) and the Rhode Island Child Health Study (RICHS, n=141), we performed an epigenome-wide association study (EWAS) between Cd and DNAM, adjusting for tissue heterogeneity using a reference-free method. Cohort-specific results were aggregated via inverse variance weighted fixed effects meta-analysis, and variably methylated CpGs were associated with gene expression. We then performed functional enrichment analysis and tests for associations between gene expression and birth size metrics. RESULTS We identified 17 Cd-associated differentially methylated CpG sites with meta-analysis p-values<1×10−5, two of which were within a 5% false discovery rate (FDR). DNAM levels at 9 of the 17 loci were associated with increased expression of 6 genes (5% FDR): TNFAIP2, EXOC3L4, GAS7, SREBF1, ACOT7, and RORA. Higher placental expression of TNFAIP2 and ACOT7 and lower expression of RORA were associated with lower birth weight z-scores (p-values<0.05). CONCLUSION Cd-associated differential DNAM and corresponding DNAM-expression associations were observed at loci involved in inflammatory signaling and cell growth. The expression levels of genes involved in inflammatory signaling (TNFAIP2, ACOT7, and RORA) were also associated with birth weight, suggesting a role for inflammatory processes in Cd-associated reproductive toxicity. https://doi.org/10.1289/EHP2192.
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Affiliation(s)
- Todd M Everson
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Tracy Punshon
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Brian P Jackson
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Ke Hao
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luca Lambertini
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire, USA
- Children’s Environmental Health and Disease Prevention Research Center at Dartmouth, Dartmouth College, Lebanon, New Hampshire, USA
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Children’s Environmental Health and Disease Prevention Research Center at Dartmouth, Dartmouth College, Lebanon, New Hampshire, USA
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44
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Agarwal P, Morriseau TS, Kereliuk SM, Doucette CA, Wicklow BA, Dolinsky VW. Maternal obesity, diabetes during pregnancy and epigenetic mechanisms that influence the developmental origins of cardiometabolic disease in the offspring. Crit Rev Clin Lab Sci 2018; 55:71-101. [DOI: 10.1080/10408363.2017.1422109] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Prasoon Agarwal
- Department of Pharmacology & Therapeutics, University of Manitoba, Winnipeg, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
| | - Taylor S. Morriseau
- Department of Pharmacology & Therapeutics, University of Manitoba, Winnipeg, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
| | - Stephanie M. Kereliuk
- Department of Pharmacology & Therapeutics, University of Manitoba, Winnipeg, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
| | - Christine A. Doucette
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
- Department of Physiology & Pathophysiology, University of Manitoba, Winnipeg, Canada
| | - Brandy A. Wicklow
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
- Department of Pediatrics & Child Health, University of Manitoba, Winnipeg, Canada
| | - Vernon W. Dolinsky
- Department of Pharmacology & Therapeutics, University of Manitoba, Winnipeg, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
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45
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Gao X, Zhang Y, Breitling LP, Brenner H. Relationship of tobacco smoking and smoking-related DNA methylation with epigenetic age acceleration. Oncotarget 2018; 7:46878-46889. [PMID: 27276709 PMCID: PMC5216910 DOI: 10.18632/oncotarget.9795] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/14/2016] [Indexed: 01/05/2023] Open
Abstract
Recent studies have identified biomarkers of chronological age based on DNA methylation levels. Since active smoking contributes to a wide spectrum of aging-related diseases in adults, this study intended to examine whether active smoking exposure could accelerate the DNA methylation age in forms of age acceleration (AA, residuals of the DNA methylation age estimate regressed on chronological age). We obtained the DNA methylation profiles in whole blood samples by Illumina Infinium Human Methylation450 Beadchip array in two independent subsamples of the ESTHER study and calculated their DNA methylation ages by two recently proposed algorithms. None of the self-reported smoking indicators (smoking status, cumulative exposure and smoking cessation time) or serum cotinine levels was significantly associated with AA. On the contrary, we successfully confirmed that 66 out of 150 smoking-related CpG sites were associated with AA, even after correction for multiple testing (FDR <0.05). We further built a smoking index (SI) based on these loci and demonstrated a monotonic dose-response relationship of this index with AA. In conclusion, DNA methylation-based biological indicators for current and past smoking exposure, but not self-reported smoking information or serum cotinine levels, were found to be related to DNA methylation defined AA. Further research should address potential mechanisms underlying the observed patterns, such as potential reflections of susceptibility to environmental hazards in both smoking related methylation changes and methylation defined AA.
