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Eichenauer H, Ehlert U. The association between prenatal famine, DNA methylation and mental disorders: a systematic review and meta-analysis. Clin Epigenetics 2023; 15:152. [PMID: 37716973 PMCID: PMC10505322 DOI: 10.1186/s13148-023-01557-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/14/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND Undernutrition in pregnant women is an unfavorable environmental condition that can affect the intrauterine development via epigenetic mechanisms and thus have long-lasting detrimental consequences for the mental health of the offspring later in life. One epigenetic mechanism that has been associated with mental disorders and undernutrition is alterations in DNA methylation. The effect of prenatal undernutrition on the mental health of adult offspring can be analyzed through quasi-experimental studies such as famine studies. The present systematic review and meta-analysis aims to analyze the association between prenatal famine exposure, DNA methylation, and mental disorders in adult offspring. We further investigate whether altered DNA methylation as a result of prenatal famine exposure is prospectively linked to mental disorders. METHODS We conducted a systematic search of the databases PubMed and PsycINFO to identify relevant records up to September 2022 on offspring whose mothers experienced famine directly before and/or during pregnancy, examining the impact of prenatal famine exposure on the offspring's DNA methylation and/or mental disorders or symptoms. RESULTS The systematic review showed that adults who were prenatally exposed to famine had an increased risk of schizophrenia and depression. Several studies reported an association between prenatal famine exposure and hyper- or hypomethylation of specific genes. The largest number of studies reported differences in DNA methylation of the IGF2 gene. Altered DNA methylation of the DUSP22 gene mediated the association between prenatal famine exposure and schizophrenia in adult offspring. Meta-analysis confirmed the increased risk of schizophrenia following prenatal famine exposure. For DNA methylation, meta-analysis was not suitable due to different microarrays/data processing approaches and/or unavailable data. CONCLUSION Prenatal famine exposure is associated with an increased risk of mental disorders and DNA methylation changes. The findings suggest that changes in DNA methylation of genes involved in neuronal, neuroendocrine, and immune processes may be a mechanism that promotes the development of mental disorders such as schizophrenia and depression in adult offspring. Such findings are crucial given that undernutrition has risen worldwide, increasing the risk of famine and thus also of negative effects on mental health.
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Affiliation(s)
- Heike Eichenauer
- Clinical Psychology and Psychotherapy, University of Zurich, Binzmühlestrasse 14, 8050, Zurich, Switzerland
| | - Ulrike Ehlert
- Clinical Psychology and Psychotherapy, University of Zurich, Binzmühlestrasse 14, 8050, Zurich, Switzerland.
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Beltrán-Sánchez H, Palloni A, Huangfu Y, McEniry M. Population-level impact of adverse early life conditions on adult healthy life expectancy in low- and middle-income countries. POPULATION STUDIES 2022; 76:19-36. [PMID: 34110269 PMCID: PMC8660937 DOI: 10.1080/00324728.2021.1933149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Evidence from theories of Developmental Origins of Health and Disease (DOHaD) suggests that experiencing adverse early life conditions subsequently leads to detrimental adult health outcomes. The bulk of empirical DOHaD literature does not consider the nature and magnitude of the impact of adverse early life conditions at the population level. In particular, it ignores the distortion of age and cohort patterns of adult health and mortality and the increased load of chronic illness and disability that ensues. In this paper, we use a microsimulation model combined with empirical estimates of incidence and prevalence of obesity, type 2 diabetes, and associated disability in low- and middle-income countries to assess the magnitude of delayed effects on adult healthy life expectancy and on compression (or expansion) of morbidity at older ages. The main goal is to determine if, in what ways, and to what extent delayed effects due to early conditions can influence cohorts' chronic illness and disability profiles.
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Affiliation(s)
- Hiram Beltrán-Sánchez
- Department of Community Health Sciences, Fielding School of Public Health and California Center for Population Research, UCLA
| | - Alberto Palloni
- Center for Demography and Ecology, University of Wisconsin-Madison. Consejo Superior de Investigaciones (CSIC), Madrid-Spain
| | - Yiyue Huangfu
- Center for Demography and Ecology, University of Wisconsin-Madison
| | - Mary McEniry
- Center for Demography and Health of Aging, University of Wisconsin-Madison
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3
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Beltrán-Sánchez H, Palloni A, Huangfu Y, McEniry M. Population-level impact of adverse early life conditions on adult healthy life expectancy in low- and middle-income countries. POPULATION STUDIES 2022. [PMID: 34110269 DOI: 10.1080/00324728.2021.1933149/suppl_file/rpst_a_1933149_sm6882.pdf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Evidence from theories of Developmental Origins of Health and Disease (DOHaD) suggests that experiencing adverse early life conditions subsequently leads to detrimental adult health outcomes. The bulk of empirical DOHaD literature does not consider the nature and magnitude of the impact of adverse early life conditions at the population level. In particular, it ignores the distortion of age and cohort patterns of adult health and mortality and the increased load of chronic illness and disability that ensues. In this paper, we use a microsimulation model combined with empirical estimates of incidence and prevalence of obesity, type 2 diabetes, and associated disability in low- and middle-income countries to assess the magnitude of delayed effects on adult healthy life expectancy and on compression (or expansion) of morbidity at older ages. The main goal is to determine if, in what ways, and to what extent delayed effects due to early conditions can influence cohorts' chronic illness and disability profiles.
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Affiliation(s)
| | - Alberto Palloni
- University of Wisconsin-Madison
- Consejo Superior de Investigaciones
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4
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Vaiserman A, Lushchak O. Prenatal famine exposure and adult health outcomes: an epigenetic link. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab013. [PMID: 34881050 PMCID: PMC8648067 DOI: 10.1093/eep/dvab013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 08/30/2021] [Accepted: 10/15/2021] [Indexed: 05/09/2023]
Abstract
Numerous human chronic pathological conditions depend on epigenetic modifications induced by environmental triggers throughout sensitive stages early in development. Developmental malnutrition is regarded as one of the most important risk factors in these processes. We present an overview of studies that the initiation and progression of many diseases are largely dependent on persisting epigenetic dysregulation caused by environmental insults early in life. For particular disorders, candidate genes were identified that underlie these associations. The current study assessed the most convincing evidence for the epigenetic link between developmental malnutrition and adult-life disease in the human population. These findings were obtained from quasi-experimental studies (so-called 'natural experiments'), i.e. naturally occurring environmental conditions in which certain subsets of the population have differing levels of exposure to a supposed causal factor. Most of this evidence was derived on the DNA methylation level. We discussed DNA methylation as a key player in epigenetic modifications that can be inherited through multiple cell divisions. In this Perspective article, an overview of the quasi-experimental epidemiological evidence for the role of epigenetic mechanisms in the developmental programming by early-life undernutrition is provided.
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Affiliation(s)
- Alexander Vaiserman
- Laboratory of Epigenetics, D.F. Chebotarev Institute of Gerontology, NAMS, 67 Vyshgorodska St., Kyiv 04114, Ukraine
| | - Oleh Lushchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenka St., Ivano-Frankivsk 76018, Ukraine
- Research and Development University, 13A Shota Rustaveli St., Ivano-Frankivsk 76000, Ukraine
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5
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Effects of vanadium (sodium metavanadate) and aflatoxin-B1 on cytochrome p450 activities, DNA damage and DNA methylation in human liver cell lines. Toxicol In Vitro 2020; 70:105036. [PMID: 33164849 DOI: 10.1016/j.tiv.2020.105036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 01/15/2023]
Abstract
Vanadium is considered as "possibly carcinogenic to humans" (V2O5, IARC Group 2B), yet uncertainties persist related to the toxicity mechanisms of the multiple forms of vanadium. Exposure to vanadium often co-occurs with other metals or with organic compounds that can be transformed by cytochrome p450 (CYP) enzymes into DNA-reactive carcinogens. Therefore, effects of a soluble form of vanadium (sodium metavanadate, NaVO3) and aflatoxin-B1 (AFB1) were tested separately and together, for induction of CYP activities, DNA damage (γH2AX and DNA alkaline unwinding assays), and DNA methylation changes (global genome and DNA repeats) in HepaRG or HepG2 liver cell lines. NaVO3 (≥ 2.3 μM) reduced CYP1A1 and CYP3A4 activities and induced DNA damage, butcaused important cell proliferation only in HepaRG cells. As a binary mixture, NaVO3 did not modify the effects of AFB1. There was no reproducible effect of NaVO3 (<21 μM) on DNA methylation in AluYb8, satellite-α, satellite-2, and by the luminometric methylation assay, but DNA methylation flow-cytometry signals in HepG2 cells (25-50 μM) increased at the G1 and G2 cell cycle phases. In conclusion, cell lines responded differently to NaVO3 supporting the importance of investigating more than one cell line, and a carcinogenic role of NaVO3 might reside at low concentrations by stimulating the proliferation of tumorigenic cells.
