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Carreras-Gallo N, Dwaraka VB, Jima DD, Skaar DA, Mendez TL, Planchart A, Zhou W, Jirtle RL, Smith R, Hoyo C. Creation and Validation of the First Infinium DNA Methylation Array for the Human Imprintome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575646. [PMID: 38293193 PMCID: PMC10827131 DOI: 10.1101/2024.01.15.575646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Differentially methylated imprint control regions (ICRs) regulate the monoallelic expression of imprinted genes. Their epigenetic dysregulation by environmental exposures throughout life results in the formation of common chronic diseases. Unfortunately, existing Infinium methylation arrays lack the ability to profile these regions adequately. Whole genome bisulfite sequencing (WGBS) is the unique method able to profile these regions, but it is very expensive and it requires not only a high coverage but it is also computationally intensive to assess those regions. Findings To address this deficiency, we developed a custom methylation array containing 22,819 probes. Among them, 9,757 probes map to 1,088 out of the 1,488 candidate ICRs recently described. To assess the performance of the array, we created matched samples processed with the Human Imprintome array and WGBS, which is the current standard method for assessing the methylation of the Human Imprintome. We compared the methylation levels from the shared CpG sites and obtained a mean R 2 = 0.569. We also created matched samples processed with the Human Imprintome array and the Infinium Methylation EPIC v2 array and obtained a mean R 2 = 0.796. Furthermore, replication experiments demonstrated high reliability (ICC: 0.799-0.945). Conclusions Our custom array will be useful for replicable and accurate assessment, mechanistic insight, and targeted investigation of ICRs. This tool should accelerate the discovery of ICRs associated with a wide range of diseases and exposures, and advance our understanding of genomic imprinting and its relevance in development and disease formation throughout the life course.
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2
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Vidal AC, Moylan CA, Wilder J, Grant DJ, Murphy SK, Hoyo C. Racial disparities in liver cancer: Evidence for a role of environmental contaminants and the epigenome. Front Oncol 2022; 12:959852. [PMID: 36072796 PMCID: PMC9441658 DOI: 10.3389/fonc.2022.959852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/21/2022] [Indexed: 01/09/2023] Open
Abstract
Liver cancer incidence has tripled since the early 1980s, making this disease one of the fastest rising types of cancer and the third leading cause of cancer-related deaths worldwide. In the US, incidence varies by geographic location and race, with the highest incidence in the southwestern and southeastern states and among racial minorities such as Hispanic and Black individuals. Prognosis is also poorer among these populations. The observed ethnic disparities do not fully reflect differences in the prevalence of risk factors, e.g., for cirrhosis that may progress to liver cancer or from genetic predisposition. Likely substantial contributors to risk are environmental factors, including chemical and non-chemical stressors; yet, the paucity of mechanistic insights impedes prevention efforts. Here, we review the current literature and evaluate challenges to reducing liver cancer disparities. We also discuss the hypothesis that epigenetic mediators may provide biomarkers for early detection to support interventions that reduce disparities.
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Affiliation(s)
- Adriana C. Vidal
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
| | - Cynthia A. Moylan
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Duke University, Durham, NC, United States
| | - Julius Wilder
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Duke University, Durham, NC, United States
| | - Delores J. Grant
- Department of Biomedical and Biological Sciences, Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, United States
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Division of Research, School of Medicine, Duke University, Durham, NC, United States
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
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3
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Jima DD, Skaar DA, Planchart A, Motsinger-Reif A, Cevik SE, Park SS, Cowley M, Wright F, House J, Liu A, Jirtle RL, Hoyo C. Genomic map of candidate human imprint control regions: the imprintome. Epigenetics 2022; 17:1920-1943. [PMID: 35786392 PMCID: PMC9665137 DOI: 10.1080/15592294.2022.2091815] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Imprinted genes – critical for growth, metabolism, and neuronal function – are expressed from one parental allele. Parent-of-origin-dependent CpG methylation regulates this expression at imprint control regions (ICRs). Since ICRs are established before tissue specification, these methylation marks are similar across cell types. Thus, they are attractive for investigating the developmental origins of adult diseases using accessible tissues, but remain unknown. We determined genome-wide candidate ICRs in humans by performing whole-genome bisulphite sequencing (WGBS) of DNA derived from the three germ layers and from gametes. We identified 1,488 hemi-methylated candidate ICRs, including 19 of 25 previously characterized ICRs (https://humanicr.org/). Gamete methylation approached 0% or 100% in 332 ICRs (178 paternally and 154 maternally methylated), supporting parent-of-origin-specific methylation, and 65% were in well-described CTCF-binding or DNaseI hypersensitive regions. This draft of the human imprintome will allow for the systematic determination of the role of early-acquired imprinting dysregulation in the pathogenesis of human diseases and developmental and behavioural disorders.
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Affiliation(s)
- 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
| | - David A Skaar
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Antonio Planchart
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Sebnem E Cevik
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Sarah S Park
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.,Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Michael Cowley
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Fred Wright
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - John House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Andy Liu
- Department of Neurology, Duke University, School of Medicine, Durham, NC, USA
| | - Randy L Jirtle
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
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4
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Maternal Dietary Quality and Dietary Inflammation Associations with Offspring Growth, Placental Development, and DNA Methylation. Nutrients 2021; 13:nu13093130. [PMID: 34579008 PMCID: PMC8468062 DOI: 10.3390/nu13093130] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/31/2021] [Accepted: 09/04/2021] [Indexed: 12/14/2022] Open
Abstract
The ‘Developmental Origins of Health and Diseases’ hypothesis posits that prenatal maternal diet influences offspring growth and later life health outcomes. Dietary assessment has focused on selected nutrients. However, this approach does not consider the complex interactions between foods and nutrients. To provide a more comprehensive approach to public health, dietary indices have been developed to assess dietary quality, dietary inflammation and risk factors for non-communicable diseases. Thus far, their use in the context of placental development is limited and associations with offspring outcomes have been inconsistent. Although epidemiological studies have focused on the role of maternal diet on foetal programming, the underlying mechanisms are still poorly understood. Some evidence suggests these associations may be driven by placental and epigenetic changes. In this narrative review, we examine the current literature regarding relationships between key validated diet quality scores (Dietary Inflammatory Index [DII], Mediterranean diet [MD], Healthy Eating Index [HEI], Alternative Healthy Eating Index [AHEI], Dietary Approaches to Stop Hypertension [DASH], Glycaemic Index [GI] and Glycaemic Load [GL]) in pregnancy and birth and long-term offspring outcomes. We summarise findings, discuss potential underlying placental and epigenetic mechanisms, in particular DNA methylation, and highlight the need for further research and public health strategies that incorporate diet quality and epigenetics.
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5
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Maternal DNA Methylation During Pregnancy: a Review. Reprod Sci 2021; 28:2758-2769. [PMID: 33469876 DOI: 10.1007/s43032-020-00456-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/29/2020] [Indexed: 12/19/2022]
Abstract
Multiple environmental, behavioral, and hereditary factors affect pregnancy. Recent studies suggest that epigenetic modifications, such as DNA methylation (DNAm), affect both maternal and fetal health during the period of gestation. Some of the pregnancy-related risk factors can influence maternal DNAm, thus predisposing both the mother and the neonate to clinical adversities with long-lasting consequences. DNAm alterations in the promoter and enhancer regions modulate gene expression changes which play vital physiological role. In this review, we have discussed the recent advances in our understanding of maternal DNA methylation changes during pregnancy and its associated complications such as gestational diabetes and anemia, adverse pregnancy outcomes like preterm birth, and preeclampsia. We have also highlighted some major gaps and limitations in the area which if addressed might improve our understanding of pregnancy and its associated adverse clinical conditions, ultimately leading to healthy pregnancies and reduction of public health burden.
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6
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Soubry A, Murphy SK, Vansant G, He Y, Price TM, Hoyo C. Opposing Epigenetic Signatures in Human Sperm by Intake of Fast Food Versus Healthy Food. Front Endocrinol (Lausanne) 2021; 12:625204. [PMID: 33967953 PMCID: PMC8103543 DOI: 10.3389/fendo.2021.625204] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/15/2021] [Indexed: 01/01/2023] Open
Abstract
Animal experiments have demonstrated that diets high in fats create a harmful environment for developing sperm cells, contributing to impaired reproductive health and induced risk for chronic diseases in the next generation. Changes at the level of the epigenome have been suggested to underlie these observations. Human data are limited to verify this hypothesis. While we earlier demonstrated a link between male obesity and DNA methylation changes at imprinted genes in mature sperm cells and newborns, it is currently unknown if -or how- a paternal eating pattern (related to obesity) is related to indices for epigenetic inheritance. We here aim to examine a yet unexplored link between consumption of healthy (rich in vitamins and fibers) or unhealthy ("fast") foods and methylation at imprint regulatory regions in DNA of sperm. We obtained semen and data from 67 men, as part of a North Carolina-based study: The Influence of the Environment on Gametic Epigenetic Reprogramming (TIEGER) study. Dietary data included intake of fruits/nuts, vegetables/soups, whole grain bread, meat, seafood/fish, and fatty or processed food items. Multiple regression models were used to explore the association between dietary habits and clinical sperm parameters as well as DNA methylation levels, quantified using bisulfite pyrosequencing at 12 differentially methylated regions (DMRs) of the following imprinted genes: GRB10, IGF2, H19, MEG3, NDN, NNAT, PEG1/MEST, PEG3, PLAGL1, SNRPN, and SGCE/PEG10. After adjusting for age, obesity status and recruitment method, we found that Total Motile Count (TMC) was significantly higher if men consumed fruits/nuts (β=+6.9, SE=1.9, p=0.0005) and vegetables (β=+5.4, SE=1.9, p=0.006), whereas consumption of fries was associated with lower TMC (β=-20.2, SE=8.7, p=0.024). Semen volume was also higher if vegetables or fruits/nuts were frequently consumed (β=+0.06, SE=0.03, p=0.03). Similarly, our sperm epigenetic analyses showed opposing associations for healthy versus fast food items. Frequent consumption of fries was related to a higher chance of sperm being methylated at the MEG3-IG CpG4 site (OR=1.073, 95%CI: 1.035-1.112), and high consumption of vegetables was associated with a lower risk of DNA methylation at the NNAT CpG3 site (OR=0.941, 95%CI: 0.914-0.968). These results remained significant after adjusting for multiple testing. We conclude that dietary habits are linked to sperm epigenetic outcomes. If carried into the next generation paternal unhealthy dietary patterns may result in adverse metabolic conditions and increased risk for chronic diseases in offspring.
