151
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Joo JE, Hiden U, Lassance L, Gordon L, Martino DJ, Desoye G, Saffery R. Variable promoter methylation contributes to differential expression of key genes in human placenta-derived venous and arterial endothelial cells. BMC Genomics 2013; 14:475. [PMID: 23855827 PMCID: PMC3729658 DOI: 10.1186/1471-2164-14-475] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 07/10/2013] [Indexed: 11/26/2022] Open
Abstract
Background The endothelial compartment, comprising arterial, venous and lymphatic cell types, is established prenatally in association with rapid phenotypic and functional changes. The molecular mechanisms underpinning this process in utero have yet to be fully elucidated. The aim of this study was to investigate the potential for DNA methylation to act as a driver of the specific gene expression profiles of arterial and venous endothelial cells. Results Placenta-derived venous and arterial endothelial cells were collected at birth prior to culturing. DNA methylation was measured at >450,000 CpG sites in parallel with expression measurements taken from 25,000 annotated genes. A consistent set of genomic loci was found to show coordinate differential methylation between the arterial and venous cell types. This included many loci previously not investigated in relation to endothelial function. An inverse relationship was observed between gene expression and promoter methylation levels for a limited subset of genes implicated in endothelial function, including NOS3, encoding endothelial Nitric Oxide Synthase. Conclusion Endothelial cells derived from the placental vasculature at birth contain widespread methylation of key regulatory genes. These are candidates involved in the specification of different endothelial cell types and represent potential target genes for environmentally mediated epigenetic disruption in utero in association with cardiovascular disease risk later in life.
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Affiliation(s)
- Jihoon E Joo
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Melbourne, Australia
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152
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Pathways by which the interplay of organismic and environmental factors lead to phenotypic variation within and across generations. ADVANCES IN CHILD DEVELOPMENT AND BEHAVIOR 2013; 44:325-54. [PMID: 23834011 DOI: 10.1016/b978-0-12-397947-6.00012-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The range of responses made to environmental exigencies by animals, including humans, may be impacted by the experiences of their progenitors. In mammals, pathways have been documented ranging from transactions between a mother and her developing fetus in the womb through continuity of parenting practices and cultural inheritance. In addition, phenotypic plasticity may be constrained by factors transmitted by the gametes that are involved in the regulation of gene expression rather than modifications to the genome itself. Possible mediators for this kind of inheritance are examined, and the conditions that might have led to the evolution of such transmission are considered. Anticipatory adjustments to possible environmental exigencies are likely to occur when such conditions recur regularly, but intermittently across generations and endure for substantial periods of time, and when adjusting to them after the fact is likely to be biologically costly, even life-threatening. It appears that physical growth and responses to nutrient availability are domains in which anticipatory, epigenetically inherited adjustments occur. In addition, given the fact that humans have oppressed one another repeatedly and for relatively long periods of time, such behavioral tendencies as boldness or innovativeness may be behavioral traits subject to such effects. The implications of these factors for research and policy are discussed.
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153
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Herzog E, Galvez J, Roks A, Stolk L, Verbiest M, Eilers P, Cornelissen J, Steegers E, Steegers-Theunissen R. Tissue-specific DNA methylation profiles in newborns. Clin Epigenetics 2013; 5:8. [PMID: 23724794 PMCID: PMC3684550 DOI: 10.1186/1868-7083-5-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/24/2013] [Indexed: 12/30/2022] Open
Abstract
Background Epidemiological studies demonstrate that foetal growth restriction and low birth weight affect long-term health. Derangements in tissue-specific epigenetic programming of foetal and placental tissues are a suggested underlying mechanism of which DNA methylation is best understood. DNA methylation has been mostly investigated in DNA from white blood cells. To improve baseline understanding of tissue-specific DNA methylation, we examined variation in DNA methylation profiles of the imprinted foetal growth genes IGF2 and H19 in three different tissues from the same newborn obtained at the same time. Findings We obtained DNA from umbilical cord blood mononuclear cells (MNC; CD34+ and CD34–, n = 6), foetal side of the placenta (n = 5) and umbilical cord Wharton jelly (n = 5). DNA methylation of the IGF2 differentially methylated region (DMR) and H19 DMR was measured using quantitative mass spectrometry. Analysis of variance testing showed no statistical difference between total mean methylation of CD34+ and CD34– MNC. Further comparisons were made with the pooled total MNC fraction. Mean IGF2 DMR methylation of Wharton jelly was 1.3 times higher (P = 0.001) than mean methylation of the pooled MNC. Placental mean methylation was 0.8 times lower (P <0.001) and Wharton jelly 0.9 times lower (P <0.001) than the pooled MNC of H19 DMR. Conclusion The total MNC fraction is a rather homogeneous cell population for methylation studies of imprinted genes in umbilical cord blood white blood cells, but may not always reflect the methylation levels of IGF2 and H19 in other organs.
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Affiliation(s)
- Emilie Herzog
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Centre Rotterdam, dr, Molewaterplein 50, Rotterdam, GE 3015, the Netherlands.
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Martino D, Loke YJ, Gordon L, Ollikainen M, Cruickshank MN, Saffery R, Craig JM. Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance. Genome Biol 2013; 14:R42. [PMID: 23697701 PMCID: PMC4054827 DOI: 10.1186/gb-2013-14-5-r42] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 05/22/2013] [Indexed: 02/02/2023] Open
Abstract
Background The extent to which development- and age-associated epigenetic changes are influenced by genetic, environmental and stochastic factors remains to be discovered. Twins provide an ideal model with which to investigate these influences but previous cross-sectional twin studies provide contradictory evidence of within-pair epigenetic drift over time. Longitudinal twin studies can potentially address this discrepancy. Results In a pilot, genome-scale study of DNA from buccal epithelium, a relatively homogeneous tissue, we show that one-third of the CpGs assayed show dynamic methylation between birth and 18 months. Although all classes of annotated genomic regions assessed show an increase in DNA methylation over time, probes located in intragenic regions, enhancers and low-density CpG promoters are significantly over-represented, while CpG islands and high-CpG density promoters are depleted among the most dynamic probes. Comparison of co-twins demonstrated that within-pair drift in DNA methylation in our cohort is specific to a subset of pairs, who show more differences at 18 months. The rest of the pairs show either minimal change in methylation discordance, or more similar, converging methylation profiles at 18 months. As with age-associated regions, sites that change in their level of within-pair discordance between birth and 18 months are enriched in genes involved in development, but the average magnitude of change is smaller than for longitudinal change. Conclusions Our findings suggest that DNA methylation in buccal epithelium is influenced by non-shared stochastic and environmental factors that could reflect a degree of epigenetic plasticity within an otherwise constrained developmental program.
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155
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Kirchner H, Osler ME, Krook A, Zierath JR. Epigenetic flexibility in metabolic regulation: disease cause and prevention? Trends Cell Biol 2013; 23:203-9. [DOI: 10.1016/j.tcb.2012.11.008] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 11/28/2012] [Accepted: 11/29/2012] [Indexed: 12/21/2022]
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Tsai PC, Spector TD, Bell JT. Using epigenome-wide association scans of DNA methylation in age-related complex human traits. Epigenomics 2013; 4:511-26. [PMID: 23130833 DOI: 10.2217/epi.12.45] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
With rapid technological advancements emerging epigenetic studies of complex traits have shifted from candidate gene analyses towards epigenome-wide association studies (EWAS). EWAS aim to systematically identify epigenetic variants across the genome that associate with complex phenotypes. Recent EWAS using case-control and disease-discordant identical twin designs have identified phenotype-associated differentially methylated regions for several traits. However, EWAS still face many challenges related to methodology, design and interpretation, owing to the dynamic nature of epigenetic variants over time. This article reviews analytical considerations in conducting EWAS and recent applications of this approach to human aging and age-related complex traits.