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Denomme MM, Haywood ME, Parks JC, Schoolcraft WB, Katz‐Jaffe MG. The inherited methylome landscape is directly altered with paternal aging and associated with offspring neurodevelopmental disorders. Aging Cell 2020; 19:e13178. [PMID: 32610362 PMCID: PMC7431824 DOI: 10.1111/acel.13178] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/22/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022] Open
Abstract
Paternal aging and the prevalence of neurodevelopmental disorders in offspring are well documented. Yet, the underlying mechanism and the mode of inheritance have not been conclusively established. Advancing paternal age is a subtle and varying phenotype. As such, it is likely that a threshold for cumulative risk may exist that, if surpassed, culminates in a predisposition to disease and ultimately an observed phenotype in offspring. Epigenetic regulation provides a plausible explanation for the nongenetic paternal transmission of disease susceptibility. With the use of whole‐genome methylation sequencing, the data described herein substantiate an increasingly compromised DNA methylation profile as sperm ages and, for the first time, also demonstrate a generational correlation in sperm and blastocyst of an altered methylome associated with advanced paternal age. Methylation alterations are not randomly distributed across the genome, but appear clustered at certain chromosomal locations, and significantly colocalize with regions of nucleosome retention. Genes associated with autism spectrum disorder, schizophrenia, and bipolar disorder are significantly enriched with causative methylation aberrations in both sperm and embryos from aged fathers. The long‐term health burden and societal economic impact of these conditions are substantial and will continue with increasingly prevalent diagnosis. This work provides a mechanistic link between the paternal age effect and offspring neurodevelopmental disorders leading to a better understanding of causation and investigation into potential future therapy.
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Affiliation(s)
| | | | | | | | - Mandy G. Katz‐Jaffe
- Fertility Labs of Colorado Lone Tree CO USA
- Fertility Genetics Lone Tree CO USA
- Colorado Center for Reproductive Medicine Lone Tree CO USA
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Lima RS, Assis Silva Gomes J, Moreira PR. An overview about DNA methylation in childhood obesity: Characteristics of the studies and main findings. J Cell Biochem 2020; 121:3042-3057. [DOI: 10.1002/jcb.29544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Rafael Silva Lima
- Laboratory of Cell‐Cell Interactions, Department of Morphology, Institute of Biological SciencesFederal University of Minas Gerais Minas Gerais Brazil
| | - Juliana Assis Silva Gomes
- Laboratory of Cell‐Cell Interactions, Department of Morphology, Institute of Biological SciencesFederal University of Minas Gerais Minas Gerais Brazil
| | - Paula Rocha Moreira
- Laboratory of Cell‐Cell Interactions, Department of Morphology, Institute of Biological SciencesFederal University of Minas Gerais Minas Gerais Brazil
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Jackson CM, Mukherjee S, Wilburn AN, Cates C, Lewkowich IP, Deshmukh H, Zacharias WJ, Chougnet CA. Pulmonary Consequences of Prenatal Inflammatory Exposures: Clinical Perspective and Review of Basic Immunological Mechanisms. Front Immunol 2020; 11:1285. [PMID: 32636848 PMCID: PMC7318112 DOI: 10.3389/fimmu.2020.01285] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/21/2020] [Indexed: 12/12/2022] Open
Abstract
Chorioamnionitis, a potentially serious inflammatory complication of pregnancy, is associated with the development of an inflammatory milieu within the amniotic fluid surrounding the developing fetus. When chorioamnionitis occurs, the fetal lung finds itself in the unique position of being constantly exposed to the consequent inflammatory meditators and/or microbial products found in the amniotic fluid. This exposure results in significant changes to the fetal lung, such as increased leukocyte infiltration, altered cytokine, and surfactant production, and diminished alveolarization. These alterations can have potentially lasting impacts on lung development and function. However, studies to date have only begun to elucidate the association between such inflammatory exposures and lifelong consequences such as lung dysfunction. In this review, we discuss the pathogenesis of and fetal immune response to chorioamnionitis, detail the consequences of chorioamnionitis exposure on the developing fetal lung, highlighting the various animal models that have contributed to our current understanding and discuss the importance of fetal exposures in regard to the development of chronic respiratory disease. Finally, we focus on the clinical, basic, and therapeutic challenges in fetal inflammatory injury to the lung, and propose next steps and future directions to improve our therapeutic understanding of this important perinatal stress.
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Affiliation(s)
- Courtney M. Jackson
- Division of Immunobiology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, United States
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Shibabrata Mukherjee
- Division of Immunobiology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, United States
| | - Adrienne N. Wilburn
- Division of Immunobiology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, United States
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Chris Cates
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Ian P. Lewkowich
- Division of Immunobiology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Hitesh Deshmukh
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Division of Neonatology/Pulmonary Biology, The Perinatal Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
| | - William J. Zacharias
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Division of Neonatology/Pulmonary Biology, The Perinatal Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
| | - Claire A. Chougnet
- Division of Immunobiology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- *Correspondence: Claire A. Chougnet
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9
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Vaiserman A, Lushchak O. Developmental origins of type 2 diabetes: Focus on epigenetics. Ageing Res Rev 2019; 55:100957. [PMID: 31473332 DOI: 10.1016/j.arr.2019.100957] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 08/19/2019] [Accepted: 08/28/2019] [Indexed: 12/15/2022]
Abstract
Traditionally, genetics and lifestyle are considered as main determinants of aging-associated pathological conditions. Accumulating evidence, however, suggests that risk of many age-related diseases is not only determined by genetic and adult lifestyle factors but also by factors acting during early development. Type 2 diabetes (T2D), an age-related disease generally manifested after the age of 40, is among such disorders. Since several age-related conditions, such as pro-inflammatory states, are characteristic of both T2D and aging, this disease is conceptualized by many authors as a kind of premature or accelerated aging. There is substantial evidence that intrauterine growth restriction (IUGR), induced by poor or unbalanced nutrient intake, exposure to xenobiotics, maternal substance abuse etc., may impair fetal development, thereby causing the fetal adipose tissue and pancreatic beta cell dysfunction. Consequently, persisting adaptive changes may occur in the glucose-insulin metabolism, including reduced capacity for insulin secretion and insulin resistance. These changes can lead to an improved ability to store fat, thus predisposing to T2D development in later life. The modulation of epigenetic regulation of gene expression likely plays a central role in linking the adverse environmental conditions early in life to the risk of T2D in adulthood. In animal models of IUGR, long-term persistent changes in both DNA methylation and expression of genes implicated in metabolic processes have been repeatedly reported. Findings from human studies confirming the role of epigenetic mechanisms in linking early-life adverse experiences to the risk for T2D in adult life are scarce compared to data from animal studies, mainly because of limited access to suitable biological samples. It is, however, convincing evidence that these mechanisms may also operate in human beings. In this review, theoretical models and research findings evidencing the role of developmental epigenetic variation in the pathogenesis of T2D are summarized and discussed.
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Affiliation(s)
| | - Oleh Lushchak
- Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
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Prenatal Malnutrition-Induced Epigenetic Dysregulation as a Risk Factor for Type 2 Diabetes. Int J Genomics 2019; 2019:3821409. [PMID: 30944826 PMCID: PMC6421750 DOI: 10.1155/2019/3821409] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 02/06/2019] [Indexed: 02/08/2023] Open
Abstract
Type 2 diabetes (T2D) is commonly regarded as a disease originating from lifestyle-related factors and typically occurring after the age of 40. There is, however, consistent experimental and epidemiological data evidencing that the risk for developing T2D may largely depend on conditions early in life. In particular, intrauterine growth restriction (IUGR) induced by poor or unbalanced nutrient intake can impair fetal growth and also cause fetal adipose tissue and pancreatic β-cell dysfunction. On account of these processes, persisting adaptive changes can occur in the glucose-insulin metabolism. These changes can include reduced ability for insulin secretion and insulin resistance, and they may result in an improved capacity to store fat, thereby predisposing to the development of T2D and obesity in adulthood. Accumulating research findings indicate that epigenetic regulation of gene expression plays a critical role in linking prenatal malnutrition to the risk of later-life metabolic disorders including T2D. In animal models of IUGR, changes in both DNA methylation and expression levels of key metabolic genes were repeatedly found which persisted until adulthood. The causal link between epigenetic disturbances during development and the risk for T2D was also confirmed in several human studies. In this review, the conceptual models and empirical data are summarized and discussed regarding the contribution of epigenetic mechanisms in developmental nutritional programming of T2D.