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Affiliation(s)
- Xu Gao
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lutz Philipp Breitling
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Pneumology and Respiratory Critical Care Medicine, Thoraxklinik, University of Heidelberg, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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46
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Mighdoll MI, Hyde TM. Brain donation at autopsy: clinical characterization and toxicologic analyses. HANDBOOK OF CLINICAL NEUROLOGY 2018; 150:143-154. [PMID: 29496137 DOI: 10.1016/b978-0-444-63639-3.00011-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The study of postmortem human brain tissue is central to the advancement of neurobiologic studies of psychiatric and neurologic illnesses, particularly the study of brain-specific isoforms and molecules. Due to tissue demands, especially pertaining to brain regions strongly implicated in the pathophysiology of neuropsychiatric disorders, the success and future of this research depend on the availability of high-quality brain specimens from large numbers of subjects, including nonpsychiatric controls, both of which may be obtained from brain banks. In this chapter, we elaborate on the need for and acquisition of well-curated and properly diagnosed postmortem human brains, relying upon our experience with the Human Brain and Tissue Repository located at the Lieber Institute for Brain Development in Baltimore, MD. We explain the advantages of sourcing postmortem human tissue from medical examiner offices, which provide access to cases of all ages, both with and without central nervous system disorders. Neuropathology analyses and toxicologic screenings, along with autopsy reports and extensive interviews with family members and treating physicians, are invaluable to the diagnoses of postmortem cases. Ultimately, the study of psychiatric and neurologic disorders is the study of brain disease, and accordingly, there is no substitution for human brain tissue.
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Affiliation(s)
- Michelle I Mighdoll
- Lieber Institute for Brain Development, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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47
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McAllister K, Mechanic LE, Amos C, Aschard H, Blair IA, Chatterjee N, Conti D, Gauderman WJ, Hsu L, Hutter CM, Jankowska MM, Kerr J, Kraft P, Montgomery SB, Mukherjee B, Papanicolaou GJ, Patel CJ, Ritchie MD, Ritz BR, Thomas DC, Wei P, Witte JS. Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. Am J Epidemiol 2017; 186:753-761. [PMID: 28978193 PMCID: PMC5860428 DOI: 10.1093/aje/kwx227] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 03/14/2017] [Accepted: 03/16/2017] [Indexed: 12/25/2022] Open
Abstract
Recently, many new approaches, study designs, and statistical and analytical methods have emerged for studying gene-environment interactions (G×Es) in large-scale studies of human populations. There are opportunities in this field, particularly with respect to the incorporation of -omics and next-generation sequencing data and continual improvement in measures of environmental exposures implicated in complex disease outcomes. In a workshop called "Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases," held October 17-18, 2014, by the National Institute of Environmental Health Sciences and the National Cancer Institute in conjunction with the annual American Society of Human Genetics meeting, participants explored new approaches and tools that have been developed in recent years for G×E discovery. This paper highlights current and critical issues and themes in G×E research that need additional consideration, including the improved data analytical methods, environmental exposure assessment, and incorporation of functional data and annotations.
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Affiliation(s)
| | - Leah E. Mechanic
- Correspondence to Dr. Leah E. Mechanic, Genomic Epidemiology Branch, Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, 9609 Medical Center Drive, Room 4E104, MSC 9763, Bethesda, MD 20892 (e-mail: )
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48
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Chen S, Mukherjee N, Janjanam VD, Arshad SH, Kurukulaaratchy RJ, Holloway JW, Zhang H, Karmaus W. Consistency and Variability of DNA Methylation in Women During Puberty, Young Adulthood, and Pregnancy. GENETICS & EPIGENETICS 2017; 9:1179237X17721540. [PMID: 28811741 PMCID: PMC5536379 DOI: 10.1177/1179237x17721540] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/03/2017] [Indexed: 12/12/2022]
Abstract
Prior DNA methylation (DNA-m) analyses have identified cytosine-phosphate-guanine (CpG) sites, which show either a significant change or consistency during lifetime. However, the proportion of CpGs that are neither significantly different nor consistent over time (indifferent CpGs) is unknown. We investigated the methylation dynamics, both longitudinal changes and consistency, in women from preadolescence to late pregnancy using DNA-m of peripheral blood cells. Consistency of cell type–adjusted DNA-m between paired individuals was assessed by regressing CpGs of subsequent age on the prior, stability by intraclass correlation coefficients (>0.5), and changes by linear mixed models. In the first 2 transitions (10-18 years and 18 years to early pregnancy), 19.5% and 20.9% CpGs were consistent, but only 0.35% in the third transition (from early to late pregnancy). Significant changes in methylation were found in 0.7%, 5.6%, and 0% CpGs, respectively. Functional enrichment analyses of genes with significant changes in DNA-m in early pregnancy (5.6%) showed that the maternal DNA-m seems to reflect signaling pathways between the uterus and the trophoblast. The transition from early to late pregnancy showed low consistency/stability and no changes, suggesting the presence of a large proportion of indifferent CpGs in late pregnancy.
