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Gu W, Wang T, Lin Y, Wang Y, Chen Y, Dai Y, Duan H. Particulate polycyclic aromatic hydrocarbons and metals, DNA methylation and DNA methyltransferase among middle-school students in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172087. [PMID: 38561129 DOI: 10.1016/j.scitotenv.2024.172087] [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: 02/05/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
The main components of particulate matter (PM) had been reported to change DNA methylation levels. However, the mixed effect of PM and its constituents on DNA methylation and the underlying mechanism in children has not been well characterized. To investigate the association between single or mixture exposures and global DNA methylation or DNA methyltransferases (DNMTs), 273 children were recruited (110 in low-exposed area and 163 in high-exposed area) in China. Serum benzo[a]pyridin-7,8-dihydroglycol-9, 10-epoxide (BPDE)-albumin adduct and urinary metals were determined as exposure markers. The global DNA methylation (% 5mC) and the mRNA expression of DNMT1, and DNMT3A were measured. The linear regression, quantile-based g-computation (QGC), and mediation analyses were performed to investigate the effects of individual and mixture exposure. We found that significantly lower levels of % 5mC (P < 0.001) and the mRNA expression of DNMT3A in high-PM exposed group (P = 0.031). After adjustment for age, gender, BMI z-score, detecting status of urinary cotinine, serum folate, and white blood cells, urinary arsenic (As) was negatively correlated with the % 5mC. One IQR increase in urinary As (19.97 μmol/mol creatinine) was associated with a 11.06 % decrease in % 5mC (P = 0.026). Serum BPDE-albumin adduct and urinary cadmium (Cd) were negatively correlated with the levels of DNMT1 and DNMT3A (P < 0.05). Mixture exposure was negatively associated with expression of DNMT3A in QGC analysis (β: -0.19, P < 0.001). Mixture exposure was significantly associated with decreased % 5mC in the children with non-detected cotinine or normal serum folate (P < 0.05), which the most contributors were PAHs and As. The mediated effect of hypomethylation through DNMT1 or DNMT3A pathway was not observed. Our findings indicated that individual and mixture exposure PAHs and metal components had negative associations with global DNA methylation and decreased DNMT3A expression significantly in school-age individuals.
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Affiliation(s)
- Wen Gu
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Ting Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Yang Lin
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; Beijing Chaoyang District Center for Disease Prevention and Control, Beijing 100021, China
| | - Yanhua Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; State Key Laboratory of Trauma and Chemical Poisoning, China
| | - Yuanyuan Chen
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Yufei Dai
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Huawei Duan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; State Key Laboratory of Trauma and Chemical Poisoning, China.
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Milicic L, Porter T, Vacher M, Laws SM. Utility of DNA Methylation as a Biomarker in Aging and Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:475-503. [PMID: 37313495 PMCID: PMC10259073 DOI: 10.3233/adr-220109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/23/2023] [Indexed: 06/15/2023] Open
Abstract
Epigenetic mechanisms such as DNA methylation have been implicated in a number of diseases including cancer, heart disease, autoimmune disorders, and neurodegenerative diseases. While it is recognized that DNA methylation is tissue-specific, a limitation for many studies is the ability to sample the tissue of interest, which is why there is a need for a proxy tissue such as blood, that is reflective of the methylation state of the target tissue. In the last decade, DNA methylation has been utilized in the design of epigenetic clocks, which aim to predict an individual's biological age based on an algorithmically defined set of CpGs. A number of studies have found associations between disease and/or disease risk with increased biological age, adding weight to the theory of increased biological age being linked with disease processes. Hence, this review takes a closer look at the utility of DNA methylation as a biomarker in aging and disease, with a particular focus on Alzheimer's disease.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- CSIRO Health and Biosecurity, Australian e-Health Research Centre, Floreat, Western Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
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Mortillo M, Marsit CJ. Select Early-Life Environmental Exposures and DNA Methylation in the Placenta. Curr Environ Health Rep 2023; 10:22-34. [PMID: 36469294 PMCID: PMC10152976 DOI: 10.1007/s40572-022-00385-1] [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: 10/03/2022] [Indexed: 12/07/2022]
Abstract
PURPOSE OF REVIEW To summarize recent literature relating early-life environmental exposures on DNA methylation in the placenta, to identify how variation in placental methylation is regulated in an exposure-specific manner, and to encourage additional work in this area. RECENT FINDINGS Multiple studies have evaluated associations between prenatal environmental exposures and placental methylation in both gene-specific and epigenome-wide frameworks. Specific exposures lead to unique variability in methylation, and cross-exposure assessments have uncovered certain genes that demonstrate consistency in differential placental methylation. Exposure studies that assess methylation effects in a trimester-specific approach tend to find larger effects during the 1st trimester exposure. Earlier studies have more targeted gene-specific approaches to methylation, while later studies have shifted towards epigenome-wide, array-based approaches. Studies focusing on exposures such as air pollution, maternal smoking, environmental contaminants, and trace metals appear to be more abundant, while studies of socioeconomic adversity and circadian disruption are scarce but demonstrate remarkable effects. Understanding the impacts of early-life environmental exposures on placental methylation is critical to establishing the link between the maternal environment, epigenetic variation, and long-term health. Future studies into this field should incorporate repeated measures of exposure throughout pregnancy, in order to determine the critical windows in which placental methylation is most heavily affected. Additionally, the use of methylation-based scores and sequencing technology could provide important insights into epigenetic gestational age and uncovering more genomic regions where methylation is affected. Studies examining the impact of other exposures on methylation, including pesticides, alcohol, and other chemicals are also warranted.