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Verhulst A, Beltran-Sanchez H, Palloni A. Impact of delayed effects on human old-age mortality 1. DEMOGRAPHIC RESEARCH 2019; 40:1167-1210. [PMID: 31452626 PMCID: PMC6709713 DOI: 10.4054/demres.2019.40.41] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND There is growing empirical evidence supporting theories of developmental origins of health and disease (DOHaD). However, the implications of DOHaD conjectures for aggregate population patterns of human disease, disability, mortality and aging are poorly understood. OBJECTIVE We empirically test two predictions derived from a formal model of aggregate population-level impacts of DOHaD. This model predicts that populations potentially influenced by delayed effects should experience singularities in their adult mortality patterns that can be empirically detected from aggregate data. METHODS We test predictions using a large mortality database for populations in the Latin American and Caribbean region (LAC) spanning nearly one hundred years of mortality history. RESULTS Results are consistent. within explicit bounds of uncertainty, with expected patterns. We find that younger cohorts in countries whose mortality decline starts more recently experience deceleration in survival gains at older ages, attenuation of the rate of aging at older ages and a decline in the association between early childhood and adult mortality. CONCLUSIONS Results point to the importance of adverse early conditions for human longevity. Future research should shed light on the impact on morbidity, disability and healthy life expectancy. CONTRIBUTION To our knowledge this is the first time that implications of DOHaD conjectures for populations' mortality patterns are formulated precisely and empirically tested with aggregate population data.
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Affiliation(s)
- Andrea Verhulst
- Population Studies Center, University of Pennsylvania, Philadelphia, USA
| | - Hiram Beltran-Sanchez
- Department of Community Health Sciences, Fielding School of Public Health and California Center for Population Research, UCLA, Los Angeles, USA
| | - Alberto Palloni
- Labor and Population Unit, RAND Corporation and Center for Demography and Health of Aging, University of Wisconsin-Madison, USA
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Abstract
Research in the field of gerontology has traditionally focused on later life stages. There is increasing evidence, however, that both the rate of age-related functional decline and the later-life health status can be programmed during early development. The central role of epigenetic mechanisms (methylation of DNA, histone modifications and regulation by non-coding RNAs) in mediating these long-term effects has been elucidated. Both rate and direction of age-associated change of epigenetic patterns (“epigenetic drift”) were shown to be largely dependent on early-life environmental conditions. Inter-individual divergences in epigenetic profiles may arise following the stochastic errors in maintaining epigenetic marks, but they may also be adaptively mediated by specific environmental cues. Recent cohort studies indicate that ticking rate of epigenetic clock, estimated by a DNA methylation-based methods, may be developmentally adjusted, and that individual’s discrepancies among epigenetic and chronological age would be likely programmed early in development. In this Perspective article, recent findings suggesting the importance of early-life determinants for life-course dynamics of epigenetic drift are summarized and discussed.
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Abstract
Epigenetics is the study of heritable mechanisms that can modify gene activity and phenotype without modifying the genetic code. The basis for the concept of epigenetics originated more than 2,000 yr ago as a theory to explain organismal development. However, the definition of epigenetics continues to evolve as we identify more of the components that make up the epigenome and dissect the complex manner by which they regulate and are regulated by cellular functions. A substantial and growing body of research shows that nutrition plays a significant role in regulating the epigenome. Here, we critically assess this diverse body of evidence elucidating the role of nutrition in modulating the epigenome and summarize the impact such changes have on molecular and physiological outcomes with regards to human health.
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Affiliation(s)
- Folami Y Ideraabdullah
- Departments of Genetics and Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina; and Departments of Nutrition and Pediatrics, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
| | - Steven H Zeisel
- Departments of Genetics and Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina; and Departments of Nutrition and Pediatrics, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
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Hendrickx K, Van Hoyweghen I. Solidarity after nature: From biopolitics to cosmopolitics. Health (London) 2018; 24:203-219. [PMID: 30222010 DOI: 10.1177/1363459318800149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
What is sustaining the divide between nature and nurture, even though sciences like epigenetics have been challenging it for at least two decades? Evelyn Fox Keller asked this question and considered it a logical problem rooted in terminological confusion within the sciences. In this article, we propose a complementary diagnosis of the problem: the nature-nurture divide is (re-)mobilized when society faces questions of inclusion and solidarity. With examples stemming from the fields of insurance and health care, immigration policy and epigenetics, we demonstrate how the nature-nurture divide is performed through techniques of classification for a politics of solidarity. We identify a common operation to these different examples that we coin 'biopolitical imputation'. We use this term to draw attention to how (Western) societal institutions, including science, create solvable problems out of complex situations, defining human actors and their agency along the lines of the nature-nurture divide as a moral guide. We argue that the tenacity of the nature-nurture divide is therefore not only a logical problem needing better scientific concepts, but also a cosmopolitical problem asking for a more profound reflection on the ontology and ethics of solidarity in order to move beyond the biopolitics of nature versus nurture.
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Affiliation(s)
- Kim Hendrickx
- Life Sciences & Society Lab, Centre for Sociological Research (CeSO), KU Leuven, Belgium
| | - Ine Van Hoyweghen
- Life Sciences & Society Lab, Centre for Sociological Research (CeSO), KU Leuven, Belgium
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15
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Maddock J, Wulaningsih W, Fernandez JC, Ploubidis GB, Goodman A, Bell J, Kuh D, Hardy R. Associations between body size, nutrition and socioeconomic position in early life and the epigenome: A systematic review. PLoS One 2018; 13:e0201672. [PMID: 30096154 PMCID: PMC6086410 DOI: 10.1371/journal.pone.0201672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/18/2018] [Indexed: 12/19/2022] Open
Abstract
Background Body size, nutrition and socioeconomic position (SEP) in early life have been associated with a wide range of long-term health effects. Epigenetics is one possible mechanism through which these early life exposures can impact later life health. We conducted a systematic review examining the observational evidence for the impact of body size, nutrition and SEP in early life on the epigenome in humans. Methods This systematic review is registered with the PROSPERO database (registration number: CRD42016050193). Three datasets were simultaneously searched using Ovid and the resulting studies were evaluated by at least two independent reviewers. Studies measuring epigenetic markers either at the same time as, or after, the early life exposure and have a measure of body size, nutrition or SEP in early life (up to 12 years), written in English and from a community-dwelling participants were included. Results We identified 90 eligible studies. Seventeen of these papers examined more than one early life exposure of interest. Fifty six papers examined body size, 37 nutrition and 17 SEP. All of the included papers examined DNA methylation (DNAm) as the epigenetic marker. Overall there was no strong evidence for a consistent association between these early life variables in DNAm which may be due to the heterogeneous study designs, data collection methods and statistical analyses. Conclusions Despite these inconclusive results, the hypothesis that the early life environment can impact DNAm, potentially persisting into adult life, was supported by some studies and warrants further investigation. We provide recommendations for future studies.
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Affiliation(s)
- Jane Maddock
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, United Kingdom
- * E-mail:
| | - Wahyu Wulaningsih
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Juan Castillo Fernandez
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - George B. Ploubidis
- Centre for Longitudinal Studies, UCL Institute of Education, University College London, London, United Kingdom
| | - Alissa Goodman
- Centre for Longitudinal Studies, UCL Institute of Education, University College London, London, United Kingdom
| | - Jordana Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Rebecca Hardy
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, United Kingdom
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Basil P, Li Q, Gui H, Hui TCK, Ling VHM, Wong CCY, Mill J, McAlonan GM, Sham PC. Prenatal immune activation alters the adult neural epigenome but can be partly stabilised by a n-3 polyunsaturated fatty acid diet. Transl Psychiatry 2018; 8:125. [PMID: 29967385 PMCID: PMC6028639 DOI: 10.1038/s41398-018-0167-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/01/2018] [Accepted: 04/21/2018] [Indexed: 02/08/2023] Open
Abstract
An unstable epigenome is implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism. This is important because the epigenome is potentially modifiable. We have previously reported that adult offspring exposed to maternal immune activation (MIA) prenatally have significant global DNA hypomethylation in the hypothalamus. However, what genes had altered methylation state, their functional effects on gene expression and whether these changes can be moderated, have not been addressed. In this study, we used next-generation sequencing (NGS) for methylome profiling in a MIA rodent model of neurodevelopmental disorders. We assessed whether differentially methylated regions (DMRs) affected the chromatin state by mapping known DNase I hypersensitivity sites (DHSs), and selected overlapping genes to confirm a functional effect of MIA on gene expression using qPCR. Finally, we tested whether methylation differences elicited by MIA could be limited by post-natal dietary (omega) n-3 polyunsaturated fatty acid (PUFA) supplementation. These experiments were conducted using hypothalamic brain tissue from 12-week-old offspring of mice injected with viral analogue PolyI:C on gestation day 9 of pregnancy or saline on gestation day 9. Half of the animals from each group were fed a diet enriched with n-3 PUFA from weaning (MIA group, n = 12 units, n = 39 mice; Control group, n = 12 units, n = 38 mice). The results confirmed our previous finding that adult offspring exposed to MIA prenatally had significant global DNA hypomethylation. Furthermore, genes linked to synaptic plasticity were over-represented among differentially methylated genes following MIA. More than 80% of MIA-induced hypomethylated sites, including those affecting chromatin state and MECP2 binding, were stabilised by the n-3 PUFA intervention. MIA resulted in increased expression of two of the 'top five' genes identified from an integrated analysis of DMRs, DHSs and MECP2 binding sites, namely Abat (t = 2.46, p < 0.02) and Gnas9 (t = 2.96, p < 0.01), although these changes were not stabilised by dietary intervention. Thus, prenatal MIA exposure impacts upon the epigenomic regulation of gene pathways linked to neurodevelopmental conditions; and many of the changes can be attenuated by a low-cost dietary intervention.