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Affiliation(s)
- Adelheid Soubry
- Epidemiology Research Center, Department of Public Health and Primary Care, Faculty of Medicine, KU Leuven—University, Leuven, Belgium
- *Correspondence: Adelheid Soubry,
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Division of Reproductive Sciences, Duke University Medical Center, Durham, NC, United States
- Duke University School of Medicine, Duke Cancer Institute, Durham, NC, United States
| | - Greet Vansant
- Epidemiology Research Center, Department of Public Health and Primary Care, Faculty of Medicine, KU Leuven—University, Leuven, Belgium
| | - Yang He
- Epidemiology Research Center, Department of Public Health and Primary Care, Faculty of Medicine, KU Leuven—University, Leuven, Belgium
| | - Thomas M. Price
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Duke University Medical Center, Durham, NC, United States
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
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7
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Araiza-Olivera D, Gutierrez-Aguilar M, Espinosa-García AM, García-García JA, Tapia-Orozco N, Sánchez-Pérez C, Palacios-Reyes C, Escárcega D, Villalón-López DN, García-Arrazola R. From bench to bedside: Biosensing strategies to evaluate endocrine disrupting compounds based on epigenetic events and their potential use in medicine. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2020; 80:103450. [PMID: 32622887 DOI: 10.1016/j.etap.2020.103450] [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: 10/14/2019] [Revised: 06/12/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
The relationship between endocrine system disorders and health risks due to chemical environmental compounds has become a growing concern in recent years. Involuntary exposure to endocrine disruptors (EDCs) is associated with the worldwide increase of diseases such as cancer, obesity, diabetes, and neurocortical disorders. EDCs are compounds that target the nuclear hormonereceptors (NHR) leading to epigenetic changes. Consequently, the use of biosensing strategies based on epigenetic events have a great potential to provide outstanding information about the exposition of EDCs and their evaluation in human health. This review addresses the novel trends in biosensing EDCs evaluation based on DNA methylation assays associated with different human diseases.
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Affiliation(s)
- D Araiza-Olivera
- Department of Chemistry and Biomolecules, Institute of Chemistry, UNAM, Mexico.
| | | | - A M Espinosa-García
- Unidad de Medicina Genómica, Hospital General de México, Dr. Balmis 148, Mexico City, Mexico.
| | - J A García-García
- Department of Education, Hospital General de México, Dr. Balmis 148, Mexico City, Mexico.
| | - N Tapia-Orozco
- Departmentof Food Science and Biotechnology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
| | - C Sánchez-Pérez
- Institute of Applied Sciences and Technology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
| | - C Palacios-Reyes
- Laboratory of Genetics and Molecular Diagnostics, Juarez Hospital of Mexico, Mexico City, Mexico.
| | - D Escárcega
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Campus Ciudad de México, calle del Puente 222, Ejidos de Huipulco, Tlalpan 14380, Mexico City, Mexico.
| | - Demelza N Villalón-López
- Instituto Politénico Nacional-Escuela Nacional de Ciencias Biológicas, Departamento de Química Orgánica, Prolongación de Carpio y Plande Ayala, colonia Casco de Santo Tomás. Del, Miguel Hidalgo, 11350, Mexico.
| | - R García-Arrazola
- Departmentof Food Science and Biotechnology, Faculty of Chemistry, Universidad Nacional Autónoma de México, Ave. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico.
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8
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Huang KT, Shen YL, Lee CN, Chu KY, Ku WC, Liu CY, Huang RFS. Using Differential Threshold Effects of Individual and Combined Periconceptional Methyl Donor Status on Maternal Genomic LINE-1 and Imprinted H19 DNA Methylation to Predict Birth Weight Variance in the Taiwan Pregnancy-Newborn Epigenetics (TPNE) Cohort Study. J Nutr 2020; 150:108-117. [PMID: 31504733 DOI: 10.1093/jn/nxz204] [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: 03/22/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Few studies have comprehensively examined the effect of methyl donor status on maternal DNA methylation and birth outcomes. OBJECTIVES This study examined associations between periconceptional methyl donor status and genome-wide and specific imprinted gene methylation and fetal growth indices in the Taiwan Pregnancy-Newborn Epigenetics cohort. METHODS Plasma folate, choline (free form), and betaine concentrations of the participants enrolled at 7-10 weeks of gestation were analyzed. DNA methylation at regulatory sequences of the imprinted H19 gene and genomic long interspersed nuclear element 1 (LINE-1) were measured in maternal lymphocytes using bisulfite/high-resolution melt polymerase chain reaction. Associations with birth weight (BW) were estimated through multiple regressions from 112 mother-newborn pairs. RESULTS A nonlinear "L-shaped" relation and an inverse association between maternal plasma folate in T1 (mean ± SE: 17.6 ± 5.1 nmol/L) and lymphocytic LINE-1 methylation (β: -0.49, P = 0.027) were characterized. After adjusting for LINE-1 methylation, individual maternal folate concentrations were positively associated with BW variance (β = 0.24, P = 0.035), and the association was more pronounced in mothers with choline in T1 (mean ± SE: 5.4 ± 0.6 μmol/L; β: 0.40, P = 0.039). Choline status of the mothers in T2 (mean ± SE: 7.2 ± 0.6 μmol/L) was inversely associated with LINE-1 methylation (β: -0.43, P = 0.035), and a positive association was evident between T1 choline and H19 methylation (β: 0.48, P = 0.011). After adjusting for epigenetic modification, maternal choline status predicted a positive association with BW (β: 0.56, P = 0.005), but the effect was limited to mothers with high betaine concentrations in T3 (mean ± SE: 36.4 ± 8.8 μmol/L), depending on folate status. CONCLUSIONS Our data highlight the differential threshold effects of periconceptional folate, choline, and betaine status on genomic LINE-1 and H19 DNA methylation and how their interplay has a long-term effect on BW variance.
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Affiliation(s)
- Kuang-Ta Huang
- PhD Program in Nutrition and Food Science, Fu Jen Catholic University, New Taipei City, Taiwan.,Loving Care Maternity and Children's Health Centers, New Taipei City, Taiwan
| | - Yu-Li Shen
- Department of Nutritional Science, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Chien-Nan Lee
- Department of Gynecology and Obstetrics, National Taiwan University Hospital, Taipei City, Taiwan
| | - Kuan-Yu Chu
- Department of Nutritional Science, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Wei-Chi Ku
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Chieh-Yu Liu
- Biostatistical Consultant Lab, Department of Speech Language Pathology and Audiology, National Taipei University of Nursing and Health Sciences, Taipei City, Taiwan
| | - Rwei-Fen S Huang
- PhD Program in Nutrition and Food Science, Fu Jen Catholic University, New Taipei City, Taiwan.,Department of Nutritional Science, Fu Jen Catholic University, New Taipei City, Taiwan
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9
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House JS, Hall J, Park SS, Planchart A, Money E, Maguire RL, Huang Z, Mattingly CJ, Skaar D, Tzeng JY, Darrah TH, Vengosh A, Murphy SK, Jirtle RL, Hoyo C. Cadmium exposure and MEG3 methylation differences between Whites and African Americans in the NEST Cohort. ENVIRONMENTAL EPIGENETICS 2019; 5:dvz014. [PMID: 31528362 PMCID: PMC6736358 DOI: 10.1093/eep/dvz014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/21/2019] [Accepted: 07/19/2019] [Indexed: 05/06/2023]
Abstract
Cadmium (Cd) is a ubiquitous environmental pollutant associated with a wide range of health outcomes including cancer. However, obscure exposure sources often hinder prevention efforts. Further, although epigenetic mechanisms are suspected to link these associations, gene sequence regions targeted by Cd are unclear. Aberrant methylation of a differentially methylated region (DMR) on the MEG3 gene that regulates the expression of a cluster of genes including MEG3, DLK1, MEG8, MEG9 and DIO3 has been associated with multiple cancers. In 287 infant-mother pairs, we used a combination of linear regression and the Getis-Ord Gi* statistic to determine if maternal blood Cd concentrations were associated with offspring CpG methylation of the sequence region regulating a cluster of imprinted genes including MEG3. Correlations were used to examine potential sources and routes. We observed a significant geographic co-clustering of elevated prenatal Cd levels and MEG3 DMR hypermethylation in cord blood (P = 0.01), and these findings were substantiated in our statistical models (β = 1.70, se = 0.80, P = 0.03). These associations were strongest in those born to African American women (β = 3.52, se = 1.32, P = 0.01) compared with those born to White women (β = 1.24, se = 2.11, P = 0.56) or Hispanic women (β = 1.18, se = 1.24, P = 0.34). Consistent with Cd bioaccumulation during the life course, blood Cd levels increased with age (β = 0.015 µg/dl/year, P = 0.003), and Cd concentrations were significantly correlated between blood and urine (ρ > 0.47, P < 0.01), but not hand wipe, soil or house dust concentrations (P > 0.05). Together, these data support that prenatal Cd exposure is associated with aberrant methylation of the imprint regulatory element for the MEG3 gene cluster at birth. However, neither house-dust nor water are likely exposure sources, and ingestion via contaminated hands is also unlikely to be a significant exposure route in this population. Larger studies are required to identify routes and sources of exposure.