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Affiliation(s)
- Michael Mortillo
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, USA.
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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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Dias S, Willmer T, Adam S, Pheiffer C. The role of maternal DNA methylation in pregnancies complicated by gestational diabetes. FRONTIERS IN CLINICAL DIABETES AND HEALTHCARE 2022; 3:982665. [PMID: 36992770 PMCID: PMC10012132 DOI: 10.3389/fcdhc.2022.982665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022]
Abstract
Diabetes in pregnancy is associated with adverse pregnancy outcomes and poses a serious threat to the health of mother and child. Although the pathophysiological mechanisms that underlie the association between maternal diabetes and pregnancy complications have not yet been elucidated, it has been suggested that the frequency and severity of pregnancy complications are linked to the degree of hyperglycemia. Epigenetic mechanisms reflect gene-environment interactions and have emerged as key players in metabolic adaptation to pregnancy and the development of complications. DNA methylation, the best characterized epigenetic mechanism, has been reported to be dysregulated during various pregnancy complications, including pre-eclampsia, hypertension, diabetes, early pregnancy loss and preterm birth. The identification of altered DNA methylation patterns may serve to elucidate the pathophysiological mechanisms that underlie the different types of maternal diabetes during pregnancy. This review aims to provide a summary of existing knowledge on DNA methylation patterns in pregnancies complicated by pregestational type 1 (T1DM) and type 2 diabetes mellitus (T2DM), and gestational diabetes mellitus (GDM). Four databases, CINAHL, Scopus, PubMed and Google Scholar, were searched for studies on DNA methylation profiling in pregnancies complicated with diabetes. A total of 1985 articles were identified, of which 32 met the inclusion criteria and are included in this review. All studies profiled DNA methylation during GDM or impaired glucose tolerance (IGT), while no studies investigated T1DM or T2DM. We highlight the increased methylation of two genes, Hypoxia‐inducible Factor‐3α (HIF3α) and Peroxisome Proliferator-activated Receptor Gamma-coactivator-Alpha (PGC1-α), and the decreased methylation of one gene, Peroxisome Proliferator Activated Receptor Alpha (PPARα), in women with GDM compared to pregnant women with normoglycemia that were consistently methylated across diverse populations with varying pregnancy durations, and using different diagnostic criteria, methodologies and biological sources. These findings support the candidacy of these three differentially methylated genes as biomarkers for GDM. Furthermore, these genes may provide insight into the pathways that are epigenetically influenced during maternal diabetes and which should be prioritized and replicated in longitudinal studies and in larger populations to ensure their clinical applicability. Finally, we discuss the challenges and limitations of DNA methylation analysis, and the need for DNA methylation profiling to be conducted in different types of maternal diabetes in pregnancy.