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Affiliation(s)
- Pei-Chien Tsai
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
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157
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Effects of early-life environment and epigenetics on cardiovascular disease risk in children: highlighting the role of twin studies. Pediatr Res 2013; 73:523-30. [PMID: 23314296 DOI: 10.1038/pr.2013.6] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of death worldwide and originates in early life. The exact mechanisms of this early-life origin are unclear, but a likely mediator at the molecular level is epigenetic dysregulation of gene expression. Epigenetic factors have thus been posited as the likely drivers of early-life programming of adult-onset diseases. This review summarizes recent advances in epidemiology and epigenetic research of CVD risk in children, with a particular focus on twin studies. Classic twin studies enable partitioning of phenotypic variance within a population into additive genetic, shared, and nonshared environmental variances, and are invaluable in research in this area. Longitudinal cohort twin studies, in particular, may provide important insights into the role of epigenetics in the pathogenesis of CVD. We describe candidate gene and epigenome-wide association studies (EWASs) and transgenerational epigenetic inheritance of CVD, and discuss the potential for evidence-based interventions. Identifying epigenetic changes associated with CVD-risk biomarkers in children will provide new opportunities to unravel the underlying biological mechanism of the origins of CVD and enable identification of those at risk for early-life interventions to alter the risk trajectory and potentially reduce CVD incidence later in life.
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158
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Ogino S, Lochhead P, Chan AT, Nishihara R, Cho E, Wolpin BM, Meyerhardt JA, Meissner A, Schernhammer ES, Fuchs CS, Giovannucci E. Molecular pathological epidemiology of epigenetics: emerging integrative science to analyze environment, host, and disease. Mod Pathol 2013; 26:465-84. [PMID: 23307060 PMCID: PMC3637979 DOI: 10.1038/modpathol.2012.214] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetics acts as an interface between environmental/exogenous factors, cellular responses, and pathological processes. Aberrant epigenetic signatures are a hallmark of complex multifactorial diseases (including neoplasms and malignancies such as leukemias, lymphomas, sarcomas, and breast, lung, prostate, liver, and colorectal cancers). Epigenetic signatures (DNA methylation, mRNA and microRNA expression, etc) may serve as biomarkers for risk stratification, early detection, and disease classification, as well as targets for therapy and chemoprevention. In particular, DNA methylation assays are widely applied to formalin-fixed, paraffin-embedded archival tissue specimens as clinical pathology tests. To better understand the interplay between etiological factors, cellular molecular characteristics, and disease evolution, the field of 'molecular pathological epidemiology (MPE)' has emerged as an interdisciplinary integration of 'molecular pathology' and 'epidemiology'. In contrast to traditional epidemiological research including genome-wide association studies (GWAS), MPE is founded on the unique disease principle, that is, each disease process results from unique profiles of exposomes, epigenomes, transcriptomes, proteomes, metabolomes, microbiomes, and interactomes in relation to the macroenvironment and tissue microenvironment. MPE may represent a logical evolution of GWAS, termed 'GWAS-MPE approach'. Although epigenome-wide association study attracts increasing attention, currently, it has a fundamental problem in that each cell within one individual has a unique, time-varying epigenome. Having a similar conceptual framework to systems biology, the holistic MPE approach enables us to link potential etiological factors to specific molecular pathology, and gain novel pathogenic insights on causality. The widespread application of epigenome (eg, methylome) analyses will enhance our understanding of disease heterogeneity, epigenotypes (CpG island methylator phenotype, LINE-1 (long interspersed nucleotide element-1; also called long interspersed nuclear element-1; long interspersed element-1; L1) hypomethylation, etc), and host-disease interactions. In this article, we illustrate increasing contribution of modern pathology to broader public health sciences, which attests pivotal roles of pathologists in the new integrated MPE science towards our ultimate goal of personalized medicine and prevention.
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Affiliation(s)
- Shuji Ogino
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA 02215, USA.
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159
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Sasaki A, de Vega WC, McGowan PO. Biological embedding in mental health: an epigenomic perspective. Biochem Cell Biol 2013; 91:14-21. [PMID: 23442137 DOI: 10.1139/bcb-2012-0070] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Human epidemiological studies and studies of animal models provide many examples by which early life experiences influence health in a long-term manner, a concept known as biological embedding. Such experiences can have profound impacts during periods of high plasticity in prenatal and early postnatal life. Epigenetic mechanisms influence gene function in the absence of changes in gene sequence. In contrast to the relative stability of gene sequences, epigenetic mechanisms appear, at least to some extent, responsive to environmental signals. To date, a few examples appear to clearly link early social experiences to epigenetic changes in pathways relevant for mental health in adulthood. Our recent work using high-throughput epigenomic techniques points to large-scale changes in gene pathways in addition to candidate genes involved in the response to psychosocial stress and neuroplasticity. Elucidation of which pathways are epigenetically labile under what conditions will enable a more complete understanding of how the epigenome can mediate environmental interactions with the genome that are relevant for mental health. In this mini-review, we provide examples of nascent research into the influence of early life experience on mental health outcomes, discuss evidence of epigenetic mechanisms that may underlie these effects, and describe challenges for research in this area.
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Affiliation(s)
- Aya Sasaki
- Department of Biological Sciences, University of Toronto, Scarborough, Canada
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160
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Soubry A, Schildkraut JM, Murtha A, Wang F, Huang Z, Bernal A, Kurtzberg J, Jirtle RL, Murphy SK, Hoyo C. Paternal obesity is associated with IGF2 hypomethylation in newborns: results from a Newborn Epigenetics Study (NEST) cohort. BMC Med 2013; 11:29. [PMID: 23388414 PMCID: PMC3584733 DOI: 10.1186/1741-7015-11-29] [Citation(s) in RCA: 260] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 02/06/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Data from epidemiological and animal model studies suggest that nutrition during pregnancy may affect the health status of subsequent generations. These transgenerational effects are now being explained by disruptions at the level of the epigenetic machinery. Besides in vitro environmental exposures, the possible impact on the reprogramming of methylation profiles at imprinted genes at a much earlier time point, such as during spermatogenesis or oogenesis, has not previously been considered. In this study, our aim was to determine associations between preconceptional obesity and DNA methylation profiles in the offspring, particularly at the differentially methylated regions (DMRs) of the imprinted Insulin-like Growth Factor 2 (IGF2) gene. METHODS We examined DNA from umbilical cord blood leukocytes from 79 newborns, born between July 2005 and November 2006 at Duke University Hospital, Durham, NC. Their mothers participated in the Newborn Epigenetics Study (NEST) during pregnancy. Parental characteristics were obtained via standardized questionnaires and medical records. DNA methylation patterns at two DMRs were analyzed by bisulfite pyrosequencing; one DMR upstream of IGF2 (IGF2 DMR), and one DMR upstream of the neighboring H19 gene (H19 DMR). Multiple regression models were used to determine potential associations between the offspring's DNA methylation patterns and parental obesity before conception. Obesity was defined as body mass index (BMI) ≥30 kg/m². RESULTS Hypomethylation at the IGF2 DMR was associated with paternal obesity. Even after adjusting for several maternal and newborn characteristics, we observed a persistent inverse association between DNA methylation in the offspring and paternal obesity (β-coefficient was -5.28, P = 0.003). At the H19 DMR, no significant associations were detected between methylation patterns and paternal obesity. Our data suggest an increase in DNA methylation at the IGF2 and H19 DMRs among newborns from obese mothers, but a larger study is warranted to further explore the potential effects of maternal obesity or lifestyle on the offspring's epigenome. CONCLUSIONS While our small sample size is limited, our data indicate a preconceptional impact of paternal obesity on the reprogramming of imprint marks during spermatogenesis. Given the biological importance of imprinting fidelity, our study provides evidence for transgenerational effects of paternal obesity that may influence the offspring's future health status.