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Affiliation(s)
- Paul Basil
- Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong SAR China ,0000 0001 2160 926Xgrid.39382.33Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Qi Li
- Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong SAR China ,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR China
| | - Hongsheng Gui
- Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong SAR China
| | - Tomy C. K. Hui
- Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong SAR China
| | - Vicki H. M. Ling
- Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong SAR China
| | - Chloe C. Y. Wong
- 0000 0001 2322 6764grid.13097.3cMRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, De Crespigny Park, Denmark Hill, London, SE5 8AF UK
| | - Jonathan Mill
- 0000 0001 2322 6764grid.13097.3cMRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, De Crespigny Park, Denmark Hill, London, SE5 8AF UK ,0000 0004 1936 8024grid.8391.3University of Exeter Medical School, Exeter University, St Luke’s Campus, Magdalen Street, Exeter, EX1 2LU UK
| | - Grainne M. McAlonan
- Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong SAR China ,0000 0001 2322 6764grid.13097.3cDepartment of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, King’s College London, De Crespigny Park, Denmark Hill, London, SE5 8AF UK
| | - Pak-Chung Sham
- Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. .,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. .,Centre for Genomic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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18
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Effects of early-life malnutrition on neurodevelopment and neuropsychiatric disorders and the potential mechanisms. Prog Neuropsychopharmacol Biol Psychiatry 2018; 83:64-75. [PMID: 29287829 DOI: 10.1016/j.pnpbp.2017.12.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/21/2017] [Accepted: 12/24/2017] [Indexed: 02/08/2023]
Abstract
Lines of evidence have demonstrated that early-life malnutrition is highly correlated with neurodevelopment and adulthood neuropsychiatric disorders, while some findings are conflicting with each other. In addition, the biological mechanisms are less investigated. We systematically reviewed the evidence linking early-life nutrition status with neurodevelopment and clinical observations in human and animal models. We summarized the effects of special nutritious on neuropsychiatric disorders and explored the underlying potential mechanisms. The further understanding of the biological regulation of early-life nutritional status on neurodevelopment might shed light on precision nutrition at an integrative systems biology framework.
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Vaiserman AM, Koliada AK. Early-life adversity and long-term neurobehavioral outcomes: epigenome as a bridge? Hum Genomics 2017; 11:34. [PMID: 29246185 PMCID: PMC5732459 DOI: 10.1186/s40246-017-0129-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022] Open
Abstract
Accumulating evidence suggests that adversities at critical periods in early life, both pre- and postnatal, can lead to neuroendocrine perturbations, including hypothalamic-pituitary-adrenal axis dysregulation and inflammation persisting up to adulthood. This process, commonly referred to as biological embedding, may cause abnormal cognitive and behavioral functioning, including impaired learning, memory, and depressive- and anxiety-like behaviors, as well as neuropsychiatric outcomes in later life. Currently, the regulation of gene activity by epigenetic mechanisms is suggested to be a key player in mediating the link between adverse early-life events and adult neurobehavioral outcomes. Role of particular genes, including those encoding glucocorticoid receptor, brain-derived neurotrophic factor, as well as arginine vasopressin and corticotropin-releasing factor, has been demonstrated in triggering early adversity-associated pathological conditions. This review is focused on the results from human studies highlighting the causal role of epigenetic mechanisms in mediating the link between the adversity during early development, from prenatal stages through infancy, and adult neuropsychiatric outcomes. The modulation of epigenetic pathways involved in biological embedding may provide promising direction toward novel therapeutic strategies against neurological and cognitive dysfunctions in adult life.
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Affiliation(s)
- Alexander M Vaiserman
- Laboratory of Epigenetics, Institute of Gerontology, Vyshgorodskaya st. 67, Kiev, 04114, Ukraine.
| | - Alexander K Koliada
- Laboratory of Epigenetics, Institute of Gerontology, Vyshgorodskaya st. 67, Kiev, 04114, Ukraine
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Pirini F, Rodriguez-Torres S, Ayandibu BG, Orera-Clemente M, Gonzalez-de la Vega A, Lawson F, Thorpe RJ, Sidransky D, Guerrero-Preston R. INSIG2 rs7566605 single nucleotide variant and global DNA methylation index levels are associated with weight loss in a personalized weight reduction program. Mol Med Rep 2017; 17:1699-1709. [PMID: 29138870 PMCID: PMC5780113 DOI: 10.3892/mmr.2017.8039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 08/17/2017] [Indexed: 12/27/2022] Open
Abstract
Single nucleotide polymorphisms associated with lipid metabolism and energy balance are implicated in the weight loss response caused by nutritional interventions. Diet-induced weight loss is also associated with differential global DNA methylation. DNA methylation has been proposed as a predictive biomarker for weight loss response. Personalized biomarkers for successful weight loss may inform clinical decisions when deciding between behavioral and surgical weight loss interventions. The aim of the present study was to investigate the association between global DNA methylation, genetic variants associated with energy balance and lipid metabolism, and weight loss following a non-surgical weight loss regimen. The present study included 105 obese participants that were enrolled in a personalized weight loss program based on their allelic composition of the following five energy balance and lipid metabolism-associated loci: Near insulin-induced gene 2 (INSIG2); melanocortin 4 receptor; adrenoceptor β2; apolipoprotein A5; and G-protein subunit β3. The present study investigated the association between a global DNA methylation index (GDMI), the allelic composition of the five energy balance and lipid metabolism-associated loci, and weight loss during a 12 month program, after controlling for age, sex and body mass index (BMI). The results demonstrated a significant association between the GDMI and near INSIG2 locus, after adjusting for BMI and weight loss, and significant trends were observed when stratifying by gender. In conclusion, a combination of genetic and epigenetic biomarkers may be used to design personalized weight loss interventions, enabling adherence and ensuring improved outcomes for obesity treatment programs. Precision weight loss programs designed based on molecular information may enable the creation of personalized interventions for patients, that use genomic biomarkers for treatment design and for treatment adherence monitoring, thus improving response to treatment.
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Affiliation(s)
- Francesca Pirini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, I‑47014 Meldola, Italy
| | | | - Bola Grace Ayandibu
- Department of Otolaryngology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - María Orera-Clemente
- Genetic Laboratory, University General Hospital Gregorio Marañón, 28007 Madrid, Spain
| | | | - Fahcina Lawson
- Department of Otolaryngology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Roland J Thorpe
- Johns Hopkins University Centre for Health Disparities Solutions, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - David Sidransky
- Department of Otolaryngology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Rafael Guerrero-Preston
- Department of Otolaryngology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
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Vaiserman AM. Early-Life Nutritional Programming of Type 2 Diabetes: Experimental and Quasi-Experimental Evidence. Nutrients 2017; 9:nu9030236. [PMID: 28273874 PMCID: PMC5372899 DOI: 10.3390/nu9030236] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 02/11/2017] [Accepted: 02/23/2017] [Indexed: 12/24/2022] Open
Abstract
Consistent evidence from both experimental and human studies suggest that inadequate nutrition in early life can contribute to risk of developing metabolic disorders including type 2 diabetes (T2D) in adult life. In human populations, most findings supporting a causative relationship between early-life malnutrition and subsequent risk of T2D were obtained from quasi-experimental studies (‘natural experiments’). Prenatal and/or early postnatal exposures to famine were demonstrated to be associated with higher risk of T2D in many cohorts around the world. Recent studies have highlighted the importance of epigenetic regulation of gene expression as a possible major contributor to the link between the early-life famine exposure and T2D in adulthood. Findings from these studies suggest that prenatal exposure to the famine may result in induction of persistent epigenetic changes that have adaptive significance in postnatal development but can predispose to metabolic disorders including T2D at the late stages of life. In this review, quasi-experimental data on the developmental programming of T2D are summarized and recent research findings on changes in DNA methylation that mediate these effects are discussed.