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Affiliation(s)
- Stephanie Dias
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa
| | - Tarryn Willmer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa
- Centre for Cardio-Metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Sumaiya Adam
- Department of Obstetrics and Gynecology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- Diabetes Research Center, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa
- Centre for Cardio-Metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Obstetrics and Gynecology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Noro F, Marotta A, Bonaccio M, Costanzo S, Santonastaso F, Orlandi S, Tirozzi A, Parisi R, De Curtis A, Persichillo M, Gianfagna F, Di Castelnuovo A, Donati MB, Cerletti C, de Gaetano G, Iacoviello L, Gialluisi A, Izzi B. Fine-grained investigation of the relationship between human nutrition and global DNA methylation patterns. Eur J Nutr 2021; 61:1231-1243. [PMID: 34741648 DOI: 10.1007/s00394-021-02716-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022]
Abstract
PURPOSE Nutrition is an important, modifiable, environmental factor affecting human health by modulating epigenetic processes, including DNA methylation (5mC). Numerous studies investigated the association of nutrition with global and gene-specific DNA methylation and evidences on animal models highlighted a role in DNA hydroxymethylation (5hmC) regulation. However, a more comprehensive analysis of different layers of nutrition in association with global levels of 5mC and 5hmC is lacking. We investigated the association between global levels of 5mC and 5hmC and human nutrition, through the stratification and analysis of dietary patterns into different nutritional layers: adherence to Mediterranean diet (MD), main food groups, macronutrients and micronutrients intake. METHODS ELISA technique was used to measure global 5mC and 5hmC levels in 1080 subjects from the Moli-sani cohort. Food intake during the 12 months before enrolment was assessed using the semi-quantitative EPIC food frequency questionnaire. Complementary approaches involving both classical statistics and supervised machine learning analyses were used to investigate the associations between global 5mC and 5hmC levels and adherence to Mediterranean diet, main food groups, macronutrients and micronutrients intake. RESULTS We found that global DNA methylation, but not hydroxymethylation, was associated with daily intake of zinc and vitamin B3. Random Forests algorithms predicting 5mC and 5hmC through intakes of food groups, macronutrients and micronutrients revealed a significant contribution of zinc, while vitamin B3 was reported among the most influential features. CONCLUSION We found that nutrition may affect global DNA methylation, suggesting a contribution of micronutrients previously implicated as cofactors in methylation pathways.
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Affiliation(s)
- Fabrizia Noro
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Annalisa Marotta
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Marialaura Bonaccio
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Simona Costanzo
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Federica Santonastaso
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Sabatino Orlandi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Alfonsina Tirozzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Roberta Parisi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Amalia De Curtis
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Mariarosaria Persichillo
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Francesco Gianfagna
- Mediterranea Cardiocentro, Naples, Italy.,Department of Medicine and Surgery, EPIMED Research Center, University of Insubria, Varese, Italy
| | | | - Maria Benedetta Donati
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Chiara Cerletti
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Giovanni de Gaetano
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Licia Iacoviello
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy. .,Department of Medicine and Surgery, EPIMED Research Center, University of Insubria, Varese, Italy.
| | - Alessandro Gialluisi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Benedetta Izzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
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Lizárraga D, García-Gasca A. The Placenta as a Target of Epigenetic Alterations in Women with Gestational Diabetes Mellitus and Potential Implications for the Offspring. EPIGENOMES 2021; 5:epigenomes5020013. [PMID: 34968300 PMCID: PMC8594713 DOI: 10.3390/epigenomes5020013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 12/14/2022] Open
Abstract
Gestational diabetes mellitus (GDM) is a pregnancy complication first detected in the second or third trimester in women that did not show evident glucose intolerance or diabetes before gestation. In 2019, the International Diabetes Federation reported that 15.8% of live births were affected by hyperglycemia during pregnancy, of which 83.6% were due to gestational diabetes mellitus, 8.5% were due to diabetes first detected in pregnancy, and 7.9% were due to diabetes detected before pregnancy. GDM increases the susceptibility to developing chronic diseases for both the mother and the baby later in life. Under GDM conditions, the intrauterine environment becomes hyperglycemic, while also showing high concentrations of fatty acids and proinflammatory cytokines, producing morphological, structural, and molecular modifications in the placenta, affecting its function; these alterations may predispose the baby to disease in adult life. Molecular alterations include epigenetic mechanisms such as DNA and RNA methylation, chromatin remodeling, histone modifications, and expression of noncoding RNAs (ncRNAs). The placenta is a unique organ that originates only in pregnancy, and its main function is communication between the mother and the fetus, ensuring healthy development. Thus, this review provides up-to-date information regarding two of the best-documented (epigenetic) mechanisms (DNA methylation and miRNA expression) altered in the human placenta under GDM conditions, as well as potential implications for the offspring.