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Affiliation(s)
- Adelheid Soubry
- Duke Cancer Institute, Duke University Medical Center 2715, Durham, NC 27710, USA.
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161
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Scarr E, Craig JM, Cairns MJ, Seo MS, Galati JC, Beveridge NJ, Gibbons A, Juzva S, Weinrich B, Parkinson-Bates M, Carroll AP, Saffery R, Dean B. Decreased cortical muscarinic M1 receptors in schizophrenia are associated with changes in gene promoter methylation, mRNA and gene targeting microRNA. Transl Psychiatry 2013; 3:e230. [PMID: 23423139 PMCID: PMC3594731 DOI: 10.1038/tp.2013.3] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Many studies have shown decreased cortical muscarinic M1 receptors (CHRM1) in schizophrenia (Sz), with one study showing Sz can be separated into two populations based on a marked loss of CHRM1 (-75%) in -25% of people (Def-Sz) with the disorder. To better understand the mechanism contributing to the loss of CHRM1 in Def-Sz, we measured specific markers of gene expression in the cortex of people with Sz as a whole, people differentiated into Def-Sz and people with Sz that do not have a deficit in cortical CHRM1 (Non-Def-Sz) and health controls. We now report that cortical CHRM1 gene promoter methylation and CHRM1 mRNA are decrease in Sz, Def-Sz and Non-Def-Sz but levels of the micro RNA (miR)-107, a CHRM1 targeting miR, are increased only in Def-Sz. We also report in vitro data strongly supporting the notion that miR-107 levels regulate CHRM1 expression. These data suggest there is a reversal of the expected inverse relationship between gene promoter methylation and CHRM1 mRNA in people with Sz and that a breakdown in gene promoter methylation control of CHRM1 expression is contributing to the global pathophysiology of the syndrome. In addition, our data argues that increased levels of at least one miR, miR-107, is contributing to the marked loss of cortical CHRM1 in Def-Sz and this may be a differentiating pathophysiology. These latter data continue to support the hypothesis that microRNAs (miRNA) have a role in the underlying neurobiology of Sz but argue they are differentially affected in subsets of people within that syndrome.
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Affiliation(s)
- E Scarr
- The Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia
| | - J M Craig
- The Early Life Epigenetic Group, The Murdoch's Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia,The Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - M J Cairns
- The School of Biomedical Sciences and Pharmacy, and Hunter Medical Research Institute, University of Newcastle, Callaghan, New South Wales, Australia,The Schizophrenia Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - M S Seo
- The Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia,The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - J C Galati
- The Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia,Department of Mathematics and Statistics, La Trobe University, Bundoora, Victoria, Australia
| | - N J Beveridge
- The School of Biomedical Sciences and Pharmacy, and Hunter Medical Research Institute, University of Newcastle, Callaghan, New South Wales, Australia,The Schizophrenia Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - A Gibbons
- The Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia,The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - S Juzva
- The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - B Weinrich
- The Early Life Epigenetic Group, The Murdoch's Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - M Parkinson-Bates
- The Cancer and the Developmental Epigenetics Group, The Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - A P Carroll
- The School of Biomedical Sciences and Pharmacy, and Hunter Medical Research Institute, University of Newcastle, Callaghan, New South Wales, Australia,The Schizophrenia Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - R Saffery
- The Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia,The Cancer and the Developmental Epigenetics Group, The Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - B Dean
- The Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia,The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia,Molecular Psychiatry Laboratory, The Mental Health Research Institute, The Kenneth Myer Building, The University of Melbourne, Genetics Lane, Parkville, Victoria 3010, Australia. E-mail:
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162
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Epigenetics and early life origins of chronic noncommunicable diseases. J Adolesc Health 2013; 52:S14-21. [PMID: 23332566 DOI: 10.1016/j.jadohealth.2012.04.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 04/26/2012] [Accepted: 04/27/2012] [Indexed: 12/31/2022]
Abstract
In light of the increasing threats of chronic noncommunicable diseases in developing countries, the growing recognition of the early life origins of chronic disease, and innovative breakthroughs in biomedical research and technology, it is imperative that we harness cutting-edge data to improve health promotion and maintenance. It is well recognized that chronic diseases are complex traits affected by a wide range of environmental and genetic factors; however, the role of epigenetic factors, particularly with regard to early life origins, remains largely unexplored. Given the unique properties of the epigenome-functionality during critical time windows, such as the intrauterine period, heritability, and reversibility-enhancing our understanding of epigenetic mechanisms may offer new opportunities for the development of novel early prediction and prevention paradigms. This may present an unparalleled opportunity to offer maternal and child health professionals important tools with the translational value to predict, detect, and prevent disease at an early age, long before its clinical occurrence, and as such, break lifelong and transgenerational cycles of disease. In doing so, modern technology can be leveraged to make great contributions to population health, quality of life, and reducing the burdensome economic costs of noncommunicable diseases in developing countries.
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163
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Novakovic B, Saffery R. The importance of the intrauterine environment in shaping the human neonatal epigenome. Epigenomics 2013; 5:1-4. [DOI: 10.2217/epi.12.77] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Boris Novakovic
- Cancer, Disease & Developmental Epigenetics, Murdoch Childrens Research Institute, Royal Children’s Hospital & Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Richard Saffery
- Cancer, Disease & Developmental Epigenetics, Murdoch Childrens Research Institute, Royal Children’s Hospital & Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3052, Australia
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164
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Haahtela T, Holgate S, Pawankar R, Akdis CA, Benjaponpitak S, Caraballo L, Demain J, Portnoy J, von Hertzen L. The biodiversity hypothesis and allergic disease: world allergy organization position statement. World Allergy Organ J 2013; 6:3. [PMID: 23663440 PMCID: PMC3646540 DOI: 10.1186/1939-4551-6-3] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 01/17/2013] [Indexed: 12/21/2022] Open
Abstract
Biodiversity loss and climate change secondary to human activities are now being associated with various adverse health effects. However, less attention is being paid to the effects of biodiversity loss on environmental and commensal (indigenous) microbiotas. Metagenomic and other studies of healthy and diseased individuals reveal that reduced biodiversity and alterations in the composition of the gut and skin microbiota are associated with various inflammatory conditions, including asthma, allergic and inflammatory bowel diseases (IBD), type1 diabetes, and obesity. Altered indigenous microbiota and the general microbial deprivation characterizing the lifestyle of urban people in affluent countries appear to be risk factors for immune dysregulation and impaired tolerance. The risk is further enhanced by physical inactivity and a western diet poor in fresh fruit and vegetables, which may act in synergy with dysbiosis of the gut flora. Studies of immigrants moving from non-affluent to affluent regions indicate that tolerance mechanisms can rapidly become impaired in microbe-poor environments. The data on microbial deprivation and immune dysfunction as they relate to biodiversity loss are evaluated in this Statement of World Allergy Organization (WAO). We propose that biodiversity, the variability among living organisms from all sources are closely related, at both the macro- and micro-levels. Loss of the macrodiversity is associated with shrinking of the microdiversity, which is associated with alterations of the indigenous microbiota. Data on behavioural means to induce tolerance are outlined and a proposal made for a Global Allergy Plan to prevent and reduce the global allergy burden for affected individuals and the societies in which they live.