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Affiliation(s)
- John S House
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Jonathan Hall
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Sarah S Park
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Antonio Planchart
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Eric Money
- Center for Geospatial Analytics, North Carolina State University, Raleigh, NC, USA
- Department of Natural Resources, North Carolina State University, Raleigh, NC, USA
| | - Rachel L Maguire
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Duke University School of Medicine, Durham, NC, USA
| | - Carolyn J Mattingly
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - David Skaar
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Jung Ying Tzeng
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Thomas H Darrah
- Division of Climate, Water, and Environment, School of Earth Sciences, The Ohio State University, Columbus, OH, USA
| | - Avner Vengosh
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University School of Medicine, Durham, NC, USA
| | - Randy L Jirtle
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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10
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Giuliani C, Biggs D, Nguyen TT, Marasco E, De Fanti S, Garagnani P, Le Phan MT, Nguyen VN, Luiselli D, Romeo G. First evidence of association between past environmental exposure to dioxin and DNA methylation of CYP1A1 and IGF2 genes in present day Vietnamese population. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:976-985. [PMID: 30373043 DOI: 10.1016/j.envpol.2018.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 06/08/2023]
Abstract
During the Vietnam War, the United States military sprayed over 74 million litres of Agent Orange (AO) to destroy forest cover as a counterinsurgency tactic in Vietnam, Laos and Cambodia. The main ingredient was contaminated by 2,3,7,8-tetrachlorodibenzo-paradioxin (TCDD). DNA methylation (DNAm) differences are potential biomarker of environmental toxicants exposure. The aim of this study was to perform a preliminary investigation of the DNAm levels from peripheral blood of the present-day Vietnamese population, including individuals whose parents, according to historical data, were exposed to AO/TCDD during the war. 94 individuals from heavily sprayed areas (cases) and 94 individuals from non-sprayed areas (controls) were studied, and historical data on alleged exposure of parents collected. 94 cases were analysed considering those whose father/parents participated in the war (N = 29) and considering the place of residence of both parents (64 living in sprayed areas versus 30 in non-contaminated areas). DNAm levels in CYP1A1 and IGF2 genes were measured (MALDI-TOF technology). The analyses showed that: 1) one CpG site in the CYP1A1 and one in the IGF2 gene showed significant differences in DNAm levels between cases and controls; 2) the CYP1A1 region resulted to be hypomethylated (in 9 out of 16 sites/units; p-val<0.01) in 29 individuals whose father/parents participated in the war in the spray zones; 3) we showed that the place of residence of both parents influenced methylation levels of the CYP1A1 and IGF2 genes (p-val<0.05). In conclusion this study indicates that past environmental exposure to dioxin (AO/TCDD) shapes the DNAm profile of CYP1A1 and that the place of living for parents in former spray zones influences DNAm of CYP1A1 and IGF2 genes. These results open the way to new applications of DNAm as potential biomarker(s) of past human exposure to dioxin.
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Affiliation(s)
- Cristina Giuliani
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy; School of Anthropology and Museum Ethnography, University of Oxford, UK.
| | - David Biggs
- Department of History and School of Public Policy, University of California, Riverside, USA
| | | | - Elena Marasco
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Sara De Fanti
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy; Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, S-141 86 Stockholm, Sweden
| | | | | | - Donata Luiselli
- Department for the Cultural Heritage (DBC), Campus of Ravenna, University of Bologna, Bologna, Italy
| | - Giovanni Romeo
- Medical Genetics Unit, S. Orsola Hospital, University of Bologna, Italy and European School of Genetic Medicine, Italy
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11
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Nolan CM, Shiel RE, Buchan JG, O'Sullivan FM, Callanan JJ. Canine MAS1: monoallelic expression is suggestive of an imprinted gene. Anim Genet 2018; 49:438-446. [PMID: 30062832 DOI: 10.1111/age.12705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 12/15/2022]
Abstract
Imprinted genes are epigenetically modified in a parent-of-origin dependent manner and as a consequence are differentially expressed, with one allele typically expressed while the other is repressed. In canine, the insulin like growth factor 2 receptor gene (IGF2R) is imprinted with predominant expression of the maternally inherited allele. Because imprinted genes usually occur in clusters, we examined the allelic expression pattern of the gene encoding the canine Mas receptor (MAS1), which is located upstream of IGF2R on canine chromosome 1 and is highly conserved in mammals. In this report we describe monoallelic expression of canine MAS1 in the neonatal umbilical cord of several individuals and we identify the expressed allele as maternally inherited. These data suggest that canine MAS1 is an imprinted gene.
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Affiliation(s)
- C M Nolan
- UCD School of Biology and Environmental Science, Science Centre West, Belfield, Dublin 4, Ireland
| | - R E Shiel
- UCD School of Veterinary Medicine, Belfield, Dublin 4, Ireland
| | - J G Buchan
- UCD School of Biology and Environmental Science, Science Centre West, Belfield, Dublin 4, Ireland
| | - F M O'Sullivan
- UCD School of Biology and Environmental Science, Science Centre West, Belfield, Dublin 4, Ireland
| | - J J Callanan
- UCD School of Veterinary Medicine, Belfield, Dublin 4, Ireland
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12
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Cowley M, Skaar DA, Jima DD, Maguire RL, Hudson KM, Park SS, Sorrow P, Hoyo C. Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:037003. [PMID: 29529597 PMCID: PMC6071808 DOI: 10.1289/ehp2085] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Imprinted genes are defined by their preferential expression from one of the two parental alleles. This unique mode of gene expression is dependent on allele-specific DNA methylation profiles established at regulatory sequences called imprinting control regions (ICRs). These loci have been used as biosensors to study how environmental exposures affect methylation and transcription. However, a critical unanswered question is whether they are more, less, or equally sensitive to environmental stressors as the rest of the genome. OBJECTIVES Using cadmium exposure in humans as a model, we aimed to determine the relative sensitivity of ICRs to perturbation of methylation compared to similar, nonimprinted loci in the genome. METHODS We assayed DNA methylation genome-wide using bisulfite sequencing of 19 newborn cord blood and 20 maternal blood samples selected on the basis of maternal blood cadmium levels. Differentially methylated regions (DMRs) associated with cadmium exposure were identified. RESULTS In newborn cord blood and maternal blood, 641 and 1,945 cadmium-associated DMRs were identified, respectively. DMRs were more common at the 15 maternally methylated ICRs than at similar nonimprinted loci in newborn cord blood (p=5.64×10-8) and maternal blood (p=6.22×10-14), suggesting a higher sensitivity for ICRs to cadmium. Genome-wide, Enrichr analysis indicated that the top three functional categories for genes that overlapped DMRs in maternal blood were body mass index (BMI) (p=2.0×10-5), blood pressure (p=3.8×10-5), and body weight (p=0.0014). In newborn cord blood, the top three functional categories were BMI, atrial fibrillation, and hypertension, although associations were not significant after correction for multiple testing (p=0.098). These findings suggest that epigenetic changes may contribute to the etiology of cadmium-associated diseases. CONCLUSIONS We analyzed cord blood and maternal blood DNA methylation profiles genome-wide at nucleotide resolution in individuals selected for high and low blood cadmium levels in the first trimester. Our findings suggest that ICRs may be hot spots for perturbation by cadmium, motivating further study of these loci to investigate potential mechanisms of cadmium action. https://doi.org/10.1289/EHP2085.
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Affiliation(s)
- Michael Cowley
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
- W.M. Keck Center for Behavioral Biology , North Carolina State University , Raleigh, North Carolina, USA
| | - David A Skaar
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Dereje D Jima
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University , Raleigh, North Carolina, USA
| | - Rachel L Maguire
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Kathleen M Hudson
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Sarah S Park
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Patricia Sorrow
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
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13
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Kingsley SL, Deyssenroth MA, Kelsey KT, Awad YA, Kloog I, Schwartz JD, Lambertini L, Chen J, Marsit CJ, Wellenius GA. Maternal residential air pollution and placental imprinted gene expression. ENVIRONMENT INTERNATIONAL 2017; 108:204-211. [PMID: 28886413 PMCID: PMC5623128 DOI: 10.1016/j.envint.2017.08.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/30/2017] [Accepted: 08/30/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Maternal exposure to air pollution is associated with reduced fetal growth, but its relationship with expression of placental imprinted genes (important regulators of fetal growth) has not yet been studied. OBJECTIVES To examine relationships between maternal residential air pollution and expression of placental imprinted genes in the Rhode Island Child Health Study (RICHS). METHODS Women-infant pairs were enrolled following delivery between 2009 and 2013. We geocoded maternal residential addresses at delivery, estimated daily levels of fine particulate matter (PM2.5; n=355) and black carbon (BC; n=336) using spatial-temporal models, and estimated residential distance to nearest major roadway (n=355). Using linear regression models we investigated the associations between each exposure metric and expression of nine candidate genes previously associated with infant birthweight in RICHS, with secondary analyses of a panel of 108 imprinted genes expressed in the placenta. We also explored effect measure modification by infant sex. RESULTS PM2.5 and BC were associated with altered expression for seven and one candidate genes, respectively, previously linked with birthweight in this cohort. Adjusting for multiple comparisons, we found that PM2.5 and BC were associated with changes in expression of 41 and 12 of 108 placental imprinted genes, respectively. Infant sex modified the association between PM2.5 and expression of CHD7 and between proximity to major roadways and expression of ZDBF2. CONCLUSIONS We found that maternal exposure to residential PM2.5 and BC was associated with changes in placental imprinted gene expression, which suggests a plausible line of investigation of how air pollution affects fetal growth and development.
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Affiliation(s)
- Samantha L Kingsley
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA.
| | - Maya A Deyssenroth
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA; Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Yara Abu Awad
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Itai Kloog
- Department of Geography and Environmental Development, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Joel D Schwartz
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Luca Lambertini
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Obstetrics, Gynecology and Reproductive Science, 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; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Gregory A Wellenius
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
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14
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Gonzalez-Nahm S, Mendez M, Robinson W, Murphy SK, Hoyo C, Hogan V, Rowley D. Low maternal adherence to a Mediterranean diet is associated with increase in methylation at the MEG3-IG differentially methylated region in female infants. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx007. [PMID: 29492309 PMCID: PMC5804547 DOI: 10.1093/eep/dvx007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 02/09/2017] [Accepted: 03/12/2017] [Indexed: 05/17/2023]
Abstract
Diet is dictated by the surrounding environment, as food access and availability may change depending on where one lives. Maternal diet during pregnancy is an important part of the in utero environment, and may affect the epigenome. Studies looking at overall diet pattern in relation to DNA methylation have been lacking. The Mediterranean diet is known for its health benefits, including decreased inflammation, weight loss, and management of chronic diseases. This study assesses the association between maternal adherence to a Mediterranean diet pattern during pregnancy and infant DNA methylation at birth. Mediterranean diet adherence in early pregnancy was measured in 390 women enrolled in the Newborn Epigenetic Study, and DNA methylation was assessed in their infants at birth. Multinomial logistic regression was used to assess the association between adherence to a Mediterranean diet and infant methylation at the MEG3, MEG3-IG, pleiomorphic adenoma gene-like 1, insulin-like growth factor 2 gene, H19, mesoderm-specific transcript, neuronatin, paternally expressed gene 3, sarcoglycan and paternally expressed gene 10 regions, measured by pyrosequencing. Infants of mothers with a low adherence to a Mediterranean diet had a greater odds of hypo-methylation at the MEG3-IG differentially methylated region (DMR). Sex-stratified models showed that this association was present in girls only. This study provides early evidence on the association between overall diet pattern and methylation at the 9 DMRs included in this study, and suggests that maternal diet can have a sex-specific impact on infant DNA methylation at specific imprinted DMRs.