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Bakulski KM, Dou JF, Feinberg JI, Brieger KK, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Schmidt RJ, Fallin MD. Prenatal Multivitamin Use and MTHFR Genotype Are Associated with Newborn Cord Blood DNA Methylation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17249190. [PMID: 33317014 PMCID: PMC7764679 DOI: 10.3390/ijerph17249190] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/20/2020] [Accepted: 11/28/2020] [Indexed: 12/20/2022]
Abstract
Background: Fetal development involves cellular differentiation and epigenetic changes—complex processes that are sensitive to environmental factors. Maternal nutrient levels during pregnancy affect development, and methylene tetrahydrofolate reductase (MTHFR) is important for processing the nutrient folate. Hypothesis: We hypothesize that supplement intake before pregnancy and maternal genotype are associated with DNA methylation in newborns. Methods: In the pregnancy cohort, Early Autism Risk Longitudinal Investigation (EARLI), health history, and genotype information was obtained (n = 249 families). Cord blood DNA methylation (n = 130) was measured using the Illumina HumanMethylation450k array and global DNA methylation levels were computed over 455,698 sites. Supplement use preconception and during pregnancy were surveyed at visits during pregnancy. We evaluated associations between maternal preconception supplement intake and global DNA methylation or DNA methylation density distributions of newborn cord blood, stratified by the presence of a variant maternal MTHFR C677T allele. Results: Maternal preconceptional multivitamin intake was associated with cord blood methylation, dependent on maternal MTHFR genotype (interaction term p = 0.013). For mothers without the MTHFR variant allele, multivitamin intake was associated with 0.96% (95% CI: 0.09, 1.83) higher global cord blood methylation (p = 0.04) and was also associated with the cumulative density distribution of methylation (p = 0.03). For mothers with at least one variant allele, multivitamin intake had a null −0.06% (95% CI: −0.45, 0.33) association with global cord blood DNA methylation, and was not associated with the cumulative density distribution (p = 0.37). Conclusions: We observed that cord blood DNA methylation was associated with maternal supplement exposure preconception and maternal genotype. Genetic context should be considered when assessing DNA methylation effects of modifiable risk factors around the time of pregnancy.
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Affiliation(s)
- Kelly M. Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (K.M.B.); (J.F.D.); (K.K.B.)
| | - John F. Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (K.M.B.); (J.F.D.); (K.K.B.)
| | - Jason I. Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA;
| | - Katharine K. Brieger
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA; (K.M.B.); (J.F.D.); (K.K.B.)
| | - Lisa A. Croen
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA;
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA 95616, USA; (I.H.-P.); (R.J.S.)
| | - Craig J. Newschaffer
- College of Health and Human Development, Penn State University, State College, PA 16802, USA;
| | - Rebecca J. Schmidt
- Department of Public Health Sciences and the M.I.N.D. Institute, School of Medicine, University of California, Davis, CA 95616, USA; (I.H.-P.); (R.J.S.)
| | - M. Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA;
- Correspondence: ; Tel.: +1-(410)-955-3463
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9
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The DNA methylation landscape in cancer. Essays Biochem 2020; 63:797-811. [PMID: 31845735 PMCID: PMC6923322 DOI: 10.1042/ebc20190037] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022]
Abstract
As one of the most abundant and well-studied epigenetic modifications, DNA methylation plays an essential role in normal development and cellular biology. Global alterations to the DNA methylation landscape contribute to alterations in the transcriptome and deregulation of cellular pathways. Indeed, improved methods to study DNA methylation patterning and dynamics at base pair resolution and across individual DNA molecules on a genome-wide scale has highlighted the scope of change to the DNA methylation landscape in disease states, particularly during tumorigenesis. More recently has been the development of DNA hydroxymethylation profiling techniques, which allows differentiation between 5mC and 5hmC profiles and provides further insights into DNA methylation dynamics and remodeling in tumorigenesis. In this review, we describe the distribution of DNA methylation and DNA hydroxymethylation in different genomic contexts, first in normal cells, and how this is altered in cancer. Finally, we discuss DNA methylation profiling technologies and the most recent advances in single-cell methods, bisulfite-free approaches and ultra-long read sequencing techniques.
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Zeng M, Zhen J, Zheng X, Qiu H, Xu X, Wu J, Lin Z, Hu J. The Role of DNA Methylation in Ischemic Stroke: A Systematic Review. Front Neurol 2020; 11:566124. [PMID: 33193003 PMCID: PMC7652818 DOI: 10.3389/fneur.2020.566124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/28/2020] [Indexed: 02/05/2023] Open
Abstract
Background: Knowledge about the classic risk and protective factors of ischemic stroke is accumulating, but the underlying pathogenesis has not yet been fully understood. As emerging evidence indicates that DNA methylation plays a role in the pathological process of cerebral ischemia, this study aims to summarize the evidence of the association between DNA methylation and ischemic stroke. Methods: MEDLINE, EMBASE, PubMed, and Cochrane Central Register of Controlled Trials were searched for eligible studies. The results reported by each study were summarized narratively. Results: A total of 20 studies with 7,014 individuals finally met the inclusion criteria. Three studies focused on global methylation, 11 studies on candidate-gene methylation, and six on epigenome-wide methylation analysis. Long-interspersed nuclear element 1 was found to be hypomethylated in stroke cases in two studies. Another 16 studies reported 37 genes that were differentially methylated between stroke cases and controls. Individuals with ischemic stroke were also reported to have higher acceleration in Hanuum 's epigenetic age compared to controls. Conclusion: DNA methylation might be associated with ischemic stroke and play a role in several pathological pathways. It is potentially a promising biomarker for stroke prevention, diagnosis and treatment, but the current evidence is limited by sample size and cross-sectional or retrospective design. Therefore, studies on large asymptomatic populations with the prospective design are needed to validate the current evidence, explore new pathways and identify novel risk/protective loci.