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Affiliation(s)
- Su Chen
- Department of Mathematical Sciences, The University of Memphis, Memphis, TN, USA
| | - Nandini Mukherjee
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - Vimala Devi Janjanam
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - S Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,The David Hide Asthma and Allergy Research Centre, Newport, UK
| | - Ramesh J Kurukulaaratchy
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,The David Hide Asthma and Allergy Research Centre, Newport, UK
| | - John W Holloway
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,Academic Unit of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, The University of Memphis, Memphis, TN, USA
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49
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Lopez-Pascual A, Lasa A, Portillo MP, Arós F, Mansego ML, González-Muniesa P, Martinez JA. Low Oxygen Consumption is Related to a Hypomethylation and an Increased Secretion of IL-6 in Obese Subjects with Sleep Apnea-Hypopnea Syndrome. ANNALS OF NUTRITION AND METABOLISM 2017; 71:16-25. [DOI: 10.1159/000478276] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 06/07/2017] [Indexed: 12/17/2022]
Abstract
Background: Deoxyribonucleic acid (DNA) methylation is an epigenetic modification involved in gene expression regulation, usually via gene silencing, which contributes to the risks of many multifactorial diseases. The aim of the present study was to analyze the influence of resting oxygen consumption on global and gene DNA methylation as well as protein secretion of inflammatory markers in blood cells from obese subjects with sleep apnea-hypopnea syndrome (SAHS). Methods: A total of 44 obese participants with SAHS were categorized in 2 groups according to their resting oxygen consumption. DNA methylation levels were evaluated using a methylation-sensitive high resolution melting approach. Results: The analyzed interleukin 6 (IL6) gene cytosine phosphate guanine (CpG) islands showed a hypomethylation, while serum IL-6 was higher in the low compared to the high oxygen consumption group (p < 0.05). Moreover, an age-related loss of DNA methylation of tumor necrosis factor (B = -0.82, 95% CI -1.33 to -0.30) and long interspersed nucleotide element 1 (B = -0.46; 95% CI -0.87 to -0.04) gene CpGs were found. Finally, studied CpG methylation levels of serpin peptidase inhibitor, clade E member 1 (r = 0.43; p = 0.01), and IL6 (r = 0.41; p = 0.02) were positively associated with fat-free mass. Conclusions: These findings suggest a potential role of oxygen in the regulation of inflammatory genes. Oxygen consumption measurement at rest could be proposed as a clinical biomarker of metabolic health.
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50
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Solomon O, Yousefi P, Huen K, Gunier RB, Escudero-Fung M, Barcellos LF, Eskenazi B, Holland N. Prenatal phthalate exposure and altered patterns of DNA methylation in cord blood. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:398-410. [PMID: 28556291 PMCID: PMC6488305 DOI: 10.1002/em.22095] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 05/18/2023]
Abstract
Epigenetic changes such as DNA methylation may be a molecular mechanism through which environmental exposures affect health. Phthalates are known endocrine disruptors with ubiquitous exposures in the general population including pregnant women, and they have been linked with a number of adverse health outcomes. We examined the association between in utero phthalate exposure and altered patterns of cord blood DNA methylation in 336 Mexican-American newborns. Concentrations of 11 phthalate metabolites were analyzed in maternal urine samples collected at 13 and 26 weeks gestation as a measure of fetal exposure. DNA methylation was assessed using the Infinium HumanMethylation 450K BeadChip adjusting for cord blood cell composition. To identify differentially methylated regions (DMRs) that may be more informative than individual CpG sites, we used two different approaches, DMRcate and comb-p. Regional assessment by both methods identified 27 distinct DMRs, the majority of which were in relation to multiple phthalate metabolites. Most of the significant DMRs (67%) were observed for later pregnancy (26 weeks gestation). Further, 51% of the significant DMRs were associated with the di-(2-ethylhexyl) phthalate metabolites. Five individual CpG sites were associated with phthalate metabolite concentrations after multiple comparisons adjustment (FDR), all showing hypermethylation. Genes with DMRs were involved in inflammatory response (IRAK4 and ESM1), cancer (BRCA1 and LASP1), endocrine function (CNPY1), and male fertility (IFT140, TESC, and PRDM8). These results on differential DNA methylation in newborns with prenatal phthalate exposure provide new insights and targets to explore mechanism of adverse effects of phthalates on human health. Environ. Mol. Mutagen. 58:398-410, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Olivia Solomon
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Paul Yousefi
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Karen Huen
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert B. Gunier
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Maria Escudero-Fung
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Lisa F. Barcellos
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Brenda Eskenazi
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Nina Holland
- School of Public Health, Center for Environmental Research and Children’s Health (CERCH), University
of California, Berkeley, Berkeley, CA 94720, USA
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