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Huang JY, Gavin AR, Richardson TS, Rowhani-Rahbar A, Siscovick DS, Hochner H, Friedlander Y, Enquobahrie DA. Accounting for Life-Course Exposures in Epigenetic Biomarker Association Studies: Early Life Socioeconomic Position, Candidate Gene DNA Methylation, and Adult Cardiometabolic Risk. Am J Epidemiol 2016; 184:520-531. [PMID: 27651384 DOI: 10.1093/aje/kww014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/13/2016] [Indexed: 02/07/2023] Open
Abstract
Recent studies suggest that epigenetic programming may mediate the relationship between early life environment, including parental socioeconomic position, and adult cardiometabolic health. However, interpreting associations between early environment and adult DNA methylation may be difficult because of time-dependent confounding by life-course exposures. Among 613 adult women (mean age = 32 years) of the Jerusalem Perinatal Study Family Follow-up (2007-2009), we investigated associations between early life socioeconomic position (paternal occupation and parental education) and mean adult DNA methylation at 5 frequently studied cardiometabolic and stress-response genes (ABCA1, INS-IGF2, LEP, HSD11B2, and NR3C1). We used multivariable linear regression and marginal structural models to estimate associations under 2 causal structures for life-course exposures and timing of methylation measurement. We also examined whether methylation was associated with adult cardiometabolic phenotype. Higher maternal education was consistently associated with higher HSD11B2 methylation (e.g., 0.5%-point higher in 9-12 years vs. ≤8 years, 95% confidence interval: 0.1, 0.8). Higher HSD11B2 methylation was also associated with lower adult weight and total and low-density lipoprotein cholesterol. We found that associations with early life socioeconomic position measures were insensitive to different causal assumption; however, exploratory analysis did not find evidence for a mediating role of methylation in socioeconomic position-cardiometabolic risk associations.
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Vansant G. Effect of Maternal and Paternal Nutrition on DNA Methylation in the Offspring: A Systematic Review of Human and Animal Studies. ACTA ACUST UNITED AC 2016. [DOI: 10.15406/aowmc.2016.04.00093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Burghardt KJ, Goodrich JM, Dolinoy DC, Ellingrod VL. DNA methylation, insulin resistance and second-generation antipsychotics in bipolar disorder. Epigenomics 2015; 7:343-52. [PMID: 26077424 DOI: 10.2217/epi.15.5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIMS This study aimed to assess the effect of second-generation antipsychotic (SGA) use and insulin resistance on a global measure of DNA methylation in patients diagnosed with bipolar disorder. MATERIALS & METHODS Subjects stable on medication (either mood stabilizer monotherapy or adjuvant SGAs) were assessed for insulin resistance. Global methylation levels were assessed in leukocyte DNA from whole blood using the Luminometric Methylation Assay. Multivariable linear regression was used to investigate the effect of insulin resistance and SGA use on DNA methylation. RESULTS A total of 115 bipolar I subjects were included in this study. The average age was 43.1 ±12.2 years and 73% were on SGAs. Average% global methylation was 77.0 ± 3.26 and was significantly influenced by insulin resistance, SGA use and smoking. CONCLUSION This is the first study to show a relationship between SGA use, insulin resistance and global DNA methylation. Further work will be needed to identify tissue- and gene-specific methylation changes.
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Affiliation(s)
- Kyle J Burghardt
- Department of Pharmacy Practice, Wayne State University Eugene Applebaum College of Pharmacy & Health Sciences, 259 Mack Avenue, Suite 2190, Detroit, MI 48201, USA
| | - Jacyln M Goodrich
- Department of Environmental Sciences, University of Michigan School of Public Health, 6638 SPH Tower, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Dana C Dolinoy
- Department of Environmental Sciences, University of Michigan School of Public Health, 6638 SPH Tower, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Vicki L Ellingrod
- Department of Clinical Social & Administrative Sciences, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109, USA.,Department of Psychiatry, School of Medicine, University of Michigan, 1301 Catherine, Ann Arbor, MI 48109, USA
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Liu J, Zhao SR, Reyes T. Neurological and Epigenetic Implications of Nutritional Deficiencies on Psychopathology: Conceptualization and Review of Evidence. Int J Mol Sci 2015; 16:18129-48. [PMID: 26251900 PMCID: PMC4581239 DOI: 10.3390/ijms160818129] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/22/2015] [Accepted: 07/28/2015] [Indexed: 12/19/2022] Open
Abstract
In recent years, a role for epigenetic modifications in the pathophysiology of disease has received significant attention. Many studies are now beginning to explore the gene-environment interactions, which may mediate early-life exposure to risk factors, such as nutritional deficiencies and later development of behavioral problems in children and adults. In this paper, we review the current literature on the role of epigenetics in the development of psychopathology, with a specific focus on the potential for epigenetic modifications to link nutrition and brain development. We propose a conceptual framework whereby epigenetic modifications (e.g., DNA methylation) mediate the link between micro- and macro-nutrient deficiency early in life and brain dysfunction (e.g., structural aberration, neurotransmitter perturbation), which has been linked to development of behavior problems later on in life.
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Affiliation(s)
- Jianghong Liu
- School of Nursing, University of Pennsylvania, 418 Curie Blvd., Philadelphia, PA 19104, USA.
| | - Sophie R Zhao
- School of Nursing, University of Pennsylvania, 418 Curie Blvd., Philadelphia, PA 19104, USA.
| | - Teresa Reyes
- School of Nursing, University of Pennsylvania, 418 Curie Blvd., Philadelphia, PA 19104, USA.
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Delgado-Cruzata L, Vin-Raviv N, Tehranifar P, Flom J, Reynolds D, Gonzalez K, Santella RM, Terry MB. Correlations in global DNA methylation measures in peripheral blood mononuclear cells and granulocytes. Epigenetics 2015; 9:1504-10. [PMID: 25482109 DOI: 10.4161/15592294.2014.983364] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Alterations in global DNA methylation levels have been associated with chronic diseases. Despite the increase in the number of studies measuring markers of global methylation, few have adequately examined within-individual differences by source of DNA and whether within-individual differences by source of DNA differ by age, race and other lifestyle factors. We examined correlations between peripheral mononuclear cell (PBMC) and granulocyte DNA methylation levels measured by the luminometric methylation assay (LUMA), and in LINE-1, Sat2, and Alu by MethyLight and pyrosequencing, in the same individual in 112 women participating in The New York City Multiethnic Breast Cancer Project. Levels of DNA methylation of Sat2 by MethyLight (r = 0.57; P < 0.01) and LINE-1 by pyrosequencing (r = 0.30; P < 0.01) were correlated between PBMC and granulocyte DNA of the same individuals, but LUMA and Alu levels were not. The magnitude of the correlations for Sat2 and LINE-1 varied when stratified by selected demographic and lifestyle factors, although the study sample size limited our comparisons across subgroups. These results lend further support to the importance of considering the source of DNA in epidemiologic studies of white blood cell DNA methylation. Results from studies that combine individuals with different available DNA sources need to be interpreted with caution.
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Affiliation(s)
- Lissette Delgado-Cruzata
- a Department of Environmental Health Sciences ; Columbia University Medical Center; Mailman School of Public Health ; New York , NY USA
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Environmental Impact on DNA Methylation in the Germline: State of the Art and Gaps of Knowledge. BIOMED RESEARCH INTERNATIONAL 2015; 2015:123484. [PMID: 26339587 PMCID: PMC4538313 DOI: 10.1155/2015/123484] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 05/03/2015] [Indexed: 12/19/2022]
Abstract
The epigenome consists of chemical changes in DNA and chromatin that without modifying the DNA sequence modulate gene expression and cellular phenotype. The epigenome is highly plastic and reacts to changing external conditions with modifications that can be inherited to daughter cells and across generations. Whereas this innate plasticity allows for adaptation to a changing environment, it also implies the potential of epigenetic derailment leading to so-called epimutations. DNA methylation is the most studied epigenetic mark. DNA methylation changes have been associated with cancer, infertility, cardiovascular, respiratory, metabolic, immunologic, and neurodegenerative pathologies. Experiments in rodents demonstrate that exposure to a variety of chemical stressors, occurring during the prenatal or the adult life, may induce DNA methylation changes in germ cells, which may be transmitted across generations with phenotypic consequences. An increasing number of human biomonitoring studies show environmentally related DNA methylation changes mainly in blood leukocytes, whereas very few data have been so far collected on possible epigenetic changes induced in the germline, even by the analysis of easily accessible sperm. In this paper, we review the state of the art on factors impinging on DNA methylation in the germline, highlight gaps of knowledge, and propose priorities for future studies.