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Affiliation(s)
- Sarah Gonzalez-Nahm
- Department of Health, Behavior and Society, Bloomberg School of Public Health, Johns Hopkins University, 624 N. Broadway, HH 904, Baltimore, MD 21205, USADepartment of NutritionDepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USAOB/GYN, Duke University Medical CenterDepartment of Environmental Health Science, North Carolina State University, NC, USADepartment of Food, Health and Well-Being, W.K. Kellogg FoundationDepartment of Maternal and Child Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michelle Mendez
- Department of Health, Behavior and Society, Bloomberg School of Public Health, Johns Hopkins University, 624 N. Broadway, HH 904, Baltimore, MD 21205, USADepartment of NutritionDepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USAOB/GYN, Duke University Medical CenterDepartment of Environmental Health Science, North Carolina State University, NC, USADepartment of Food, Health and Well-Being, W.K. Kellogg FoundationDepartment of Maternal and Child Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Whitney Robinson
- Department of Health, Behavior and Society, Bloomberg School of Public Health, Johns Hopkins University, 624 N. Broadway, HH 904, Baltimore, MD 21205, USADepartment of NutritionDepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USAOB/GYN, Duke University Medical CenterDepartment of Environmental Health Science, North Carolina State University, NC, USADepartment of Food, Health and Well-Being, W.K. Kellogg FoundationDepartment of Maternal and Child Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan K. Murphy
- Department of Health, Behavior and Society, Bloomberg School of Public Health, Johns Hopkins University, 624 N. Broadway, HH 904, Baltimore, MD 21205, USADepartment of NutritionDepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USAOB/GYN, Duke University Medical CenterDepartment of Environmental Health Science, North Carolina State University, NC, USADepartment of Food, Health and Well-Being, W.K. Kellogg FoundationDepartment of Maternal and Child Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cathrine Hoyo
- Department of Health, Behavior and Society, Bloomberg School of Public Health, Johns Hopkins University, 624 N. Broadway, HH 904, Baltimore, MD 21205, USADepartment of NutritionDepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USAOB/GYN, Duke University Medical CenterDepartment of Environmental Health Science, North Carolina State University, NC, USADepartment of Food, Health and Well-Being, W.K. Kellogg FoundationDepartment of Maternal and Child Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vijaya Hogan
- Department of Health, Behavior and Society, Bloomberg School of Public Health, Johns Hopkins University, 624 N. Broadway, HH 904, Baltimore, MD 21205, USADepartment of NutritionDepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USAOB/GYN, Duke University Medical CenterDepartment of Environmental Health Science, North Carolina State University, NC, USADepartment of Food, Health and Well-Being, W.K. Kellogg FoundationDepartment of Maternal and Child Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Diane Rowley
- Department of Health, Behavior and Society, Bloomberg School of Public Health, Johns Hopkins University, 624 N. Broadway, HH 904, Baltimore, MD 21205, USADepartment of NutritionDepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USAOB/GYN, Duke University Medical CenterDepartment of Environmental Health Science, North Carolina State University, NC, USADepartment of Food, Health and Well-Being, W.K. Kellogg FoundationDepartment of Maternal and Child Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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15
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Abstract
Obesity is a complex and multifactorial disease, which likely comprises multiple subtypes. Emerging data have linked chemical exposures to obesity. As organismal response to environmental exposures includes altered gene expression, identifying the regulatory epigenetic changes involved would be key to understanding the path from exposure to phenotype and provide new tools for exposure detection and risk assessment. In this report, we summarize published data linking early-life exposure to the heavy metals, cadmium and lead, to obesity. We also discuss potential mechanisms, as well as the need for complete coverage in epigenetic screening to fully identify alterations. The keys to understanding how metal exposure contributes to obesity are improved assessment of exposure and comprehensive establishment of epigenetic profiles that may serve as markers for exposures.
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Affiliation(s)
- Sarah S Park
- Department of Biological Sciences, Center for Human Health & the Environment, North Carolina State University, Raleigh, NC 27695 USA
| | - David A Skaar
- Department of Biological Sciences, Center for Human Health & the Environment, North Carolina State University, Raleigh, NC 27695 USA
| | - Randy L Jirtle
- Department of Biological Sciences, Center for Human Health & the Environment, North Carolina State University, Raleigh, NC 27695 USA.,Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53705, USA.,Department of Sport & Exercise Sciences, Institute of Sport & Physical Activity Research, University of Bedfordshire, Bedford, Bedfordshire, UK
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health & the Environment, North Carolina State University, Raleigh, NC 27695 USA
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16
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Fuemmeler BF, Lee CT, Soubry A, Iversen ES, Huang Z, Murtha AP, Schildkraut JM, Jirtle RL, Murphy SK, Hoyo C. DNA Methylation of Regulatory Regions of Imprinted Genes at Birth and Its Relation to Infant Temperament. GENETICS & EPIGENETICS 2016; 8:59-67. [PMID: 27920589 PMCID: PMC5127604 DOI: 10.4137/geg.s40538] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/20/2016] [Accepted: 10/22/2016] [Indexed: 01/07/2023]
Abstract
BACKGROUND DNA methylation of the differentially methylated regions (DMRs) of imprinted genes is relevant to neurodevelopment. METHODS DNA methylation status of the DMRs of nine imprinted genes in umbilical cord blood leukocytes was analyzed in relation to infant behaviors and temperament (n = 158). RESULTS MEG3 DMR levels were positively associated with internalizing (β = 0.15, P = 0.044) and surgency (β = 0.19, P = 0.018) behaviors, after adjusting for birth weight, gender, gestational age at birth, maternal age at delivery, race/ethnicity, education level, smoking status, parity, and a history of anxiety or depression. Higher methylation levels at the intergenic MEG3-IG methylation regions were associated with surgency (β = 0.28, P = 0.0003) and PEG3 was positively related to externalizing (β = 0.20, P = 0.01) and negative affectivity (β = 0.18, P = 0.02). CONCLUSION While the small sample size limits inference, these pilot data support gene-specific associations between epigenetic differences in regulatory regions of imprinted domains at birth and later infant temperament.
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Affiliation(s)
- Bernard F Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, VA, USA
| | - Chien-Ti Lee
- Department of Family Life, Brigham Young University, Provo, UT, USA
| | - Adelheid Soubry
- Department of Public Health and Primary Care, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, NC, USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Amy P Murtha
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Randy L Jirtle
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.; Department of Sport and Exercise Sciences, Institute of Sport and Physical Activity Research (ISPAR), University of Bedfordshire, University Square, Luton, UK
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Cathrine Hoyo
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
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17
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Li Y, Xie C, Murphy SK, Skaar D, Nye M, Vidal AC, Cecil KM, Dietrich KN, Puga A, Jirtle RL, Hoyo C. Lead Exposure during Early Human Development and DNA Methylation of Imprinted Gene Regulatory Elements in Adulthood. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:666-73. [PMID: 26115033 PMCID: PMC4858407 DOI: 10.1289/ehp.1408577] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 06/24/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND Lead exposure during early development causes neurodevelopmental disorders by unknown mechanisms. Epidemiologic studies have focused recently on determining associations between lead exposure and global DNA methylation; however, such approaches preclude the identification of loci that may alter human disease risk. OBJECTIVES The objective of this study was to determine whether maternal, postnatal, and early childhood lead exposure can alter the differentially methylated regions (DMRs) that control the monoallelic expression of imprinted genes involved in metabolism, growth, and development. METHODS Questionnaire data and serial blood lead levels were obtained from 105 participants (64 females, 41 males) of the Cincinnati Lead Study from birth to 78 months. When participants were adults, we used Sequenom EpiTYPER assays to test peripheral blood DNA to quantify CpG methylation in peripheral blood leukocytes at DMRs of 22 human imprinted genes. Statistical analyses were conducted using linear regression. RESULTS Mean blood lead concentration from birth to 78 months was associated with a significant decrease in PEG3 DMR methylation (β = -0.0014; 95% CI: -0.0023, -0.0005, p = 0.002), stronger in males (β = -0.0024; 95% CI: -0.0038, -0.0009, p = 0.003) than in females (β = -0.0009; 95% CI: -0.0020, 0.0003, p = 0.1). Elevated mean childhood blood lead concentration was also associated with a significant decrease in IGF2/H19 (β = -0.0013; 95% CI: -0.0023, -0.0003, p = 0.01) DMR methylation, but primarily in females, (β = -0.0017; 95% CI: -0.0029, -0.0006, p = 0.005) rather than in males, (β = -0.0004; 95% CI: -0.0023, 0.0015, p = 0.7). Elevated blood lead concentration during the neonatal period was associated with higher PLAGL1/HYMAI DMR methylation regardless of sex (β = 0.0075; 95% CI: 0.0018, 0.0132, p = 0.01). The magnitude of associations between cumulative lead exposure and CpG methylation remained unaltered from 30 to 78 months. CONCLUSIONS Our findings provide evidence that early childhood lead exposure results in sex-dependent and gene-specific DNA methylation differences in the DMRs of PEG3, IGF2/H19, and PLAGL1/HYMAI in adulthood. CITATION Li Y, Xie C, Murphy SK, Skaar D, Nye M, Vidal AC, Cecil KM, Dietrich KN, Puga A, Jirtle RL, Hoyo C. 2016. Lead exposure during early human development and DNA methylation of imprinted gene regulatory elements in adulthood. Environ Health Perspect 124:666-673; http://dx.doi.org/10.1289/ehp.1408577.