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Affiliation(s)
- Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, PO Box 160, 00029, Helsinki, HUCH, Finland
| | - Stephen Holgate
- School of Medicine, University of Southampton, Southampton, UK
| | | | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research, University of Zurich, Davos, Switzerland
| | - Suwat Benjaponpitak
- Department of Pediatrics, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Luis Caraballo
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | - Jeffrey Demain
- Allergy, Asthma & Immunology Center of Alaska, Dept of Pediatrics, University of Washington, Washington, USA
| | - Jay Portnoy
- University of Missouri-Kansas City School of Medicine, Missouri, USA
| | - Leena von Hertzen
- Skin and Allergy Hospital, Helsinki University Hospital, PO Box 160, 00029, Helsinki, HUCH, Finland
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165
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Novakovic B, Gordon L, Robinson WP, Desoye G, Saffery R. Glucose as a fetal nutrient: dynamic regulation of several glucose transporter genes by DNA methylation in the human placenta across gestation. J Nutr Biochem 2013; 24:282-8. [DOI: 10.1016/j.jnutbio.2012.06.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 05/10/2012] [Accepted: 06/08/2012] [Indexed: 01/02/2023]
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166
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Pirazzini C, Giuliani C, Bacalini MG, Boattini A, Capri M, Fontanesi E, Marasco E, Mantovani V, Pierini M, Pini E, Luiselli D, Franceschi C, Garagnani P. Space/population and time/age in DNA methylation variability in humans: a study on IGF2/H19 locus in different Italian populations and in mono- and di-zygotic twins of different age. Aging (Albany NY) 2012; 4:509-20. [PMID: 22879348 PMCID: PMC3433936 DOI: 10.18632/aging.100476] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Little is known about the impact of space (geography/ancestry) and time (age of the individuals) on DNA methylation variability in humans. We investigated DNA methylation of the imprinted IGF2/H19 locus in: i) a cohort of individuals homogeneous for age and gender (males with restricted age range: 30-50 years) belonging to four Italian districts representative of the major genetic clines, informative for the geographical dimension; ii) a cohort of monozygotic (MZ) and dizygotic (DZ) twins of different ages (age-range: 22-97 years), informative for the temporal dimension. DNA methylation of the analyzed regions displayed high levels of inter-individual variability that could not be ascribed to any geographical cline. In MZ twins we identified two IGF2/H19 regions where the intra-couple variations significantly increased after the age of 60 years. The analysis of twins’ individual life histories suggests that the within twin pairs difference is likely the result of the aging process itself, as sharing a common environment for long periods had no effect on DNA methylation divergence. On the whole, the data here reported suggest that: i) aging more than population genetics is responsible for the inter-individual variability in DNA methylation patterns in humans; ii) DNA methylation variability appears to be highly region-specific.
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Affiliation(s)
- Chiara Pirazzini
- CIG - Interdipartimental Center L. Galvani, University of Bologna, Italy
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Rice WR, Friberg U, Gavrilets S. Homosexuality as a Consequence of Epigenetically Canalized Sexual Development. QUARTERLY REVIEW OF BIOLOGY 2012; 87:343-68. [DOI: 10.1086/668167] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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168
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Novakovic B, Saffery R. The ever growing complexity of placental epigenetics – Role in adverse pregnancy outcomes and fetal programming. Placenta 2012; 33:959-70. [DOI: 10.1016/j.placenta.2012.10.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/02/2012] [Accepted: 10/06/2012] [Indexed: 02/01/2023]
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169
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Mascheretti S, Bureau A, Battaglia M, Simone D, Quadrelli E, Croteau J, Cellino MR, Giorda R, Beri S, Maziade M, Marino C. An assessment of gene-by-environment interactions in developmental dyslexia-related phenotypes. GENES BRAIN AND BEHAVIOR 2012; 12:47-55. [DOI: 10.1111/gbb.12000] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 09/26/2012] [Accepted: 10/24/2012] [Indexed: 01/02/2023]
Affiliation(s)
- S. Mascheretti
- The Academic Centre for the study of Behavioural Plasticity; Vita-Salute San Raffaele University; Milan; 20132; Italy
| | | | | | - D. Simone
- Department of Child Psychiatry; Scientific Institute Eugenio Medea; Bosisio Parini; Lecco; 23842; Italy
| | - E. Quadrelli
- Department of Child Psychiatry; Scientific Institute Eugenio Medea; Bosisio Parini; Lecco; 23842; Italy
| | - J. Croteau
- Centre de Recherche de l'Institut universitaire en santé mentale de Québec; Québec; G1J 2 G3; Canada
| | - M. R. Cellino
- Centro Regionale di Riferimento per i Disturbi dell'Apprendimento - CRRDA, ULSS 20; Verona; 37122; Italy
| | - R. Giorda
- Molecular Biology Laboratory; Scientific Institute Eugenio Medea; Bosisio Parini; Lecco; 23842; Italy
| | - S. Beri
- Molecular Biology Laboratory; Scientific Institute Eugenio Medea; Bosisio Parini; Lecco; 23842; Italy
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170
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Abstract
The Peri/postnatal Epigenetic Twins Study (PETS) is a longitudinal cohort of 250 pairs of Australian twins and their mothers, who were recruited mid-way through pregnancy from January 2007 to September 2009. The study is centered on the developmental origins of health and disease paradigm (DOHaD) in which an adverse intrauterine environment predisposes the individual to complex disease in later life by reducing growth in utero and adversely altering developmental plasticity. Data concerning diet and lifestyle were collected from mothers during pregnancy, and samples of plasma and serum taken at 28 weeks’ gestation. We attended 75% of all births, at which time we collected multiple biological samples including placenta, cord blood, and neonatal cheek cells, the latter from 91% of pairs. Chorionicity was recorded and zygosity was determined by DNA testing where necessary. Approximately 40% of the twins are monozygotic, two-thirds of which are dichorionic. Twins were seen again at 18 months of age and repeat blood and cheek swabs taken where possible. Studies of gene expression and the epigenetic marks of DNA methylation have so far revealed that twins exhibit a wide range of epigenetic discordance at birth, that one-third of the epigenome changes significantly between birth and 18 months; shared (maternal) environment, genetic factors, and non-shared intrauterine environment contribute to an increasing proportion of epigenetic variation at birth, respectively, and affect tissues differently, and that within-pair birth weight discordance correlates with epigenetic discordance in genes associated with lipid metabolism, supporting an epigenetic mechanism for DOHaD.