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Demetriou CA, van Veldhoven K, Relton C, Stringhini S, Kyriacou K, Vineis P. Biological embedding of early-life exposures and disease risk in humans: a role for DNA methylation. Eur J Clin Invest 2015; 45:303-32. [PMID: 25645488 DOI: 10.1111/eci.12406] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/19/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND Following wider acceptance of 'the thrifty phenotype' hypothesis and the convincing evidence that early-life exposures can influence adult health even decades after the exposure, much interest has been placed on the mechanisms through which early-life exposures become biologically embedded. MATERIALS AND METHODS In this review, we summarize the current literature regarding biological embedding of early-life experiences. To this end, we conducted a literature search to identify studies investigating early-life exposures in relation to DNA methylation changes. In addition, we summarize the challenges faced in investigations of epigenetic effects, stemming from the peculiarities of this emergent and complex field. A proper systematic review and meta-analyses were not feasible given the nature of the evidence. RESULTS We identified seven studies on early-life socio-economic circumstances, 10 studies on childhood obesity and six studies on early-life nutrition all relating to DNA methylation changes that met the stipulated inclusion criteria. The pool of evidence gathered, albeit small, favours a role of epigenetics and DNA methylation in biological embedding, but replication of findings, multiple comparison corrections, publication bias and causality are concerns remaining to be addressed in future investigations. CONCLUSIONS Based on these results, we hypothesize that epigenetics, in particular DNA methylation, is a plausible mechanism through which early-life exposures are biologically embedded. This review describes the current status of the field and acts as a stepping stone for future, better designed investigations on how early-life exposures might become biologically embedded through epigenetic effects.
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Affiliation(s)
- Christiana A Demetriou
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK; Department of Electron Microscopy / Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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29
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Affiliation(s)
- Karen E. Charlton
- School of Medicine; Faculty of Science, Medicine and Health; University of Wollongong; New South Wales Australia
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Abstract
The molecular signatures of epigenetic regulation and chromatin architectures are fundamental to genetically determined biological processes. Covalent and post-translational chemical modification of the chromatin template can sensitize the genome to changing environmental conditions to establish diverse functional states. Recent interest and research focus surrounds the direct connections between metabolism and chromatin dynamics, which now represents an important conceptual challenge to explain many aspects of metabolic dysfunction. Several components of the epigenetic machinery require intermediates of cellular metabolism for enzymatic function. Furthermore, changes to intracellular metabolism can alter the expression of specific histone methyltransferases and acetyltransferases conferring widespread variations in epigenetic modification patterns. Specific epigenetic influences of dietary glucose and lipid consumption, as well as undernutrition, are observed across numerous organs and pathways associated with metabolism. Studies have started to define the chromatin-dependent mechanisms underlying persistent and pathophysiological changes induced by altered metabolism. Importantly, numerous recent studies demonstrate that gene regulation underlying phenotypic determinants of adult metabolic health is influenced by maternal and early postnatal diet. These emerging concepts open new perspectives to combat the rising global epidemic of metabolic disorders.
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Affiliation(s)
- Samuel T. Keating
- From the Epigenetics in Human Health and Disease Laboratory (S.T.K., A.E.-O.) and Epigenomics Profiling Facility (S.T.K., A.E.-O.), Baker IDI Heart & Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia; Department of Pathology, The University of Melbourne, Victoria, Australia (A.E.-O.); and Central Clinical School, Department of Medicine, Monash University, Melbourne, Victoria, Australia (A.E.-O.)
| | - Assam El-Osta
- From the Epigenetics in Human Health and Disease Laboratory (S.T.K., A.E.-O.) and Epigenomics Profiling Facility (S.T.K., A.E.-O.), Baker IDI Heart & Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia; Department of Pathology, The University of Melbourne, Victoria, Australia (A.E.-O.); and Central Clinical School, Department of Medicine, Monash University, Melbourne, Victoria, Australia (A.E.-O.)
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31
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DNA methylation signatures link prenatal famine exposure to growth and metabolism. Nat Commun 2014; 5:5592. [PMID: 25424739 PMCID: PMC4246417 DOI: 10.1038/ncomms6592] [Citation(s) in RCA: 366] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/16/2014] [Indexed: 12/22/2022] Open
Abstract
Periconceptional diet may persistently influence DNA methylation levels with phenotypic consequences. However, a comprehensive assessment of the characteristics of prenatal malnutrition-associated differentially methylated regions (P-DMRs) is lacking in humans. Here we report on a genome-scale analysis of differential DNA methylation in whole blood after periconceptional exposure to famine during the Dutch Hunger Winter. We show that P-DMRs preferentially occur at regulatory regions, are characterized by intermediate levels of DNA methylation and map to genes enriched for differential expression during early development. Validation and further exploratory analysis of six P-DMRs highlight the critical role of gestational timing. Interestingly, differential methylation of the P-DMRs extends along pathways related to growth and metabolism. P-DMRs located in INSR and CPT1A have enhancer activity in vitro and differential methylation is associated with birth weight and serum LDL cholesterol. Epigenetic modulation of pathways by prenatal malnutrition may promote an adverse metabolic phenotype in later life. The long-term effect of prenatal nutrition on gene regulation is largely unknown. Here the authors identify differentially methylated regions in whole blood from individuals exposed to famine early after conception, and show that these epigenetic changes may have adverse metabolic consequences later in life.
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Vaiserman AM. Epigenetic programming by early-life stress: Evidence from human populations. Dev Dyn 2014; 244:254-65. [PMID: 25298004 DOI: 10.1002/dvdy.24211] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/29/2014] [Accepted: 09/29/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A substantial body of experimental and epidemiological evidence has been accumulated suggesting that stressful events in early life including acute perinatal stress, maternal deprivation or separation, and variation in maternal care may lead to neuroendocrine perturbations thereby affecting reproductive performance, cognitive functions, and stress responses as well as the risk for infectious, cardio-metabolic and psychiatric diseases in later life. RESULTS Findings from recent studies based on both genome-wide and candidate gene approaches highlighted the importance of mechanisms that are involved in epigenetic regulation of gene expression, such as DNA methylation, histone modifications, and non-coding RNAs, in the long-term effects of exposure to stress in early life. CONCLUSIONS This review is focused on the findings from human studies indicating the role of epigenetic mechanisms in the causal link between early-life stress and later-life health outcomes.
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Affiliation(s)
- A M Vaiserman
- D.F. Chebotarev State Institute of Gerontology NAMS of Ukraine, Kiev, Ukraine
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Abstract
A growing number of studies in recent years have highlighted the importance of molecular nutrition as a potential determinant of health and disease. In particular, the ability of micronutrients to regulate the final expression of gene products via modulation of transcription and translation is now being recognised. Modulation of microRNA (miRNA) by nutrients is one pathway by which nutrition may mediate gene expression. miRNA, a class of non-coding RNA, can directly regulate gene expression post-transcriptionally. In addition, miRNA are able to indirectly influence gene expression potential at the transcriptional level via modulation of the function of components of the epigenetic machinery (DNA methylation and histone modifications). These mechanisms interact to form a complex, bi-directional regulatory circuit modulating gene expression. Disease-specific miRNA profiles have been identified in multiple disease states, including those with known dietary risk factors. Therefore, the role that nutritional components, in particular, vitamins and minerals, play in the modulation of miRNA profiles, and consequently health and disease, is increasingly being investigated, and as such is a timely subject for review. The recently posited potential for viable exogenous miRNA to enter human blood circulation from food sources adds another interesting dimension to the potential for dietary miRNA to contribute to gene modulation.