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Affiliation(s)
- Yue Li
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Changchun Xie
- Division of Epidemiology and Biostatistics, Department of Environmental Health, Center for Clinical and Translational Science and Training, University of Cincinnati (UC), Cincinnati, Ohio, USA
| | - Susan K. Murphy
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - David Skaar
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University (NCSU), Raleigh, North Carolina, USA
| | - Monica Nye
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Adriana C. Vidal
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Kim M. Cecil
- Cincinnati Children’s Environmental Health Center, Cincinnati Children’s Hospital Medical Center, UC College of Medicine, Cincinnati, Ohio, USA
- Department of Radiology,
- Department of Pediatrics,
- Department of Environmental Health,
- Center for Environmental Genetics, and
| | - Kim N. Dietrich
- Division of Epidemiology and Biostatistics, UC College of Medicine, Cincinnati, Ohio, USA
| | - Alvaro Puga
- Department of Environmental Health,
- Center for Environmental Genetics, and
| | - Randy L. Jirtle
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University (NCSU), Raleigh, North Carolina, USA
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Sport and Exercise Sciences, Institute of Sport and Physical Activity Research, University of Bedfordshire, Bedford, Bedfordshire, United Kingdom
- Address correspondence to C. Hoyo, Department of Biological Sciences, Center for Human Health and the Environment (CHHE), Program of Epidemiology and Environmental Epigenomics, North Carolina State University (NCSU), Raleigh, NC 27695-7633 USA. Telephone: (919) 515-0540. E-mail: , or R.L. Jirtle, Department of Biological Sciences, CHHE, NCSU, Raleigh, NC 27695-7633 USA. Telephone: (919) 399-3342. E-mail:
| | - Cathrine Hoyo
- Department of Community and Family Medicine, and
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University (NCSU), Raleigh, North Carolina, USA
- Address correspondence to C. Hoyo, Department of Biological Sciences, Center for Human Health and the Environment (CHHE), Program of Epidemiology and Environmental Epigenomics, North Carolina State University (NCSU), Raleigh, NC 27695-7633 USA. Telephone: (919) 515-0540. E-mail: , or R.L. Jirtle, Department of Biological Sciences, CHHE, NCSU, Raleigh, NC 27695-7633 USA. Telephone: (919) 399-3342. E-mail:
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18
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Porta M. Human contamination by persistent toxic substances: the rationale to improve exposure assessment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:14560-14565. [PMID: 25167816 DOI: 10.1007/s11356-014-3460-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/14/2014] [Indexed: 06/03/2023]
Abstract
We know quite a lot about the generalized human contamination by environmental chemical agents; this statement is fully compatible with the view that most countries lack the necessary monitoring systems. We also know quite a lot about the toxic effects of environmental pollutants; this statement is fully compatible with the proposal that we need both more research and more energetic policies to decrease human contamination by such pollutants. Unsurprisingly, we know too little about the (environmental and social) causes and the etiopathogenesis (mechanisms) of the most prevalent diseases, and we will continue to miss relevant causes and mechanisms if we neglect the toxic chemicals that commonly contaminate humans, worldwide. Basic, clinical end environmental-epidemiological research on human health should more often consider integrating biomarkers of internal dose of environmental chemical pollutants. When we act in more responsible, rational, and scientific ways; when we become less dismissive towards environmental hazards; and when we thus neglect less the generalized human contamination by environmental chemical agents and their toxic effects, we will expand mechanistic biologic knowledge, and we shall as well increase the effectiveness of interventions and policies that enable the primary prevention of human diseases which cause huge amounts of economic burden and human suffering.
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Affiliation(s)
- Miquel Porta
- Hospital del Mar Institute of Medical Research (IMIM), Barcelona, Catalonia, Spain.
- School of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA.
- CIBER en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.
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19
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Fedak KM, Bernal A, Capshaw ZA, Gross S. Applying the Bradford Hill criteria in the 21st century: how data integration has changed causal inference in molecular epidemiology. Emerg Themes Epidemiol 2015; 12:14. [PMID: 26425136 PMCID: PMC4589117 DOI: 10.1186/s12982-015-0037-4] [Citation(s) in RCA: 364] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 09/23/2015] [Indexed: 01/15/2023] Open
Abstract
In 1965, Sir Austin Bradford Hill published nine “viewpoints” to help determine if observed epidemiologic associations are causal. Since then, the “Bradford Hill Criteria” have become the most frequently cited framework for causal inference in epidemiologic studies. However, when Hill published his causal guidelines—just 12 years after the double-helix model for DNA was first suggested and 25 years before the Human Genome Project began—disease causation was understood on a more elementary level than it is today. Advancements in genetics, molecular biology, toxicology, exposure science, and statistics have increased our analytical capabilities for exploring potential cause-and-effect relationships, and have resulted in a greater understanding of the complexity behind human disease onset and progression. These additional tools for causal inference necessitate a re-evaluation of how each Bradford Hill criterion should be interpreted when considering a variety of data types beyond classic epidemiology studies. Herein, we explore the implications of data integration on the interpretation and application of the criteria. Using examples of recently discovered exposure–response associations in human disease, we discuss novel ways by which researchers can apply and interpret the Bradford Hill criteria when considering data gathered using modern molecular techniques, such as epigenetics, biomarkers, mechanistic toxicology, and genotoxicology.
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Affiliation(s)
- Kristen M Fedak
- Department of Environmental and Radiological Health Sciences, Colorado State University, 350 West Lake Street, Fort Collins, CO 80521 USA ; Cardno ChemRisk, 4840 Pearl East Circle, Suite 300 West, Boulder, CO 80301 USA
| | - Autumn Bernal
- Cardno ChemRisk, 130 Vantis Suite 170, Aliso Viejo, CA 92656 USA
| | - Zachary A Capshaw
- Cardno ChemRisk, 4840 Pearl East Circle, Suite 300 West, Boulder, CO 80301 USA
| | - Sherilyn Gross
- Cardno ChemRisk, 4840 Pearl East Circle, Suite 300 West, Boulder, CO 80301 USA
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Marsit CJ. Influence of environmental exposure on human epigenetic regulation. ACTA ACUST UNITED AC 2015; 218:71-9. [PMID: 25568453 DOI: 10.1242/jeb.106971] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Environmental toxicants can alter epigenetic regulatory features such as DNA methylation and microRNA expression. As the sensitivity of epigenomic regulatory features may be greatest during the in utero period, when critical windows are narrow, and when epigenomic profiles are being set, this review will highlight research focused on that period. I will focus on work in human populations, where the impact of environmental toxicants in utero, including cigarette smoke and toxic trace metals such as arsenic, mercury and manganese, on genome-wide, gene-specific DNA methylation has been assessed. In particular, arsenic is highlighted, as this metalloid has been the focus of a number of studies and its detoxification mechanisms are well understood. Importantly, the tissues and cells being examined must be considered in context in order to interpret the findings of these studies. For example, by studying the placenta, it is possible to identify potential epigenetic adaptations of key genes and pathways that may alter the developmental course in line with the developmental origins of health and disease paradigm. Alternatively, studies of newborn cord blood can be used to examine how environmental exposure in utero can impact the composition of cells within the peripheral blood, leading to immunological effects of exposure. The results suggest that in humans, like other vertebrates, there is a susceptibility for epigenomic alteration by the environment during intrauterine development, and this may represent a mechanism of plasticity of the organism in response to its environment as well as a mechanism through which long-term health consequences can be shaped.
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Affiliation(s)
- Carmen J Marsit
- Department of Pharmacology and Toxicology and Section of Epidemiology and Biostatistics in the Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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Vidal AC, Semenova V, Darrah T, Vengosh A, Huang Z, King K, Nye MD, Fry R, Skaar D, Maguire R, Murtha A, Schildkraut J, Murphy S, Hoyo C. Maternal cadmium, iron and zinc levels, DNA methylation and birth weight. BMC Pharmacol Toxicol 2015; 16:20. [PMID: 26173596 PMCID: PMC4502530 DOI: 10.1186/s40360-015-0020-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 07/07/2015] [Indexed: 12/27/2022] Open
Abstract
Background Cadmium (Cd) is a ubiquitous and environmentally persistent toxic metal that has been implicated in neurotoxicity, carcinogenesis and obesity and essential metals including zinc (Zn) and iron (Fe) may alter these outcomes. However mechanisms underlying these relationships remain limited. Methods We examined whether maternal Cd levels during early pregnancy were associated with offspring DNA methylation at regulatory sequences of genomically imprinted genes and weight at birth, and whether Fe and Zn altered these associations. Cd, Fe and Zn were measured in maternal blood of 319 women ≤12 weeks gestation. Offspring umbilical cord blood leukocyte DNA methylation at regulatory differentially methylated regions (DMRs) of 8 imprinted genes was measured using bisulfite pyrosequencing. Regression models were used to examine the relationships among Cd, Fe, Zn, and DMR methylation and birth weight. Results Elevated maternal blood Cd levels were associated with lower birth weight (p = 0.03). Higher maternal blood Cd levels were also associated with lower offspring methylation at the PEG3 DMR in females (β = 0.55, se = 0.17, p = 0.05), and at the MEG3 DMR in males (β = 0.72, se = 0.3, p = 0.08), however the latter association was not statistically significant. Associations between Cd and PEG3 and PLAGL1 DNA methylation were stronger in infants born to women with low concentrations of Fe (p < 0.05). Conclusions Our data suggest the association between pre-natal Cd and offspring DNA methylation at regulatory sequences of imprinted genes may be sex- and gene-specific. Essential metals such as Zn may mitigate DNA methylation response to Cd exposure. Larger studies are required.