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171
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Jacoby M, Gohrbandt S, Clausse V, Brons NH, Muller CP. Interindividual variability and co-regulation of DNA methylation differ among blood cell populations. Epigenetics 2012; 7:1421-34. [PMID: 23151460 DOI: 10.4161/epi.22845] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DNA methylation regulates gene expression in a cell-type specific way. Although peripheral blood mononuclear cells (PBMCs) comprise a heterogeneous cell population, most studies of DNA methylation in blood are performed on total mononuclear cells. In this study, we investigated high resolution methylation profiles of 58 CpG sites dispersed over eight immune response genes in multiple purified blood cells from healthy adults and newborns. Adjacent CpG sites showed methylation levels that were increasingly correlated in adult blood vs. cord blood. Thus, while interindividual variability increases from newborn to adult blood, the underlying methylation changes may not be merely stochastic, but seem to be orchestrated as clusters of adjacent CpG sites. Multiple linear regression analysis showed that interindividual methylation variability was influenced by distance of average methylation levels to the closest border (0 or 100%), presence of transcription factor binding sites, CpG conservation across species and age. Furthermore, CD4+ and CD14+ cell types were negative predictors of methylation variability. Concerns that PBMC methylation differences may be confounded by variations in blood cell composition were justified for CpG sites with large methylation differences across cell types, such as in the IFN-γ gene promoter. Taken together, our data suggest that unsorted mononuclear cells are reasonable surrogates of CD8+ and, to a lesser extent, CD4+ T cell methylation in adult peripheral, but not in neonatal, cord blood.
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Affiliation(s)
- Monique Jacoby
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Luxembourg
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172
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Huang RC, Galati JC, Burrows S, Beilin LJ, Li X, Pennell CE, van Eekelen J, Mori TA, Adams LA, Craig JM. DNA methylation of the IGF2/H19 imprinting control region and adiposity distribution in young adults. Clin Epigenetics 2012; 4:21. [PMID: 23148549 PMCID: PMC3507742 DOI: 10.1186/1868-7083-4-21] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 10/24/2012] [Indexed: 02/07/2023] Open
Abstract
Background The insulin-like growth factor 2 (IGF2) and H19 imprinted genes control growth and body composition. Adverse in-utero environments have been associated with obesity-related diseases and linked with altered DNA methylation at the IGF2/H19 locus. Postnatally, methylation at the IGF2/H19 imprinting control region (ICR) has been linked with cerebellum weight. We aimed to investigate whether decreased IGF2/H19 ICR methylation is associated with decreased birth and childhood anthropometry and increased contemporaneous adiposity. DNA methylation in peripheral blood (n = 315) at 17 years old was measured at 12 cytosine-phosphate-guanine sites (CpGs), analysed as Sequenom MassARRAY EpiTYPER units within the IGF2/H19 ICR. Birth size, childhood head circumference (HC) at six time-points and anthropometry at age 17 years were measured. DNA methylation was investigated for its association with anthropometry using linear regression. Results The principal component of IGF2/H19 ICR DNA methylation (representing mean methylation across all CpG units) positively correlated with skin fold thickness (at four CpG units) (P-values between 0.04 to 0.001) and subcutaneous adiposity (P = 0.023) at age 17, but not with weight, height, BMI, waist circumference or visceral adiposity. IGF2/H19 methylation did not associate with birth weight, length or HC, but CpG unit 13 to 14 methylation was negatively associated with HC between 1 and 10 years. β-coefficients of four out of five remaining CpG units also estimated lower methylation with increasing childhood HC. Conclusions As greater IGF2/H19 methylation was associated with greater subcutaneous fat measures, but not overall, visceral or central adiposity, we hypothesize that obesogenic pressures in youth result in excess fat being preferentially stored in peripheral fat depots via the IGF2/H19 domain. Secondly, as IGF2/H19 methylation was not associated with birth size but negatively with early childhood HC, we hypothesize that the HC may be a more sensitive marker of early life programming of the IGF axis and of fetal physiology than birth size. To verify this, investigations of the dynamics of IGF2/H19 methylation and expression from birth to adolescence are required.
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Affiliation(s)
- Rae-Chi Huang
- School of Medicine and Pharmacology, University of Western Australia (UWA), Perth, WA, Australia.
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173
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Ellis JA, Munro JE, Chavez RA, Gordon L, Joo JE, Akikusa JD, Allen RC, Ponsonby AL, Craig JM, Saffery R. Genome-scale case-control analysis of CD4+ T-cell DNA methylation in juvenile idiopathic arthritis reveals potential targets involved in disease. Clin Epigenetics 2012; 4:20. [PMID: 23148518 PMCID: PMC3536591 DOI: 10.1186/1868-7083-4-20] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 10/24/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND Juvenile Idiopathic Arthritis (JIA) is a complex autoimmune rheumatic disease of largely unknown cause. Evidence is growing that epigenetic variation, particularly DNA methylation, is associated with autoimmune disease. However, nothing is currently known about the potential role of aberrant DNA methylation in JIA. As a first step to addressing this knowledge gap, we have profiled DNA methylation in purified CD4+ T cells from JIA subjects and controls. Genomic DNA was isolated from peripheral blood CD4+ T cells from 14 oligoarticular and polyarticular JIA cases with active disease, and healthy age- and sex-matched controls. Genome-scale methylation analysis was carried out using the Illumina Infinium HumanMethylation27 BeadChip. Methylation data at >25,000 CpGs was compared in a case-control study design. RESULTS Methylation levels were significantly different (FDR adjusted p<0.1) at 145 loci. Removal of four samples exposed to methotrexate had a striking impact on the outcome of the analysis, reducing the number of differentially methylated loci to 11. The methotrexate-naive analysis identified reduced methylation at the gene encoding the pro-inflammatory cytokine IL32, which was subsequently replicated using a second analysis platform and a second set of case-control pairs. CONCLUSIONS Our data suggests that differential T cell DNA methylation may be a feature of JIA, and that reduced methylation at IL32 is associated with this disease. Further work in larger prospective and longitudinal sample collections is required to confirm these findings, assess whether the identified differences are causal or consequential of disease, and further investigate the epigenetic modifying properties of therapeutic regimens.
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Affiliation(s)
- Justine A Ellis
- Genes, Environment & Complex Disease, Murdoch Childrens Research Institute, 50 Flemington Rd, Parkville, Vic, Australia.
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174
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Wang KCW, Botting KJ, Padhee M, Zhang S, McMillen IC, Suter CM, Brooks DA, Morrison JL. Early origins of heart disease: Low birth weight and the role of the insulin-like growth factor system in cardiac hypertrophy. Clin Exp Pharmacol Physiol 2012; 39:958-64. [DOI: 10.1111/j.1440-1681.2012.05743.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kimberley CW Wang
- Early Origins of Adult Health Research Group; Sansom Institute for Health Research; School of Pharmacy and Medical Sciences; University of Adelaide; Adelaide; South Australia; Australia
| | | | - Monalisa Padhee
- Early Origins of Adult Health Research Group; Sansom Institute for Health Research; School of Pharmacy and Medical Sciences; University of Adelaide; Adelaide; South Australia; Australia
| | - Song Zhang
- Early Origins of Adult Health Research Group; Sansom Institute for Health Research; School of Pharmacy and Medical Sciences; University of Adelaide; Adelaide; South Australia; Australia
| | - I Caroline McMillen
- Early Origins of Adult Health Research Group; Sansom Institute for Health Research; School of Pharmacy and Medical Sciences; University of Adelaide; Adelaide; South Australia; Australia
| | - Catherine M Suter
- Victor Chang Cardiac Research Institute; Darlinghurst; New South Wales; Australia
| | - Doug A Brooks
- Cell Biology of Diseases Research Group; Sansom Institute for Health Research; School of Pharmacy and Medical Sciences; University of Adelaide; Adelaide; South Australia; Australia
| | - Janna L Morrison
- Early Origins of Adult Health Research Group; Sansom Institute for Health Research; School of Pharmacy and Medical Sciences; University of Adelaide; Adelaide; South Australia; Australia
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175
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Abstract
AbstractMy response is divided into four sections: (1) is devoted to a potpourri of commentaries that are essentially in agreement with the substance of my target article (with one exception); in (2) I address, in response to one of the commentaries, several issues relating to the use of candidate gene association studies in behavior genetics (in particular those proposing a specific G×E interaction); in (3) I provide a detailed response to several defenses of the twin study methodology; and in (4) I conclude with several reflections on that methodology and the conception of human nature it has fostered.