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del Rosario MC, Ossowski V, Knowler WC, Bogardus C, Baier LJ, Hanson RL. Potential epigenetic dysregulation of genes associated with MODY and type 2 diabetes in humans exposed to a diabetic intrauterine environment: an analysis of genome-wide DNA methylation. Metabolism 2014; 63:654-60. [PMID: 24582139 PMCID: PMC3995826 DOI: 10.1016/j.metabol.2014.01.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/14/2014] [Indexed: 10/25/2022]
Abstract
OBJECTIVE The aim of this study is to investigate the potential role of DNA methylation in mediating the increased risk of developing type 2 diabetes in offspring of mothers who had diabetes during pregnancy. MATERIALS AND METHODS Peripheral blood leukocytes were collected from non-diabetic Pima Indians who were either offspring of diabetic mothers (ODM; n=14) or offspring of nondiabetic mothers (ONDM; n=14). The two groups were matched for age, sex, age of mother, and fraction of Pima ethnicity. Differentially methylated regions were determined using a MeDIP-chip assay on an Affymetrix Human Tiling 2.0R Array. Data were analyzed using the model based analysis of tiling arrays (MAT) algorithm, and 4883 regions overlapping with putative promoters, were identified as differentially methylated, having met an empirically derived threshold (nominal p<0.0077). The list of genes with differentially methylated promoters was subjected to KEGG pathway analysis to determine canonical metabolic pathways enriched by these genes. RESULTS Pathway analysis of genes with differentially methylated promoters identified the top 3 enriched pathways as maturity onset diabetes of the young (MODY), type 2 diabetes, and Notch signaling. Several genes in these pathways are known to affect pancreatic development and insulin secretion. CONCLUSIONS These findings support the hypothesis that epigenetic changes may increase the risk of type 2 diabetes via an effect on β-cell function in the offspring of mothers with diabetes during pregnancy.
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Affiliation(s)
- Melissa C del Rosario
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, 1550 East Indian School Road, Phoenix, AZ, 85014
| | - Vicky Ossowski
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, 1550 East Indian School Road, Phoenix, AZ, 85014
| | - William C Knowler
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, 1550 East Indian School Road, Phoenix, AZ, 85014
| | - Clifton Bogardus
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, 1550 East Indian School Road, Phoenix, AZ, 85014
| | - Leslie J Baier
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, 1550 East Indian School Road, Phoenix, AZ, 85014
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, 1550 East Indian School Road, Phoenix, AZ, 85014.
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Ilott NE, Schneider T, Mill J, Schalkwyk L, Brolese G, Bizarro L, Stolerman IP, Dempster E, Asherson P. Long-term effects of gestational nicotine exposure and food-restriction on gene expression in the striatum of adolescent rats. PLoS One 2014; 9:e88896. [PMID: 24586432 PMCID: PMC3929494 DOI: 10.1371/journal.pone.0088896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 01/14/2014] [Indexed: 01/12/2023] Open
Abstract
Gestational exposure to environmental toxins such as nicotine may result in detectable gene expression changes in later life. To investigate the direct toxic effects of prenatal nicotine exposure on later brain development, we have used transcriptomic analysis of striatal samples to identify gene expression differences between adolescent Lister Hooded rats exposed to nicotine in utero and controls. Using an additional group of animals matched for the reduced food intake experienced in the nicotine group, we were also able to assess the impact of imposed food-restriction on gene expression profiles. We found little evidence for a role of gestational nicotine exposure on altered gene expression in the striatum of adolescent offspring at a significance level of p<0.01 and |log2 fold change >0.5|, although we cannot exclude the possibility of nicotine-induced changes in other brain regions, or at other time points. We did, however, find marked gene expression differences in response to imposed food-restriction. Food-restriction resulted in significant group differences for a number of immediate early genes (IEGs) including Fos, Fosb, Fosl2, Arc, Junb, Nr4a1 and Nr4a3. These genes are associated with stress response pathways and therefore may reflect long-term effects of nutritional deprivation on the development of the stress system.
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Affiliation(s)
- Nicholas E. Ilott
- Medical Research Council (MRC), Social, Genetic and Developmental Psychiatry (SGDP) centre, Institute of Psychiatry, King's College London, London, United Kingdom
- Computational Genomics Analysis and Training (CGAT), Medical Research Council (MRC) Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Tomasz Schneider
- Department of addictions, Institute of Psychiatry, King's College London, London, United Kingdom,
- Experimental Psychology, University of Oxford, Oxford, United Kingdom
| | - Jonathan Mill
- Medical Research Council (MRC), Social, Genetic and Developmental Psychiatry (SGDP) centre, Institute of Psychiatry, King's College London, London, United Kingdom
- University of Exeter Medical School, Exeter, United Kingdom
| | - Leonard Schalkwyk
- Medical Research Council (MRC), Social, Genetic and Developmental Psychiatry (SGDP) centre, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Giovana Brolese
- Departamento de Psicologia do Desenvolvimento e da Personalidade, Instituto de Psicologia, Universidade Federal do Rio Grande do Sul, Porto Alegre-RS, Brazil
| | - Lisiane Bizarro
- Departamento de Psicologia do Desenvolvimento e da Personalidade, Instituto de Psicologia, Universidade Federal do Rio Grande do Sul, Porto Alegre-RS, Brazil
| | - Ian P. Stolerman
- Department of addictions, Institute of Psychiatry, King's College London, London, United Kingdom,
| | - Emma Dempster
- Medical Research Council (MRC), Social, Genetic and Developmental Psychiatry (SGDP) centre, Institute of Psychiatry, King's College London, London, United Kingdom
- University of Exeter Medical School, Exeter, United Kingdom
| | - Philip Asherson
- Medical Research Council (MRC), Social, Genetic and Developmental Psychiatry (SGDP) centre, Institute of Psychiatry, King's College London, London, United Kingdom
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Zhu L, Wang X, Li XL, Towers A, Cao X, Wang P, Bowman R, Yang H, Goldstein J, Li YJ, Jiang YH. Epigenetic dysregulation of SHANK3 in brain tissues from individuals with autism spectrum disorders. Hum Mol Genet 2013; 23:1563-78. [PMID: 24186872 DOI: 10.1093/hmg/ddt547] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The molecular basis for the majority of cases of autism spectrum disorders (ASD) remains unknown. We tested the hypothesis that ASD have an epigenetic cause by performing DNA methylation profiling of five CpG islands (CGI-1 to CGI-5) in the SHANK3 gene in postmortem brain tissues from 54 ASD patients and 43 controls. We found significantly increased overall DNA methylation (epimutation) in three intragenic CGIs (CGI-2, CGI-3 and CGI-4). The increased methylation was clustered in the CGI-2 and CGI-4 in ∼15% of ASD brain tissues. SHANK3 has an extensive array of mRNA splice variants resulting from combinations of five intragenic promoters and alternative splicing of coding exons. Altered expression and alternative splicing of SHANK3 isoforms were observed in brain tissues with increased methylation of SHANK3 CGIs in ASD brain tissues. A DNA methylation inhibitor modified the methylation of CGIs and altered the isoform-specific expression of SHANK3 in cultured cells. This study is the first to find altered methylation patterns in SHANK3 in ASD brain samples. Our finding provides evidence to support an alternative approach to investigating the molecular basis of ASD. The ability to alter the epigenetic modification and expression of SHANK3 by environmental factors suggests that SHANK3 may be a valuable biomarker for dissecting the role of gene and environment interaction in the etiology of ASD.
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Vilahur N, Baccarelli AA, Bustamante M, Agramunt S, Byun HM, Fernandez MF, Sunyer J, Estivill X. Storage conditions and stability of global DNA methylation in placental tissue. Epigenomics 2013; 5:341-8. [PMID: 23750648 DOI: 10.2217/epi.13.29] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
AIM The placenta is an informative and easily available tissue for many epidemiological studies. We analyzed the extent to which storage delay affects DNA methylation. MATERIAL & METHODS Biopsies from two placentas were sequentially stored at -80°C after standing at room temperature for 30 min, 1 h, 2 h, 6 h and 24 h. Global DNA methylation was measured by bisulfite pyrosequencing of repetitive elements and the luminometric methylation assay. RESULTS Small changes in global DNA methylation in relation to time-to-storage were observed by pyrosequencing, with a coefficient of variation (COV) of 2.49% (placenta 1) and 2.86% (placenta 2), similar to the mean technical variation observed for pyrosequencing (COV: 1.91 and 1.51%, respectively). A luminometric methylation assay yielded more variable results in the two placentas analyzed, both among time points (COV: 9.13 and 10.35%, respectively) and technical replicates (COV: 11.60 and 9.80%, respectively). CONCLUSION Global DNA methylation is stable at room temperature. However, some techniques to measure methylation might be confounded by DNA degradation caused by a delay in storage.
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Affiliation(s)
- Nadia Vilahur
- Center for Research in Environmental Epidemiology CREAL, Barcelona, Catalonia, Spain.