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Affiliation(s)
- Adriana C Vidal
- Department of Surgery, Division of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
| | - Viktoriya Semenova
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA. .,Department of Public Health, Brody School of Medicine, East Carolina University, Greenville, NC, 27834, USA.
| | - Thomas Darrah
- Division of Water, Climate, and the Environment, School of Earth Sciences, The Ohio State University, Columbus, OH, 43210, USA.
| | - Avner Vengosh
- Nicholas School of the Environment, Duke University, Research Drive, Durham, NC, 27710, USA.
| | - Zhiqing Huang
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University School of Medicine, Research Drive, Durham, NC, 27710, USA.
| | - Katherine King
- Environmental Public Health Division, U.S. Environmental Protection Agency, Chapel Hill, NC, 27599, USA. .,Department of Community and Family Medicine and Duke Cancer Institute, Duke University School of Medicine, Erwin Drive, Durham, NC, 27710, USA.
| | - Monica D Nye
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University School of Medicine, Research Drive, Durham, NC, 27710, USA. .,University of North Carolina at Chapel Hill, Lineberger Comprehensive Cancer Center, 450 West Drive, Chapel Hill, NC, 27599, USA.
| | - Rebecca Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, UNC-Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - David Skaar
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Rachel Maguire
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Amy Murtha
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Duke University School of Medicine, Erwin Drive, Durham, NC, 27710, USA.
| | - Joellen Schildkraut
- Department of Community and Family Medicine and Duke Cancer Institute, Duke University School of Medicine, Erwin Drive, Durham, NC, 27710, USA.
| | - Susan Murphy
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University School of Medicine, Research Drive, Durham, NC, 27710, USA.
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA.
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22
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Nye MD, Hoyo C, Murphy SK. In vitro lead exposure changes DNA methylation and expression of IGF2 and PEG1/MEST. Toxicol In Vitro 2015; 29:544-50. [PMID: 25596546 DOI: 10.1016/j.tiv.2015.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 12/10/2014] [Accepted: 01/06/2015] [Indexed: 11/28/2022]
Abstract
Epigenetic processes, such as changes in DNA methylation, likely mediate the link between environmental exposures in utero and altered gene expression. Differentially methylated regions (DMRs) that regulate imprinted genes may be especially vulnerable to environmental exposures since imprinting is established and maintained largely through DNA methylation, resulting in expression from only one parental chromosome. We used the human embryonic kidney cell line, HEK-293, to investigate the effects of exposure to physiologically relevant doses of lead acetate (Pb) on the methylation status of nine imprinted gene DMRs. We assessed mean methylation after seventy-two hours of Pb exposure (0-25 μg/dL) using bisulfite pyrosequencing. The PEG1/MEST and IGF2 DMRs had maximum methylation decreases of 9.6% (20 μg/dL; p<0.005) and 3.8% (25 μg/dL; p<0.005), respectively. Changes at the MEG3 DMRs had a maximum decrease in methylation of 2.9% (MEG3) and 1.8% (MEG3-IG) at 5 μg/dL Pb, but were not statistically significant. The H19, NNAT, PEG3, PLAGL1, and SGCE/PEG10 DMRs showed a less than 0.5% change in methylation, across the dose range used, and were deemed non-responsive to Pb in our model. Pb exposure below reportable/actionable levels increased expression of PEG1/MEST concomitant with decreased methylation. These results suggest that Pb exposure can stably alter the regulatory capacity of multiple imprinted DMRs.
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Affiliation(s)
- Monica D Nye
- Duke University Medical Center, Department of Obstetrics and Gynecology, B225 LSRC, Research Drive, Durham, NC 27708, USA; University of North Carolina at Chapel Hill, Lineberger Comprehensive Cancer Center, 450 West Drive, Chapel Hill, NC 27599, USA.
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA.
| | - Susan K Murphy
- Duke University Medical Center, Department of Obstetrics and Gynecology, B225 LSRC, Research Drive, Durham, NC 27708, USA.
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23
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Hoyo C, Daltveit AK, Iversen E, Benjamin-Neelon SE, Fuemmeler B, Schildkraut J, Murtha AP, Overcash F, Vidal AC, Wang F, Huang Z, Kurtzberg J, Seewaldt V, Forman M, Jirtle RL, Murphy SK. Erythrocyte folate concentrations, CpG methylation at genomically imprinted domains, and birth weight in a multiethnic newborn cohort. Epigenetics 2014; 9:1120-30. [PMID: 24874916 DOI: 10.4161/epi.29332] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Epigenetic mechanisms are proposed to link maternal concentrations of methyl group donor nutrients with the risk of low birth weight. However, empirical data are lacking. We have examined the association between maternal folate and birth weight and assessed the mediating role of DNA methylation at nine differentially methylated regions (DMRs) of genomically imprinted genes in these associations. Compared with newborns of women with folate levels in the lowest quartile, birth weight was higher in newborns of mothers in the second (β = 143.2, se = 63.2, P = 0.02), third (β = 117.3, se = 64.0, P = 0.07), and fourth (β = 133.9, se = 65.2, P = 0.04) quartiles, consistent with a threshold effect. This pattern of association did not vary by race/ethnicity but was more apparent in newborns of non-obese women. DNA methylation at the PLAGL1, SGCE, DLK1/MEG3 and IGF2/H19 DMRs was associated with maternal folate levels and also birth weight, suggestive of threshold effects. MEG3 DMR methylation mediated the association between maternal folate levels and birth weight (P =0.06). While the small sample size and partial scope of examined DMRs limit our conclusions, our data suggest that, with respect to birth weight, no additional benefits may be derived from increased maternal folate concentrations, especially in non-obese women. These data also support epigenetic plasticity as a key mechanistic response to folate availability during early fetal development.
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Affiliation(s)
- Cathrine Hoyo
- Department of Biological Sciences; North Carolina State University; Raleigh, NC USA; Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Anne Kjersti Daltveit
- Department of Global Public Health and Primary Care; University of Bergen; Bergen, Norway
| | - Edwin Iversen
- Department of Statistics; Duke University; Durham, NC USA
| | - Sara E Benjamin-Neelon
- Department of Community and Family Medicine; Duke University School of Medicine and Duke Global Health Institute; Durham, NC USA
| | - Bernard Fuemmeler
- Department of Community and Family Medicine; Duke University; Durham, NC USA
| | - Joellen Schildkraut
- Department of Community and Family Medicine; Duke Cancer Institute; Duke University; Durham, NC USA
| | - Amy P Murtha
- Department of Obstetrics and Gynecology; Division of Maternal-Fetal Medicine; School of Medicine; Duke University; Durham, NC USA
| | - Francine Overcash
- Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Adriana C Vidal
- Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Frances Wang
- Department of Community and Family Medicine; Duke Cancer Institute; Duke University; Durham, NC USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology; Division of Gynecologic Oncology; School of Medicine; Duke University; Durham, NC USA
| | - Joanne Kurtzberg
- Duke University Department of Pediatrics; Duke Cancer Institute; School of Medicine; Duke University; Durham, NC USA
| | - Victoria Seewaldt
- Department of Medicine; Division of Oncology; School of Medicine; Duke University; Durham, NC USA
| | - Michele Forman
- Department of Nutritional Sciences; University of Texas; Austin, TX USA
| | - Randy L Jirtle
- Department of Oncology; McArdle Laboratory for Cancer Research; University of Wisconsin-Madison; Madison, WI USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology; Division of Gynecologic Oncology; School of Medicine; Duke University; Durham, NC USA
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24
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Chen J, Li Q, Rialdi A, Mystal E, Ly J, Finik J, Davey T, Lambertini L, Nomura Y. Influences of Maternal Stress during Pregnancy on the Epi/genome: Comparison of Placenta and Umbilical Cord Blood. ACTA ACUST UNITED AC 2014; 3. [PMID: 29963333 PMCID: PMC6020835 DOI: 10.4172/2167-1044.1000152] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background Maternal stress during pregnancy is one of the major adverse environmental factors in utero that is capable of influencing health outcomes of the offspring throughout life. Both genetic and epigenetic processes are susceptible to environmental insults in utero and are potential biomarkers of the experienced environment including maternal stress. Methods We profiled expression level of six genes in hypothalamic pituitary adrenal (HPA) axis functioning (HSD11B2, SLC6A4, NR3C1, NR3C2, CRHR1 and CRHR2), two imprinted genes (IGF2 and H19) and one neurodevelopmental gene (EGR1), from 49 pairs of placenta and umbilical cord blood (UCB) samples from a birth cohort. We also assessed global methylation levels by LUminometric Methylation Assay (LUMA) and methylation at the imprinting control region (ICR) of IGF2/H19. Results Little correlations between paired placenta and UCB were observed except H19 expression (r = 0.31, P = 0.04) and IGF2/H19 ICR methylation (r = 0.43, P = 0.01); gene expression levels were significantly higher (P < 0.001) in placenta than UCB except CRHR1 and CRHR2, which were unexpressed in placenta. Maternal stress correlated higher levels of HPA genes and lower levels of EGR1 and LUMA, but only in placenta. Positive association between maternal stress and IGF2/H19 ICR methylation was present in both placenta and UCB. Conclusions Our findings support the notion that adverse in utero environment, as measured by antenatal maternal stress, depression and anxiety, can be observed in the epi/genome of the relevant tissues, i.e. placenta and UCBs, leading to development of molecular markers for assessing in utero adversities.
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Affiliation(s)
- Jia Chen
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Qian Li
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexender Rialdi
- Graduate School, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elana Mystal
- Department of Psychology, Queens College, CUNY, Flushing, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jenny Ly
- Department of Psychology, Queens College, CUNY, Flushing, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jackie Finik
- Department of Psychology, Queens College, CUNY, Flushing, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Taira Davey
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luca Lambertini
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yoko Nomura
- Department of Psychology, Queens College, CUNY, Flushing, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,William E. Macaulay Honors College (Queens), New York, NY, USA
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Wehkalampi K, Muurinen M, Wirta SB, Hannula-Jouppi K, Hovi P, Järvenpää AL, Eriksson JG, Andersson S, Kere J, Kajantie E. Altered Methylation of IGF2 Locus 20 Years after Preterm Birth at Very Low Birth Weight. PLoS One 2013; 8:e67379. [PMID: 23840686 PMCID: PMC3686716 DOI: 10.1371/journal.pone.0067379] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/17/2013] [Indexed: 12/21/2022] Open
Abstract
Introduction People born preterm at very low birth weight (VLBW, ≤1500g) have higher rates of risk factors for adult-onset diseases, including cardiovascular diseases and type 2 diabetes. These risks may be mediated through epigenetic modification of genes that are critical to normal growth and development. Methods We measured the methylation level of an imprinted insulin-like-growth-factor 2 (IGF2) locus (IGF2/H19) in young adults born preterm at VLBW and in their peers born at term. We studied 158 VLBW and 161 control subjects aged 18 to 27 years from the Helsinki Study of Very Low Birth Weight Adults. Methylation fraction at two IGF2 differentially methylated regions (DMRs) – IGF2 antisense transcript (IGF2AS, also known as IGF2 DMR0) and last exon of IGF2 (IGF2_05, also known as IGF2 DMR2) – were measured with Sequenom Epityper. We used linear regression and adjustment for covariates to compare methylation fractions at these DMRs between VLBW and control subjects. Results At one IGF2AS CpG site, methylation was significantly lower in VLBW than in control subjects, mean difference −0.017 (95% CI; −0.028, −0.005), P = 0.004. Methylation at IGF2_05 was not different between the groups. Conclusions Methylation of IGF2AS is altered 20 years after preterm birth at VLBW. Altered methylation may be a mechanism of later increased disease risk but more data are needed to indicate causality.