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176
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Abstract
AbstractThe science of genetics is undergoing a paradigm shift. Recent discoveries, including the activity of retrotransposons, the extent of copy number variations, somatic and chromosomal mosaicism, and the nature of the epigenome as a regulator of DNA expressivity, are challenging a series of dogmas concerning the nature of the genome and the relationship between genotype and phenotype. According to three widely held dogmas, DNA is the unchanging template of heredity, is identical in all the cells and tissues of the body, and is the sole agent of inheritance. Rather than being an unchanging template, DNA appears subject to a good deal of environmentally induced change. Instead of identical DNA in all the cells of the body, somatic mosaicism appears to be the normal human condition. And DNA can no longer be considered the sole agent of inheritance. We now know that the epigenome, which regulates gene expressivity, can be inherited via the germline. These developments are particularly significant for behavior genetics for at least three reasons: First, epigenetic regulation, DNA variability, and somatic mosaicism appear to be particularly prevalent in the human brain and probably are involved in much of human behavior; second, they have important implications for the validity of heritability and gene association studies, the methodologies that largely define the discipline of behavior genetics; and third, they appear to play a critical role in development during the perinatal period and, in particular, in enabling phenotypic plasticity in offspring. I examine one of the central claims to emerge from the use of heritability studies in the behavioral sciences, the principle of minimal shared maternal effects, in light of the growing awareness that the maternal perinatal environment is a critical venue for the exercise of adaptive phenotypic plasticity. This consideration has important implications for both developmental and evolutionary biology.
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177
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Pidsley R, Dempster E, Troakes C, Al-Sarraj S, Mill J. Epigenetic and genetic variation at the IGF2/H19 imprinting control region on 11p15.5 is associated with cerebellum weight. Epigenetics 2012; 7:155-63. [PMID: 22395465 DOI: 10.4161/epi.7.2.18910] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
IGF2 is a paternally expressed imprinted gene with an important role in development and brain function. Allele-specific expression of IGF2 is regulated by DNA methylation at three differentially methylated regions (DMRs) spanning the IGF2/H19 domain on human 11p15.5. We have comprehensively assessed DNA methylation and genotype across the three DMRs and the H19 promoter using tissue from a unique collection of well-characterized and neuropathologically-dissected post-mortem human cerebellum samples (n = 106) and frontal cortex samples (n = 51). We show that DNA methylation, particularly in the vicinity of a key CTCF-binding site (CTCF3) in the imprinting control region (ICR) upstream of H19, is strongly correlated with cerebellum weight. DNA methylation at CTCF3 uniquely explains ~25% of the variance in cerebellum weight. In addition, we report that genetic variation in this ICR is strongly associated with cerebellum weight in a parental-origin specific manner, with maternally-inherited alleles associated with a 16% increase in cerebellum weight compared with paternally-inherited alleles. Given the link between structural brain abnormalities and neuropsychiatric disease, an understanding of the epigenetic and parent-of-origin specific genetic factors associated with brain morphology provides important clues about the etiology of disorders such as schizophrenia and autism.
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Affiliation(s)
- Ruth Pidsley
- Institute of Psychiatry, King's College London, London, UK
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178
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Lattuada D, Roda B, Pignatari C, Magni R, Colombo F, Cattaneo A, Zattoni A, Cetin I, Reschiglian P, Bolis G. A tag-less method for direct isolation of human umbilical vein endothelial cells by gravitational field-flow fractionation. Anal Bioanal Chem 2012; 405:977-84. [PMID: 22995996 DOI: 10.1007/s00216-012-6337-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/28/2012] [Accepted: 08/06/2012] [Indexed: 01/16/2023]
Abstract
The analysis of cellular and molecular profiles represents a powerful tool in many biomedical applications to identify the mechanisms underlying the pathological changes. The improvement of cellular starting material and the maintenance of the physiological status in the sample preparation are very useful. Human umbilical vein endothelial cells (HUVEC) are a model for prediction of endothelial dysfunction. HUVEC are enzymatically removed from the umbilical vein by collagenase. This method provides obtaining a good sample yield. However, the obtained cells are often contaminated with blood cells and fibroblasts. Methods based on negative selection by in vitro passages or on the use of defined marker are currently employed to isolate target cells. However, these approaches cannot reproduce physiological status and they require expensive instrumentation. Here we proposed a new method for an easy, tag-less and direct isolation of HUVEC from raw umbilical cord sample based on the gravitational field-flow fractionation (GrFFF). This is a low-cost, fully biocompatible method with low instrumental and training investments for flow-assisted cell fractionation. The method allows obtaining pure cells without cell culture procedures as starting material for further analysis; for example, a proper amount of RNA can be extracted. The approach can be easily integrated into clinical and biomedical procedures.
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Affiliation(s)
- Debora Lattuada
- Department of Obstetrics and Gynaecology, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
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179
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Labrie V, Pai S, Petronis A. Epigenetics of major psychosis: progress, problems and perspectives. Trends Genet 2012; 28:427-35. [PMID: 22622229 PMCID: PMC3422438 DOI: 10.1016/j.tig.2012.04.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 04/03/2012] [Accepted: 04/23/2012] [Indexed: 01/26/2023]
Abstract
Understanding the origins of normal and pathological behavior is one of the most exciting opportunities in contemporary biomedical research. There is increasing evidence that, in addition to DNA sequence and the environment, epigenetic modifications of DNA and histone proteins may contribute to complex phenotypes. Inherited and/or acquired epigenetic factors are partially stable and have regulatory roles in numerous genomic activities, thus making epigenetics a promising research path in etiological studies of psychiatric disease. In this article, we review recent epigenetic studies examining the brain and other tissues, including those from individuals with schizophrenia (SCZ) and bipolar disorder (BPD). We also highlight heuristic aspects of the epigenetic theory of psychiatric disease and discuss the future directions of psychiatric epigenetics.
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Affiliation(s)
- Viviane Labrie
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, ONT, M5T 1R8, Canada
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180
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Czyz W, Morahan JM, Ebers GC, Ramagopalan SV. Genetic, environmental and stochastic factors in monozygotic twin discordance with a focus on epigenetic differences. BMC Med 2012; 10:93. [PMID: 22898292 PMCID: PMC3566971 DOI: 10.1186/1741-7015-10-93] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 08/17/2012] [Indexed: 03/16/2023] Open
Abstract
Genetic-epidemiological studies on monozygotic (MZ) twins have been used for decades to tease out the relative contributions of genes and the environment to a trait. Phenotypic discordance in MZ twins has traditionally been ascribed to non-shared environmental factors acting after birth, however recent data indicate that this explanation is far too simple. In this paper, we review other reasons for discordance, including differences in the in utero environment, genetic mosaicism, and stochastic factors, focusing particularly on epigenetic discordance. Epigenetic differences are gaining increasing recognition. Although it is clear that in specific cases epigenetic alterations provide a causal factor in disease etiology, the overall significance of epigenetics in twin discordance remains unclear. It is also challenging to determine the causality and relative contributions of environmental, genetic, and stochastic factors to epigenetic variability. Epigenomic profiling studies have recently shed more light on the dynamics of temporal methylation change and methylome heritability, yet have not given a definite answer regarding their relevance to disease, because of limitations in establishing causality. Here, we explore the subject of epigenetics as another component in human phenotypic variability and its links to disease focusing particularly on evidence from MZ twin studies.