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Affiliation(s)
- Minyan Zeng
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Juanying Zhen
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- Department of Clinical Medicine, Shantou University Medical College, Shantou, China
| | - Xiaodan Zheng
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- Department of Clinical Medicine, Shantou University Medical College, Shantou, China
| | - Hongyan Qiu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xiaonan Xu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jun Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zhijian Lin
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- *Correspondence: Zhijian Lin
| | - Jun Hu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- Jun Hu
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11
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DNA methylation-based biological age, genome-wide average DNA methylation, and conventional breast cancer risk factors. Sci Rep 2019; 9:15055. [PMID: 31636290 PMCID: PMC6803691 DOI: 10.1038/s41598-019-51475-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/25/2019] [Indexed: 12/12/2022] Open
Abstract
DNA methylation-based biological age (DNAm age), as well as genome-wide average DNA methylation, have been reported to predict breast cancer risk. We aimed to investigate the associations between these DNA methylation-based risk factors and 18 conventional breast cancer risk factors for disease-free women. A sample of 479 individuals from the Australian Mammographic Density Twins and Sisters was used for discovery, a sample of 3354 individuals from the Melbourne Collaborative Cohort Study was used for replication, and meta-analyses pooling results from the two studies were conducted. DNAm age based on three epigenetic clocks (Hannum, Horvath and Levine) and genome-wide average DNA methylation were calculated using the HumanMethylation 450 K BeadChip assay data. The DNAm age measures were positively associated with body mass index (BMI), smoking, alcohol drinking and age at menarche (all nominal P < 0.05). Genome-wide average DNA methylation was negatively associated with smoking and number of live births, and positively associated with age at first live birth (all nominal P < 0.05). The association of DNAm age with BMI was also evident in within-twin-pair analyses that control for familial factors. This study suggests that some lifestyle and hormonal risk factors are associated with these DNA methylation-based breast cancer risk factors, and the observed associations are unlikely to be due to familial confounding but are likely causal. DNA methylation-based risk factors could interplay with conventional risk factors in modifying breast cancer risk.
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12
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Laubach ZM, Perng W, Cardenas A, Rifas-Shiman SL, Oken E, DeMeo D, Litonjua AA, Duca RC, Godderis L, Baccarelli A, Hivert MF. Socioeconomic status and DNA methylation from birth through mid-childhood: a prospective study in Project Viva. Epigenomics 2019; 11:1413-1427. [PMID: 31509016 PMCID: PMC6802709 DOI: 10.2217/epi-2019-0040] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/20/2018] [Indexed: 12/28/2022] Open
Abstract
Aim: We investigated associations of prenatal socioeconomic status (SES) with DNA methylation at birth, and to explore persistence of associations into early (∼3 years) and mid-childhood (∼7 years) among 609 mother-child pairs in a Boston-area prebirth cohort. Materials & methods: First, we created a prenatal SES index comprising individual- and neighborhood-level metrics and examined associations of low (lowest 10%) versus high (upper 90%) SES with genome-wide DNA methylation in cord blood via the Infinium HumanMethylation450 BeadChip. Next, we evaluated persistence of associations detected in cord blood with DNA methylation of the same CpG sites measured in peripheral leukocytes in early- and mid-childhood. Results & conclusion: Low prenatal SES was associated with methylation at CpG sites near ACSF3, TNRC6C-AS1, MTMR4 and LRRN4. The relationship with LRRN4 persisted into early childhood.