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Affiliation(s)
- Karoliina Wehkalampi
- Department of Health Promotion and Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Children’s Hospital, Helsinki University Central Hospital, Helsinki, Finland
- * E-mail:
| | - Mari Muurinen
- Research Programs Unit, Molecular Medicine Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
| | - Sara Bruce Wirta
- Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institute, Stockholm, Sweden
| | - Katariina Hannula-Jouppi
- Skin and Allergy Hospital, Helsinki University Central Hospital, Helsinki, Finland
- Research Programs Unit, Molecular Medicine Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
| | - Petteri Hovi
- Department of Health Promotion and Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Children’s Hospital, Helsinki University Central Hospital, Helsinki, Finland
| | | | - Johan G. Eriksson
- Department of Health Promotion and Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Unit of General Practice, Helsinki University Central Hospital, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, University of Helsinki, Helsinki, Finland
| | - Sture Andersson
- Children’s Hospital, Helsinki University Central Hospital, Helsinki, Finland
| | - Juha Kere
- Research Programs Unit, Molecular Medicine Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institute, Stockholm, Sweden
| | - Eero Kajantie
- Department of Health Promotion and Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Children’s Hospital, Helsinki University Central Hospital, Helsinki, Finland
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26
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Porta M. Human contamination by environmental chemical pollutants: can we assess it more properly? Prev Med 2012; 55:560-2. [PMID: 23036521 DOI: 10.1016/j.ypmed.2012.09.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 09/23/2012] [Accepted: 09/25/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Miquel Porta
- Hospital del Mar Institute of Medical Research (IMIM), Barcelona, Catalonia, Spain.
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27
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Murphy SK, Huang Z, Hoyo C. Differentially methylated regions of imprinted genes in prenatal, perinatal and postnatal human tissues. PLoS One 2012; 7:e40924. [PMID: 22808284 PMCID: PMC3396645 DOI: 10.1371/journal.pone.0040924] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 06/15/2012] [Indexed: 12/11/2022] Open
Abstract
Epigenetic plasticity in relation to in utero exposures may mechanistically explain observed differences in the likelihood of developing common complex diseases including hypertension, diabetes and cardiovascular disease through the cumulative effects of subtle alterations in gene expression. Imprinted genes are essential mediators of growth and development and are characterized by differentially methylated regulatory regions (DMRs) that carry parental allele-specific methylation profiles. This theoretical 50% level of methylation provides a baseline from which endogenously- or exogenously-induced deviations in methylation can be detected. We quantified DNA methylation at imprinted gene DMRs in a large panel of human conceptal tissues, in matched buccal cell specimens collected at birth and at one year of age, and in the major cell fractions of umbilical cord blood to assess the stability of methylation at these regions. DNA methylation was measured using validated pyrosequencing assays at seven DMRs regulating the IGF2/H19, DLK1/MEG3, MEST, NNAT and SGCE/PEG10 imprinted domains. DMR methylation did not significantly differ for the H19, MEST and SGCE/PEG10 DMRs across all conceptal tissues analyzed (ANOVA p>0.10). Methylation differences at several DMRs were observed in tissues from brain (IGF2 and MEG3-IG DMRs), liver (IGF2 and MEG3 DMRs) and placenta (both DLK1/MEG3 DMRs and NNAT DMR). In most infants, methylation profiles in buccal cells at birth and at one year of age were comparable, as was methylation in the major cell fractions of umbilical cord blood. Several infants showed temporal deviations in methylation at multiple DMRs. Similarity of inter-individual and intra-individual methylation at some, but not all of the DMRs analyzed supports the possibility that methylation of these regions can serve as useful biosensors of exposure.
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Affiliation(s)
- Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, United States of America.
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28
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Perkins E, Murphy SK, Murtha AP, Schildkraut J, Jirtle RL, Demark-Wahnefried W, Forman MR, Kurtzberg J, Overcash F, Huang Z, Hoyo C. Insulin-like growth factor 2/H19 methylation at birth and risk of overweight and obesity in children. J Pediatr 2012; 161:31-9. [PMID: 22341586 PMCID: PMC3360130 DOI: 10.1016/j.jpeds.2012.01.015] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 11/28/2011] [Accepted: 01/06/2012] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To determine whether aberrant DNA methylation at differentially methylated regions (DMRs) regulating insulin-like growth factor 2 (IGF2) expression in umbilical cord blood is associated with overweight or obesity in a multiethnic cohort. STUDY DESIGN Umbilical cord blood leukocytes of 204 infants born between 2005 and 2009 in Durham, North Carolina, were analyzed for DNA methylation at two IGF2 DMRs by using pyrosequencing. Anthropometric and feeding data were collected at age 1 year. Methylation differences were compared between children >85th percentile of the Centers for Disease Control and Prevention growth charts weight-for-age (WFA) and children ≤ 85th percentile of WFA at 1 year by using generalized linear models, adjusting for post-natal caloric intake, maternal cigarette smoking, and race/ethnicity. RESULTS The methylation percentages at the H19 imprint center DMR was higher in infants with WFA >85th percentile (62.7%; 95% CI, 59.9%-65.5%) than in infants with WFA ≤ 85th percentile (59.3%; 95% CI, 58.2%-60.3%; P = .02). At the intragenic IGF2 DMR, methylation levels were comparable between infants with WFA ≤ 85th percentile and infants with WFA >85th percentile. CONCLUSIONS Our findings suggest that IGF2 plasticity may be mechanistically important in early childhood overweight or obese status. If confirmed in larger studies, these findings suggest aberrant DNA methylation at sequences regulating imprinted genes may be useful identifiers of children at risk for the development of early obesity.
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Affiliation(s)
- Ellen Perkins
- Department of Community and Family Medicine, Duke University, Durham, NC 27710, USA
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29
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Byun HM, Nordio F, Coull BA, Tarantini L, Hou L, Bonzini M, Apostoli P, Bertazzi PA, Baccarelli A. Temporal stability of epigenetic markers: sequence characteristics and predictors of short-term DNA methylation variations. PLoS One 2012; 7:e39220. [PMID: 22745719 PMCID: PMC3379987 DOI: 10.1371/journal.pone.0039220] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 05/21/2012] [Indexed: 01/27/2023] Open
Abstract
Background DNA methylation is an epigenetic mechanism that has been increasingly investigated in observational human studies, particularly on blood leukocyte DNA. Characterizing the degree and determinants of DNA methylation stability can provide critical information for the design and conduction of human epigenetic studies. Methods We measured DNA methylation in 12 gene-promoter regions (APC, p16, p53, RASSF1A, CDH13, eNOS, ET-1, IFNγ, IL-6, TNFα, iNOS, and hTERT) and 2 of non-long terminal repeat elements, i.e., L1 and Alu in blood samples obtained from 63 healthy individuals at baseline (Day 1) and after three days (Day 4). DNA methylation was measured by bisulfite-PCR-Pyrosequencing. We calculated intraclass correlation coefficients (ICCs) to measure the within-individual stability of DNA methylation between Day 1 and 4, subtracted of pyrosequencing error and adjusted for multiple covariates. Results Methylation markers showed different temporal behaviors ranging from high (IL-6, ICC = 0.89) to low stability (APC, ICC = 0.08) between Day 1 and 4. Multiple sequence and marker characteristics were associated with the degree of variation. Density of CpG dinucleotides nearby the sequence analyzed (measured as CpG(o/e) or G+C content within ±200bp) was positively associated with DNA methylation stability. The 3′ proximity to repeat elements and range of DNA methylation on Day 1 were also positively associated with methylation stability. An inverted U-shaped correlation was observed between mean DNA methylation on Day 1 and stability. Conclusions The degree of short-term DNA methylation stability is marker-dependent and associated with sequence characteristics and methylation levels.
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Affiliation(s)
- Hyang-Min Byun
- Laboratory of Environmental Epigenetics, Exposure Epidemiology and Risk Program, Harvard School of Public Health, Boston, Massachusetts, United States of America.
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Hoyo C, Fortner K, Murtha AP, Schildkraut JM, Soubry A, Demark-Wahnefried W, Jirtle RL, Kurtzberg J, Forman MR, Overcash F, Huang Z, Murphy SK. Association of cord blood methylation fractions at imprinted insulin-like growth factor 2 (IGF2), plasma IGF2, and birth weight. Cancer Causes Control 2012; 23:635-45. [PMID: 22392079 PMCID: PMC3313040 DOI: 10.1007/s10552-012-9932-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 02/16/2012] [Indexed: 12/19/2022]
Abstract
Purpose Altered methylation at Insulin-like Growth Factor 2 (IGF2) regulatory regions has previously been associated with obesity, and several malignancies including colon, esophageal, and prostate adenocarcinomas, presumably via changes in expression and/or loss of imprinting, but the functional significance of these DNA methylation marks have not been demonstrated in humans. We examined associations among DNA methylation at IGF2 differentially methylated regions (DMRs), circulating IGF2 protein concentrations in umbilical cord blood (UCB) and birth weight in newborns. Methods Questionnaire data were obtained from 300 pregnant women recruited between 2005 and 2009. UCB DNA methylation was measured by bisulfite pyrosequencing. UCB plasma concentrations of soluble IGF2 were measured by ELISA assays. Generalized linear regression models were used to examine the relationship between DMR methylation and IGF2 levels. Results Lower IGF2 DMR methylation was associated with elevated plasma IGF2 protein concentrations (β = −9.87, p < 0.01); an association that was stronger in infants born to obese women (pre-pregnancy BMI > 30 kg/m2, β = −20.21, p < 0.0001). Elevated IGF2 concentrations were associated with higher birth weight (p < 0.0001) after adjusting for maternal race/ethnicity, pre-pregnancy BMI, cigarette smoking, gestational diabetes, and infant sex. These patterns of association were not apparent at the H19 DMR. Conclusion Our data suggest that variation in IGF2 DMR methylation is an important mechanism by which circulating IGF2 concentrations, a putative risk factor for obesity and cancers of the colon, esophagus, and prostate, are modulated; associations that may depend on pre-pregnancy obesity.