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Affiliation(s)
- Witold Czyz
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences (Clinical Neurology), University of Oxford, Oxford, UK
| | - Julia M Morahan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences (Clinical Neurology), University of Oxford, Oxford, UK
| | - George C Ebers
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences (Clinical Neurology), University of Oxford, Oxford, UK
| | - Sreeram V Ramagopalan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences (Clinical Neurology), University of Oxford, Oxford, UK
- Blizard Institute, Queen Mary University of London, Barts and The London School of Medicine and Dentistry, London, UK
- London School of Hygiene and Tropical Medicine, London, UK
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181
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Bönsch D, Wunschel M, Lenz B, Janssen G, Weisbrod M, Sauer H. Methylation matters? Decreased methylation status of genomic DNA in the blood of schizophrenic twins. Psychiatry Res 2012; 198:533-7. [PMID: 23102571 DOI: 10.1016/j.psychres.2011.09.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 09/02/2011] [Accepted: 09/05/2011] [Indexed: 11/25/2022]
Abstract
Studies of schizophrenia inheritance in identical twins show a concordance of about 50%, which supports an epigenetic model. In our present study we investigated methylation of genomic DNA and promoter methylation of Reelin and SOX10 genes in peripheral blood of twins suffering from schizophrenia. Global DNA methylation was reduced (52.3%) in schizophrenic twins if compared with healthy control twins (65.7%). The reduced methylation was significant in males only. We also found a similar hypomethylation in the non-affected twins of discordant pairs and a mixed group of psychiatric controls. In discordant twins there was a relative hypermethylation of the SOX10 promoter. Within-pair-difference of methylation of Reelin promoter was significantly lower in monozygotic twins than in dizygotic twins.
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Affiliation(s)
- Dominikus Bönsch
- Bezirkskrankenhaus Lohr am Main, Krankenhaus für Psychiatrie, Psychotherapie und Psychosomatische Medizin, Am Sommerberg, 97816 Lohr am Main, Germany.
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182
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Talens RP, Christensen K, Putter H, Willemsen G, Christiansen L, Kremer D, Suchiman HED, Slagboom PE, Boomsma DI, Heijmans BT. Epigenetic variation during the adult lifespan: cross-sectional and longitudinal data on monozygotic twin pairs. Aging Cell 2012; 11:694-703. [PMID: 22621408 PMCID: PMC3399918 DOI: 10.1111/j.1474-9726.2012.00835.x] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The accumulation of epigenetic changes was proposed to contribute to the age-related increase in the risk of most common diseases. In this study on 230 monozygotic twin pairs (MZ pairs), aged 18–89 years, we investigated the occurrence of epigenetic changes over the adult lifespan. Using mass spectrometry, we investigated variation in global (LINE1) DNA methylation and in DNA methylation at INS, KCNQ1OT1, IGF2, GNASAS, ABCA1, LEP, and CRH, candidate loci for common diseases. Except for KCNQ1OT1, interindividual variation in locus-specific DNA methylation was larger in old individuals than in young individuals, ranging from 1.2-fold larger at ABCA1 (P = 0.010) to 1.6-fold larger at INS (P = 3.7 × 10−07). Similarly, there was more within-MZ-pair discordance in old as compared with young MZ pairs, except for GNASAS, ranging from an 8% increase in discordance each decade at CRH (P = 8.9 × 10−06) to a 16% increase each decade at LEP (P = 2.0 × 10−08). Still, old MZ pairs with strikingly similar DNA methylation were also observed at these loci. After 10-year follow-up in elderly twins, the variation in DNA methylation showed a similar pattern of change as observed cross-sectionally. The age-related increase in methylation variation was generally attributable to unique environmental factors, except for CRH, for which familial factors may play a more important role. In conclusion, sustained epigenetic differences arise from early adulthood to old age and contribute to an increasing discordance of MZ twins during aging.
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Affiliation(s)
- Rudolf P. Talens
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kaare Christensen
- The Danish Aging Research Center and The Danish Twin Registry, University of Southern Denmark, Odense C, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark
| | - Hein Putter
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Lene Christiansen
- The Danish Aging Research Center and The Danish Twin Registry, University of Southern Denmark, Odense C, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark
| | - Dennis Kremer
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - H. Eka D. Suchiman
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - P. Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Bastiaan T. Heijmans
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
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183
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Abstract
The classical twin study has been a powerful heuristic in biomedical, psychiatric and behavioural research for decades. Twin registries worldwide have collected biological material and longitudinal phenotypic data on tens of thousands of twins, providing a valuable resource for studying complex phenotypes and their underlying biology. In this Review, we consider the continuing value of twin studies in the current era of molecular genetic studies. We conclude that classical twin methods combined with novel technologies represent a powerful approach towards identifying and understanding the molecular pathways that underlie complex traits.
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184
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Gordon L, Joo JE, Powell JE, Ollikainen M, Novakovic B, Li X, Andronikos R, Cruickshank MN, Conneely KN, Smith AK, Alisch RS, Morley R, Visscher PM, Craig JM, Saffery R. Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence. Genome Res 2012; 22:1395-406. [PMID: 22800725 PMCID: PMC3409253 DOI: 10.1101/gr.136598.111] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Comparison between groups of monozygotic (MZ) and dizygotic (DZ) twins enables an estimation of the relative contribution of genetic and shared and nonshared environmental factors to phenotypic variability. Using DNA methylation profiling of ∼20,000 CpG sites as a phenotype, we have examined discordance levels in three neonatal tissues from 22 MZ and 12 DZ twin pairs. MZ twins exhibit a wide range of within-pair differences at birth, but show discordance levels generally lower than DZ pairs. Within-pair methylation discordance was lowest in CpG islands in all twins and increased as a function of distance from islands. Variance component decomposition analysis of DNA methylation in MZ and DZ pairs revealed a low mean heritability across all tissues, although a wide range of heritabilities was detected for specific genomic CpG sites. The largest component of variation was attributed to the combined effects of nonshared intrauterine environment and stochastic factors. Regression analysis of methylation on birth weight revealed a general association between methylation of genes involved in metabolism and biosynthesis, providing further support for epigenetic change in the previously described link between low birth weight and increasing risk for cardiovascular, metabolic, and other complex diseases. Finally, comparison of our data with that of several older twins revealed little evidence for genome-wide epigenetic drift with increasing age. This is the first study to analyze DNA methylation on a genome scale in twins at birth, further highlighting the importance of the intrauterine environment on shaping the neonatal epigenome.