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Affiliation(s)
- Zachary M Laubach
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Wei Perng
- Department of Epidemiology, Colorado School of Public Health, Anschutz Medical Center, Aurora, CO 80045, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School/Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School/Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Dawn DeMeo
- Center for Chest Diseases, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Augusto A Litonjua
- Division of Pediatric Pulmonary Medicine, Golisano Children's Hospital at Strong, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Radu-Corneliu Duca
- Centre for Environment & Health, Department of Public Health & Primary Care, University of Leuven (KU Leuven), 3000, Belgium
| | - Lode Godderis
- Centre for Environment & Health, Department of Public Health & Primary Care, University of Leuven (KU Leuven), 3000, Belgium
- IDEWE, External Service for Prevention at Protection at Work, Heverlee, 3001, Belgium
| | - Andrea Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY 10032, USA
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School/Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
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13
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Laubach ZM, Faulk CD, Dolinoy DC, Montrose L, Jones TR, Ray D, Pioon MO, Holekamp KE. Early life social and ecological determinants of global DNA methylation in wild spotted hyenas. Mol Ecol 2019; 28:3799-3812. [PMID: 31291495 DOI: 10.1111/mec.15174] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/14/2019] [Accepted: 06/19/2019] [Indexed: 12/26/2022]
Abstract
Environmental factors early in life can have lasting influence on the development and phenotypes of animals, but the underlying molecular modifications remain poorly understood. We examined cross-sectional associations among early life socioecological factors and global DNA methylation in 293 wild spotted hyenas (Crocuta crocuta) in the Masai Mara National Reserve, Kenya, grouped according to three age classes (cub, subadult and adult). Explanatory variables of interest included annual maternal rank based on outcomes of dyadic agonistic interactions, litter size, wild ungulate prey density and anthropogenic disturbance in the year each hyena was born based on counts of illegal livestock in the Reserve. The dependent variable of interest was global DNA methylation, assessed via the LUminometric Methylation Assay, which provides a percentage methylation value calculated at CCGG sites across the genome. Among cubs, we observed approximately 2.75% higher CCGG methylation in offspring born to high- than low-ranking mothers. Among cubs and subadults, higher anthropogenic disturbance corresponded with greater %CCGG methylation. In both cubs and adults, we found an inverse association between prey density measured before a hyena was 3 months old and %CCGG methylation. Our results suggest that maternal rank, anthropogenic disturbance and prey availability early in life are associated with later life global DNA methylation. Future studies are required to understand the extent to which these DNA methylation patterns relate to adult phenotypes and fitness outcomes.
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Affiliation(s)
- Zachary M Laubach
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, USA.,BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.,Mara Hyena Project, Michigan State University, Masai Mara National Reserve, Talek, Kenya
| | | | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Luke Montrose
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Donna Ray
- Divisions of Geriatric Medicine and Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Malit O Pioon
- Mara Hyena Project, Michigan State University, Masai Mara National Reserve, Talek, Kenya
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, USA.,BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.,Mara Hyena Project, Michigan State University, Masai Mara National Reserve, Talek, Kenya
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14
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Bodelon C, Ambatipudi S, Dugué PA, Johansson A, Sampson JN, Hicks B, Karlins E, Hutchinson A, Cuenin C, Chajès V, Southey MC, Romieu I, Giles GG, English D, Polidoro S, Assumma M, Baglietto L, Vineis P, Severi G, Herceg Z, Flanagan JM, Milne RL, Garcia-Closas M. Blood DNA methylation and breast cancer risk: a meta-analysis of four prospective cohort studies. Breast Cancer Res 2019; 21:62. [PMID: 31101124 PMCID: PMC6525390 DOI: 10.1186/s13058-019-1145-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Environmental and genetic factors play an important role in the etiology of breast cancer. Several small blood-based DNA methylation studies have reported risk associations with methylation at individual CpGs and average methylation levels; however, these findings require validation in larger prospective cohort studies. To investigate the role of blood DNA methylation on breast cancer risk, we conducted a meta-analysis of four prospective cohort studies, including a total of 1663 incident cases and 1885 controls, the largest study of blood DNA methylation and breast cancer risk to date. METHODS We assessed associations with methylation at 365,145 CpGs present in the HumanMethylation450 (HM450K) Beadchip, after excluding CpGs that did not pass quality controls in all studies. Each of the four cohorts estimated odds ratios (ORs) and 95% confidence intervals (CI) for the association between each individual CpG and breast cancer risk. In addition, each study assessed the association between average methylation measures and breast cancer risk, adjusted and unadjusted for cell-type composition. Study-specific ORs were combined using fixed-effect meta-analysis with inverse variance weights. Stratified analyses were conducted by age at diagnosis (< 50, ≥ 50), estrogen receptor (ER) status (+/-), and time since blood collection (< 5, 5-10, > 10 years). The false discovery rate (q value) was used to account for multiple testing. RESULTS The average age at blood draw ranged from 52.2 to 62.2 years across the four cohorts. Median follow-up time ranged from 6.6 to 8.4 years. The methylation measured at individual CpGs was not associated with breast cancer risk (q value > 0.59). In addition, higher average methylation level was not associated with risk of breast cancer (OR = 0.94, 95% CI = 0.85, 1.05; P = 0.26; P for study heterogeneity = 0.86). We found no evidence of modification of this association by age at diagnosis (P = 0.17), ER status (P = 0.88), time since blood collection (P = 0.98), or CpG location (P = 0.98). CONCLUSIONS Our data indicate that DNA methylation measured in the blood prior to breast cancer diagnosis in predominantly postmenopausal women is unlikely to be associated with substantial breast cancer risk on the HM450K array. Larger studies or with greater methylation coverage are needed to determine if associations exist between blood DNA methylation and breast cancer risk.