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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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Soriano-Tárraga C, Jiménez-Conde J, Giralt-Steinhauer E, Ois Á, Rodríguez-Campello A, Cuadrado-Godia E, Fernández-Cadenas I, Montaner J, Lucas G, Elosua R, Roquer J. DNA isolation method is a source of global DNA methylation variability measured with LUMA. Experimental analysis and a systematic review. PLoS One 2013; 8:e60750. [PMID: 23585847 PMCID: PMC3621987 DOI: 10.1371/journal.pone.0060750] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/02/2013] [Indexed: 11/19/2022] Open
Abstract
In DNA methylation, methyl groups are covalently bound to CpG dinucleotides. However, the assumption that methyl groups are not lost during routine DNA extraction has not been empirically tested. To avoid nonbiological associations in DNA methylation studies, it is essential to account for potential batch effect bias in the assessment of this epigenetic mechanism. Our purpose was to determine if the DNA isolation method is an independent source of variability in methylation status. We quantified Global DNA Methylation (GDM) by luminometric methylation assay (LUMA), comparing the results from 3 different DNA isolation methods. In the controlled analysis (n = 9), GDM differed slightly for the same individual depending on extraction method. In the population analysis (n = 580) there were significant differences in GDM between the 3 DNA isolation methods (medians, 78.1%, 76.5% and 75.1%; p<0.001). A systematic review of published data from LUMA GDM studies that specify DNA extraction methods is concordant with our findings. DNA isolation method is a source of GDM variability measured with LUMA. To avoid possible bias, the method used should be reported and taken into account in future DNA methylation studies.
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Affiliation(s)
- Carolina Soriano-Tárraga
- Neurovascular Research Group. Neurology Department. Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
- * E-mail:
| | - Jordi Jiménez-Conde
- Neurovascular Research Group. Neurology Department. Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Eva Giralt-Steinhauer
- Neurovascular Research Group. Neurology Department. Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Ángel Ois
- Neurovascular Research Group. Neurology Department. Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Ana Rodríguez-Campello
- Neurovascular Research Group. Neurology Department. Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Elisa Cuadrado-Godia
- Neurovascular Research Group. Neurology Department. Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Israel Fernández-Cadenas
- Neurovascular Research Laboratory. Institut de Recerca, Universitat Autònoma de Barcelona, Hospital Vall d’Hebron, Barcelona, Spain
- Laboratory of neurovascular pharmacogenomics and genetics, Fundació per la Docència i Recerca Mutua Terrassa, Terrassa (Barcelona), Spain
| | - Joan Montaner
- Neurovascular Research Laboratory. Institut de Recerca, Universitat Autònoma de Barcelona, Hospital Vall d’Hebron, Barcelona, Spain
| | - Gavin Lucas
- Cardiovascular Epidemiology and Genetics group. Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics group. Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Jaume Roquer
- Neurovascular Research Group. Neurology Department. Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
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Davey Smith G. If data could talk back: Anzia Yezierska, Paul de Kruif and thousands of pages of ‘research’. Int J Epidemiol 2013; 42:1-6. [DOI: 10.1093/ije/dyt039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Newman AB, Murabito JM. The epidemiology of longevity and exceptional survival. Epidemiol Rev 2013; 35:181-97. [PMID: 23372024 DOI: 10.1093/epirev/mxs013] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2012] [Indexed: 12/12/2022] Open
Abstract
The field of the "epidemiology of longevity" has been expanding rapidly in recent years. Several long-term cohort studies have followed older adults long enough to identify the most long-lived and to define many factors that lead to a long life span. Very long-lived people such as centenarians have been examined using case-control study designs. Both cohort and case-control studies have been the subject of genome-wide association studies that have identified genetic variants associated with longevity. With growing recognition of the importance of rare variations, family studies of longevity will be useful. Most recently, exome and whole-genome sequencing, gene expression, and epigenetic studies have been undertaken to better define functional variation and regulation of the genome. In this review, we consider how these studies are leading to a deeper understanding of the underlying biologic pathways to longevity.
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Prenatal and Perinatal Environmental Influences on the Human Fetal and Placental Epigenome. Clin Pharmacol Ther 2012; 92:716-26. [DOI: 10.1038/clpt.2012.141] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Ng JWY, Barrett LM, Wong A, Kuh D, Smith GD, Relton CL. The role of longitudinal cohort studies in epigenetic epidemiology: challenges and opportunities. Genome Biol 2012; 13:246. [PMID: 22747597 PMCID: PMC3446311 DOI: 10.1186/gb-2012-13-6-246] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Longitudinal cohort studies are ideal for investigating how epigenetic patterns change over time and relate to changing exposure patterns and the development of disease. We highlight the challenges and opportunities in this approach.
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Kirkbride JB, Susser E, Kundakovic M, Kresovich JK, Davey Smith G, Relton CL. Prenatal nutrition, epigenetics and schizophrenia risk: can we test causal effects? Epigenomics 2012; 4:303-15. [PMID: 22690666 PMCID: PMC3970193 DOI: 10.2217/epi.12.20] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We posit that maternal prenatal nutrition can influence offspring schizophrenia risk via epigenetic effects. In this article, we consider evidence that prenatal nutrition is linked to epigenetic outcomes in offspring and schizophrenia in offspring, and that schizophrenia is associated with epigenetic changes. We focus upon one-carbon metabolism as a mediator of the pathway between perturbed prenatal nutrition and the subsequent risk of schizophrenia. Although post-mortem human studies demonstrate DNA methylation changes in brains of people with schizophrenia, such studies cannot establish causality. We suggest a testable hypothesis that utilizes a novel two-step Mendelian randomization approach, to test the component parts of the proposed causal pathway leading from prenatal nutritional exposure to schizophrenia. Applied here to a specific example, such an approach is applicable for wider use to strengthen causal inference of the mediating role of epigenetic factors linking exposures to health outcomes in population-based studies.
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Affiliation(s)
- James B Kirkbride
- EpiCentre group, Department of Psychiatry, University of Cambridge, Herchel Smith Building for Brain & Mind Sciences, Forvie Site, Robinson Way, Cambridge, UK.
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Tobi EW, Slagboom PE, van Dongen J, Kremer D, Stein AD, Putter H, Heijmans BT, Lumey LH. Prenatal famine and genetic variation are independently and additively associated with DNA methylation at regulatory loci within IGF2/H19. PLoS One 2012; 7:e37933. [PMID: 22666415 PMCID: PMC3364289 DOI: 10.1371/journal.pone.0037933] [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: 01/15/2012] [Accepted: 04/25/2012] [Indexed: 02/07/2023] Open
Abstract
Both the early environment and genetic variation may affect DNA methylation, which is one of the major molecular marks of the epigenome. The combined effect of these factors on a well-defined locus has not been studied to date. We evaluated the association of periconceptional exposure to the Dutch Famine of 1944-45, as an example of an early environmental exposure, and single nucleotide polymorphisms covering the genetic variation (tagging SNPs) with DNA methylation at the imprinted IGF2/H19 region, a model for an epigenetically regulated genomic region. DNA methylation was measured at five differentially methylated regions (DMRs) that regulate the imprinted status of the IGF2/H19 region. Small but consistent differences in DNA methylation were observed comparing 60 individuals with periconceptional famine exposure with unexposed same-sex siblings at all IGF2 DMRs (P(BH)<0.05 after adjustment for multiple testing), but not at the H19 DMR. IGF2 DMR0 methylation was associated with IGF2 SNP rs2239681 (P(BH) = 0.027) and INS promoter methylation with INS SNPs, including rs689, which tags the INS VNTR, suggesting a mechanism for the reported effect of the VNTR on INS expression (P(BH) = 3.4 × 10(-3)). Prenatal famine and genetic variation showed similar associations with IGF2/H19 methylation and their contributions were additive. They were small in absolute terms (<3%), but on average 0.5 standard deviations relative to the variation in the population. Our analyses suggest that environmental and genetic factors could have independent and additive similarly sized effects on DNA methylation at the same regulatory site.
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Affiliation(s)
- Elmar W. Tobi
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - P. Eline Slagboom
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- The Netherlands consortium for Healthy Ageing, Leiden University Medical Center, Leiden, The Netherlands
| | - Jenny van Dongen
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Dennis Kremer
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Aryeh D. Stein
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Hein Putter
- Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Bastiaan T. Heijmans
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- The Netherlands consortium for Healthy Ageing, Leiden University Medical Center, Leiden, The Netherlands
| | - L. H. Lumey
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, United States of America
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Michels KB. Commentary: Marking the epigenome--in search of the fingerprints of intrauterine nutritional deficiencies. Int J Epidemiol 2012; 41:123-5. [PMID: 22269255 DOI: 10.1093/ije/dyr228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Karin B Michels
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Ng JWY, Barrett LM, Wong A, Kuh D, Smith G, Relton CL. The role of longitudinal cohort studies in epigenetic epidemiology: challenges and opportunities. Genome Biol 2012. [DOI: 10.1186/gb4029] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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