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Affiliation(s)
- Cathrine Hoyo
- Department of Community and Family Medicine, Duke University Medical Center, 2200 West Main Street, Ste. 600, Durham, NC 27705, USA.
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Murphy SK, Adigun A, Huang Z, Overcash F, Wang F, Jirtle RL, Schildkraut JM, Murtha AP, Iversen ES, Hoyo C. Gender-specific methylation differences in relation to prenatal exposure to cigarette smoke. Gene 2011; 494:36-43. [PMID: 22202639 DOI: 10.1016/j.gene.2011.11.062] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/25/2011] [Accepted: 11/30/2011] [Indexed: 12/15/2022]
Abstract
Epigenetic alterations may mechanistically explain the developmental origins of adult disease, namely the hypothesis that many complex adult chronic diseases originate as a result of conditions encountered in utero. If true, epigenetically regulated imprinted genes, critical to normal growth and development, may partially mediate these outcomes. We determined the influence of in utero exposure to cigarette smoking on methylation at two differentially methylated regions (DMRs) regulating Insulin-like Growth Factor 2 (IGF2) and H19, and how this might relate to birth weight of infants born to 418 pregnant women. Smoking status was ascertained through self-report and medical records. Bisulfite pyrosequencing was used to measure methylation in umbilical cord blood DNAs. Least squares DNA methylation means at each DMR and birth weight were compared between infants of smokers and non-smokers, using generalized linear models. While there were no significant differences at the H19 DMR, infants born to smokers had higher methylation at the IGF2 DMR than those born to never smokers or those who quit during pregnancy (49.5%, SD=8.0 versus 46.6%, SD=5.6 and 45.8%, SD=6.3, respectively; p=0.0002). The smoking-related increase in methylation was most pronounced in male offspring (p for sex interaction=0.03), for whom approximately 20% of smoking-related low birth weight was mediated by DNA methylation at the IGF2 DMR. Our findings suggest that IGF2 DMR plasticity is an important mechanism by which in utero adjustments to environmental toxicants are conferred. Larger studies to replicate these findings are required.
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Affiliation(s)
- Susan K Murphy
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Duke University Medical Center, Durham, NC 27708, USA.
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Talens RP, Jukema JW, Trompet S, Kremer D, Westendorp RGJ, Lumey LH, Sattar N, Putter H, Slagboom PE, Heijmans BT. Hypermethylation at loci sensitive to the prenatal environment is associated with increased incidence of myocardial infarction. Int J Epidemiol 2011; 41:106-15. [PMID: 22101166 DOI: 10.1093/ije/dyr153] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Human epidemiological studies suggest that small size at birth and food deprivation during gestation confer an excess risk of coronary heart diseases (CHD) in adulthood, frequently in a sex-specific manner. Prior epigenetic studies indicate that such prenatal conditions are marked by persistent and sometimes sex-specific changes in DNA methylation. Here, we have investigated the association between DNA methylation and myocardial infarction (MI) at six loci sensitive to prenatal nutrition, anticipating potential sex-specificity. Method Within the placebo group of the PROSPER trial on pravastatin and the risk of CHD, we compared all individuals who were event free at baseline and developed MI during 3 years' follow-up (n = 122) with a similar-sized control group. Methylation at IL10, LEP, ABCA1, IGF2, INS and GNASAS was measured in DNA extracted from leucocytes using mass spectrometry. RESULTS DNA methylation at GNASAS was modestly higher in MI cases compared with controls (P = 0.030). A significant sex interaction was observed for INS (P = 0.014) and GNASAS (P = 0.031). Higher DNA methylation at these loci was associated with MI among women (INS: +2.5%, P = 0.002; GNASAS: +4.2%, P = 0.001). Hypermethylation at one locus and at both loci was associated with odds ratios (ORs) of 2.8 and 8.6, respectively (P(trend) = 3.0 × 10(-4)). No association was observed among men. CONCLUSIONS The risk of MI in women is associated with DNA methylation marks at specific loci previously shown to be sensitive to prenatal conditions. This observation may reflect a developmental component of MI.
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Affiliation(s)
- Rudolf P Talens
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
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Soubry A, Murphy S, Huang Z, Murtha A, Schildkraut J, Jirtle R, Wang F, Kurtzberg J, Demark-Wahnefried W, Forman M, Hoyo C. The effects of depression and use of antidepressive medicines during pregnancy on the methylation status of the IGF2 imprinted control regions in the offspring. Clin Epigenetics 2011; 3:2. [PMID: 22414206 PMCID: PMC3257545 DOI: 10.1186/1868-7083-3-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 10/26/2011] [Indexed: 12/31/2022] Open
Abstract
In utero exposures to environmental factors may result in persistent epigenetic modifications affecting normal development and susceptibility to chronic diseases in later life. We explored the relationship between exposure of the growing fetus to maternal depression or antidepressants and DNA methylation at two differentially methylated regions (DMRs) of the imprinted Insulin-like Growth Factor 2 (IGF2) gene. Aberrant DNA methylation at the IGF2 and neighboring H19 DMRs has been associated with deregulated IGF2 expression, childhood cancers and several chronic diseases during adulthood. Our study population is comprised of pregnant mothers and their newborns (n = 436), as part of the Newborn Epigenetics Study (NEST). A standardized questionnaire was completed and medical record data were abstracted to ascertain maternal depression and antidepressive drug use. DMR methylation levels in umbilical cord blood leukocytes were quantified using pyrosequencing. From the 436 newborns, laboratory data were obtained for 356 individuals at the IGF2 DMRs, and for 411 individuals at the H19 DMRs; about half of each group was African American or Caucasian. While overall no association between depression and methylation profiles was found, we observed a significant hypermethylation of the H19 DMRs in newborns of African American (n = 177) but not Caucasian (n = 168) mothers who reported the use of antidepressive drugs during pregnancy (β = +6.89, p = 0.01). Of note, our data reveal a race-independent association between smoking during pregnancy and methylation at the IGF2 DMR (+3.05%, p = 0.01). In conclusion, our findings suggest a race-dependent response related to maternal use of antidepressants at one of the IGF2 DMRs in the offspring.
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Affiliation(s)
- A Soubry
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.
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Hoyo C, Murtha AP, Schildkraut JM, Jirtle RL, Demark-Wahnefried W, Forman MR, Iversen ES, Kurtzberg J, Overcash F, Huang Z, Murphy SK. Methylation variation at IGF2 differentially methylated regions and maternal folic acid use before and during pregnancy. Epigenetics 2011; 6:928-36. [PMID: 21636975 DOI: 10.4161/epi.6.7.16263] [Citation(s) in RCA: 184] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Folic acid (FA) supplementation before and during pregnancy has been associated with decreased risk of neural tube defects although recent reports suggest it may also increase the risk of other chronic diseases. We evaluated exposure to maternal FA supplementation before and during pregnancy in relation to aberrant DNA methylation at two differentially methylated regions (DMRs) regulating Insulin-like Growth Factor 2 (IGF2) expression in infants. Aberrant methylation at these regions has been associated with IGF2 deregulation and increased susceptibility to several chronic diseases. Using a self-administered questionnaire, we assessed FA intake before and during pregnancy in 438 pregnant women. Pyrosequencing was used to measure methylation at two IGF2 DMRs in umbilical cord blood leukocytes. Mixed models were used to determine relationships between maternal FA supplementation before or during pregnancy and DNA methylation levels at birth. Average methylation at the H19 DMR was 61.2%. Compared to infants born to women reporting no FA intake before or during pregnancy, methylation levels at the H19 DMR decreased with increasing FA intake (2.8%, p=0.03, and 4.9%, p=0.04, for intake before and during pregnancy, respectively). This methylation decrease was most pronounced in male infants (p=0.01). Methylation alterations at the H19 DMR are likely an important mechanism by which FA risks and/or benefits are conferred in utero. Because stable methylation marks at DMRs regulating imprinted genes are acquired before gastrulation, they may serve as archives of early exposures with the potential to improve our understanding of developmental origins of adult disease.
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Affiliation(s)
- Cathrine Hoyo
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA.
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Bernal AJ, Jirtle RL. Epigenomic disruption: the effects of early developmental exposures. BIRTH DEFECTS RESEARCH. PART A, CLINICAL AND MOLECULAR TERATOLOGY 2010; 88:938-44. [PMID: 20568270 PMCID: PMC2945443 DOI: 10.1002/bdra.20685] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Through DNA methylation, histone modifications, and small regulatory RNAs the epigenome systematically controls gene expression during development, both in utero and throughout life. The epigenome is also a very reactive system; its labile nature allows it to sense and respond to environmental perturbations to ensure survival during fetal growth. This pliability can lead to aberrant epigenetic modifications that persist into later life and induce numerous disease states. Endocrine-disrupting compounds (EDCs) are ubiquitous chemicals that interfere with growth and development. Several EDCs also interfere with epigenetic programming. The investigation of the epigenotoxic effects of bisphenol A (BPA), an EDC used in the production of plastics and resins, has further raised concern over the impact of EDCs on the epigenome. Using the Agouti viable yellow (A(vy)) mouse model, dietary BPA exposure was shown to hypomethylate both the A(vy) and the Cabp(IAP) metastable epialleles. This hypomethylating effect was counteracted with dietary supplementation of methyl donors or genistein. These results are consistent with reports of BPA and other EDCs causing epigenetic effects. Epigenotoxicity could lead to numerous developmental, metabolic, and behavioral disorders in exposed populations. The heritable nature of epigenetic changes also increases the risk for transgenerational inheritance of phenotypes. Thus, epigenotoxicity must be considered when assessing these compounds for safety.
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Affiliation(s)
- Autumn J. Bernal
- Department of Radiation Oncology Duke University Medical Center Durham, North Carolina, 27710 USA
| | - Randy L. Jirtle
- Department of Radiation Oncology Duke University Medical Center Durham, North Carolina, 27710 USA
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