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Affiliation(s)
- Clara Bodelon
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Srikant Ambatipudi
- International Agency for Research on Cancer (IARC), Lyon, France
- AMCHSS, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Pierre-Antoine Dugué
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | | | - Joshua N. Sampson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Belynda Hicks
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Eric Karlins
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Amy Hutchinson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Veronique Chajès
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Australia
| | - Isabelle Romieu
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Graham G. Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | - Dallas English
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | - Silvia Polidoro
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Manuela Assumma
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Paolo Vineis
- MRC-PHE Center for Environment and Health, School of Public Health, Imperial College, London, UK
| | - Gianluca Severi
- CESP (U1018 INSERM, Équipe Générations et Santé), Facultés de médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Roger L. Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
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15
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Chamberlain JA, Dugué PA, Bassett JK, Hodge AM, Brinkman MT, Joo JE, Jung CH, Makalic E, Schmidt DF, Hopper JL, Buchanan DD, English DR, Southey MC, Giles GG, Milne RL. Dietary intake of one-carbon metabolism nutrients and DNA methylation in peripheral blood. Am J Clin Nutr 2018; 108:611-621. [PMID: 30101351 DOI: 10.1093/ajcn/nqy119] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 05/09/2018] [Indexed: 12/28/2022] Open
Abstract
Background Folate and other one-carbon metabolism nutrients are essential to enable DNA methylation to occur, but the extent to which their dietary intake influences methylation in adulthood is unclear. Objective We assessed associations between dietary intake of these nutrients and DNA methylation in peripheral blood, overall and at specific genomic locations. Design We conducted a cross-sectional study using baseline data and samples from 5186 adult participants in the Melbourne Collaborative Cohort Study (MCCS). Nutrient intake was estimated from a food-frequency questionnaire. DNA methylation was measured by using the Illumina Infinium HumanMethylation450 BeadChip array (HM450K). We assessed associations of intakes of folate, riboflavin, vitamins B-6 and B-12, methionine, choline, and betaine with methylation at individual cytosine-guanine dinucleotides (CpGs), and with median (genome-wide) methylation across all CpGs, CpGs in gene bodies, and CpGs in gene promoters. We also assessed associations with methylation at long interspersed nuclear element 1 (LINE-1), satellite 2 (Sat2), and Arthrobacter luteus restriction endonuclease (Alu) repetitive elements for a subset of participants. We used linear mixed regression, adjusting for age, sex, country of birth, smoking, energy intake from food, alcohol intake, Mediterranean diet score, and batch effects to assess log-linear associations with dietary intake of each nutrient. In secondary analyses, we assessed associations with low or high intakes defined by extreme quintiles. Results No evidence of log-linear association was observed at P < 10-7 between the intake of one-carbon metabolism nutrients and methylation at individual CpGs. Low intake of riboflavin was associated with higher methylation at CpG cg21230392 in the first exon of PROM1 (P = 5.0 × 10-8). No consistent evidence of association was observed with genome-wide or repetitive element measures of methylation. Conclusion Our findings suggest that dietary intake of one-carbon metabolism nutrients in adulthood, as measured by a food-frequency questionnaire, has little association with blood DNA methylation. An association with low intake of riboflavin requires replication in independent cohorts. This study was registered at http://www.clinicaltrials.gov as NCT03227003.
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Affiliation(s)
- James A Chamberlain
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Pierre-Antoine Dugué
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Julie K Bassett
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Allison M Hodge
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Maree T Brinkman
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - JiHoon E Joo
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, The University of Melbourne, Parkville, Victoria, Australia
| | - Enes Makalic
- Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Daniel F Schmidt
- Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - John L Hopper
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia.,Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria, Australia.,Genetic Medicine and Familial Cancer Center, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Melissa C Southey
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Roger L Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
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16
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Loke YJ, Muggli E, Nguyen L, Ryan J, Saffery R, Elliott EJ, Halliday J, Craig JM. Time- and sex-dependent associations between prenatal alcohol exposure and placental global DNA methylation. Epigenomics 2018; 10:981-991. [PMID: 29956547 DOI: 10.2217/epi-2017-0147] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AIM Epigenetic changes, in particular in the placenta, may mediate the effects of prenatal alcohol exposure (PAE) on children's health. We examined the relationship between PAE patterns, based on dose and timing, and placental global DNA methylation. METHODS Using linear regression analysis, we examined the association between different PAE categories and placental global DNA methylation (n = 187), using the proxy measure of Alu-interspersed repeats. RESULTS Following adjustment for important covariates, we found no evidence of an association between PAE and placental global DNA methylation overall. However, when stratifying by newborn sex, PAE throughout pregnancy was associated with higher placental global DNA methylation (1.5%; p = 0.01) of male newborns. CONCLUSION PAE may have sex-specific effects on placental global DNA methylation if alcohol is consumed throughout pregnancy.
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Affiliation(s)
- Yuk Jing Loke
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, the Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
| | - Evelyne Muggli
- Public Health Genetics, Murdoch Children's Research Institute, the Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Linh Nguyen
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, the Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
| | - Joanne Ryan
- Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Epidemiology & Preventive Medicine, Monash University, Melbourne, Victoria 3004, Australia.,Cancer & Disease Epigenetics, Murdoch Children's Research Institute, the Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
| | - Richard Saffery
- Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia.,Cancer & Disease Epigenetics, Murdoch Children's Research Institute, the Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
| | - Elizabeth J Elliott
- Discipline of Child & Adolescent Health, School of Medicine and Health, University of Sydney, Sydney 2006, New South Wales, Australia.,Australian Paediatric Surveillance Unit, Sydney Childrens Hospitals Network, Westmead, Sydney, New South Wales, Australia
| | - Jane Halliday
- Public Health Genetics, Murdoch Children's Research Institute, the Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Jeffrey M Craig
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, the Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia.,Centre for Molecular and Medical Research, Deakin University, Geelong Waurn Ponds Campus, Locked Bag 20000, Geelong, Victoria 3220, Australia
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17
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Singh G, Singh V, Wang ZX, Voisin G, Lefebvre F, Navenot JM, Evans B, Verma M, Anderson DW, Schneider JS. Effects of developmental lead exposure on the hippocampal methylome: Influences of sex and timing and level of exposure. Toxicol Lett 2018; 290:63-72. [PMID: 29571894 DOI: 10.1016/j.toxlet.2018.03.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/15/2018] [Accepted: 03/19/2018] [Indexed: 12/21/2022]
Abstract
Developmental lead (Pb) exposure results in persistent cognitive/behavioral impairments as well as an elevated risk for developing a variety of diseases in later life. Environmental exposures during development can result in a variety of epigenetic changes, including alterations in DNA methylation, that can influence gene expression patterns and affect the function and development of the nervous system. The present promoter-based methylation microarray profiling study explored the extent to which developmental Pb exposure may modify the methylome of a brain region, hippocampus, known to be sensitive to the effects of Pb exposure. Male and female Long Evans rats were exposed to 0 ppm, 150 ppm, 375 ppm, or 750 ppm Pb through perinatal exposures (gestation through lactation), early postnatal exposures (birth through weaning), or long-term postnatal exposures (birth through postnatal day 55). Results showed a significant contribution of sex to the hippocampal methylome and effects of Pb exposure level, with non-linear dose response effects on methylation. Surprisingly, the developmental period of exposure contributed only a small amount of variance to the overall data and gene ontology (GO) analysis revealed the largest number of overrepresented GO terms in the groups with the lowest level of exposure. The highest number of significant differentially methylated regions was found in females exposed to Pb at the lowest exposure level. Our data reinforce the significant effect that low level Pb exposure may have on gene-specific DNA methylation patterns in brain and that this occurs in a sex-dependent manner.
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Affiliation(s)
- G Singh
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA.
| | - V Singh
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zi-Xuan Wang
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - G Voisin
- Atelerics S.E.N.C, Montreal, QC, Canada
| | - F Lefebvre
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - J-M Navenot
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - B Evans
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - M Verma
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - D W Anderson
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - J S Schneider
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
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18
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Rawat S, Kaur G, Yadav S, Khan MA, Kallur Nava S. Global DNA methylation and depression: Preliminary result from community based epidemiological study. Meta Gene 2018. [DOI: 10.1016/j.mgene.2017.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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