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Affiliation(s)
- Lavinia Gordon
- Bioinformatics Unit, Murdoch Childrens Research Institute, Parkville, Victoria 3052, Australia
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185
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Hong X, Wang X. Early life precursors, epigenetics, and the development of food allergy. Semin Immunopathol 2012; 34:655-69. [PMID: 22777545 DOI: 10.1007/s00281-012-0323-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 06/19/2012] [Indexed: 12/21/2022]
Abstract
Food allergy (FA), a major clinical and public health concern worldwide, is caused by a complex interplay of environmental exposures, genetic variants, gene-environment interactions, and epigenetic alterations. This review summarizes recent advances surrounding these key factors, with a particular focus on the potential role of epigenetics in the development of FA. Epidemiologic studies have reported a number of nongenetic factors that may influence the risk of FA, such as timing of food introduction and feeding pattern, diet/nutrition, exposure to environmental tobacco smoking, prematurity and low birth weight, microbial exposure, and race/ethnicity. Current studies on the genetics of FA are mainly conducted using candidate gene approaches, which have linked more than 10 genes to the genetic susceptibility of FA. Studies on gene-environment interactions of FA are very limited. Epigenetic alteration has been proposed as one of the mechanisms to mediate the influence of early life environmental exposures and gene-environment interactions on the development of diseases later in life. The role of epigenetics in the regulation of the immune system and the epigenetic effects of some FA-associated environmental exposures are discussed in this review. There is a particular lack of large-scale prospective birth cohort studies that simultaneously assess the interrelationships of early life exposures, genetic susceptibility, epigenomic alterations, and the development of FA. The identification of these key factors and their independent and joint contributions to FA will allow us to gain important insight into the biological mechanisms by which environmental exposures and genetic susceptibility affect the risk of FA and will provide essential information to develop more effective new paradigms in the diagnosis, prevention, and management of FA.
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Affiliation(s)
- Xiumei Hong
- Center on the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205-2179, USA.
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186
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Stünkel W, Pan H, Chew SB, Tng E, Tan JH, Chen L, Joseph R, Cheong CY, Ong ML, Lee YS, Chong YS, Saw SM, Meaney MJ, Kwek K, Sheppard AM, Gluckman PD, Holbrook JD. Transcriptome changes affecting Hedgehog and cytokine signalling in the umbilical cord: implications for disease risk. PLoS One 2012; 7:e39744. [PMID: 22808055 PMCID: PMC3393728 DOI: 10.1371/journal.pone.0039744] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 05/25/2012] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Babies born at lower gestational ages or smaller birthweights have a greater risk of poorer health in later life. Both the causes of these sub-optimal birth outcomes and the mechanism by which the effects are transmitted over decades are the subject of extensive study. We investigated whether a transcriptomic signature of either birthweight or gestational age could be detected in umbilical cord RNA. METHODS The gene expression patterns of 32 umbilical cords from Singaporean babies of Chinese ethnicity across a range of birthweights (1698-4151 g) and gestational ages (35-41 weeks) were determined. We confirmed the differential expression pattern by gestational age for 12 genes in a series of 127 umbilical cords of Chinese, Malay and Indian ethnicity. RESULTS We found that the transcriptome is substantially influenced by gestational age; but less so by birthweight. We show that some of the expression changes dependent on gestational age are enriched in signal transduction pathways, such as Hedgehog and in genes with roles in cytokine signalling and angiogenesis. We show that some of the gene expression changes we report are reflected in the epigenome. CONCLUSIONS We studied the umbilical cord which is peripheral to disease susceptible tissues. The results suggest that soma-wide transcriptome changes, preserved at the epigenetic level, may be a mechanism whereby birth outcomes are linked to the risk of adult metabolic and arthritic disease and suggest that greater attention be given to the association between premature birth and later disease risk.
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Affiliation(s)
- Walter Stünkel
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Hong Pan
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Siew Boom Chew
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Emilia Tng
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Jun Hao Tan
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Li Chen
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Roy Joseph
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Clara Y. Cheong
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Mei-Lyn Ong
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Yung Seng Lee
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Yap-Seng Chong
- Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Seang Mei Saw
- Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, Singapore
| | - Michael J. Meaney
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
| | - Kenneth Kwek
- Department of Maternal Fetal Medicine, KK Women’s and Children’s Hospital, Singapore, Singapore
| | | | - Peter D. Gluckman
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - Joanna D. Holbrook
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
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187
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Prenatal famine exposure, health in later life and promoter methylation of four candidate genes. J Dev Orig Health Dis 2012; 3:450-7. [DOI: 10.1017/s2040174412000396] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Poor nutrition during fetal development can permanently alter growth, cardiovascular physiology and metabolic function. Animal studies have shown that prenatal undernutrition followed by balanced postnatal nutrition alters deoxyribonucleic acid (DNA) methylation of gene promoter regions of candidate metabolic control genes in the liver. The aim of this study was to investigate whether methylation status of the proximal promoter regions of four candidate genes differed between individuals exposed to the Dutch famine in utero. In addition, we determined whether methylation status of these genes was associated with markers of metabolic and cardiovascular disease and adult lifestyle. Methylation status of the GR1-C (glucocorticoid receptor), PPARγ (peroxisome proliferator-activated receptor gamma), lipoprotein lipase and phosphatidylinositol 3 kinase p85 proximal promoters was investigated in DNA isolated from peripheral blood samples of 759 58-year-old subjects born around the time of the 1944–45 Dutch famine. We observed no differences in methylation levels of the promoters between exposed and unexposed men and women. Methylation status of PPARγ was associated with levels of high-density lipoprotein cholesterol and triglycerides as well as with exercise and smoking. Hypomethylation of the GR promoter was associated with adverse adult lifestyle factors, including higher body mass index, less exercise and more smoking. The previously reported increased risk of cardiovascular and metabolic disease after prenatal famine exposure was not associated with differences in methylation status across the promoter regions of these candidate genes measured in peripheral blood. The adult environment seems to affect GR and PPARγ promoter methylation.
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188
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Novakovic B, Galati JC, Chen A, Morley R, Craig JM, Saffery R. Maternal vitamin D predominates over genetic factors in determining neonatal circulating vitamin D concentrations. Am J Clin Nutr 2012; 96:188-95. [PMID: 22648713 DOI: 10.3945/ajcn.112.035683] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND There are multiple potential regulators of neonatal vitamin D status of environmental, genetic, and epigenetic origins. The relation between these factors and circulating neonatal vitamin D has yet to be fully characterized. OBJECTIVE The aim of this study was to examine the relative contribution of genetic factors, maternal circulating 25-hydroxyvitamin D [25(OH)D] concentrations, and the placental methylation level of the gene that encodes the primary catabolic enzyme of active vitamin D [25(OH)D-24-hydroxylase encoded by CYP24A1] to neonatal 25(OH)D concentrations. DESIGN We used the classical twin study design to determine the genetic contribution to neonatal 25(OH)D. A total of 86 twin pairs (32 monozygotic and 54 dizygotic twin pairs) were included in this study. Serum 25(OH)D was measured by using a 25(OH)D kit. CYP24A1 promoter DNA methylation was measured by means of matrix-assisted laser desorption time-of-flight mass spectrometry. RESULTS Maternal and neonatal 25(OH)D showed a strong association (R² = 0.19). Monozygotic and dizygotic within-pair serum 25(OH)D correlations were similar (R² = 0.71 and 0.67, respectively), which suggested no genetic effect. Placental CYP24A1 methylation did not show an association with maternal or neonatal 25(OH)D concentrations. CONCLUSIONS Our results suggest that maternal circulating 25(OH)D is the most significant regulator of neonatal circulating 25(OH)D concentrations, with underlying genetic factors playing a limited role. The placental methylation of the CYP24A1 promoter appears subject to a genetic influence, although no evidence of a relation between the methylation level of this gene and circulating maternal or neonatal 25(OH)D was apparent.
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Affiliation(s)
- Boris Novakovic
- Cancer and Disease Epigenetics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
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189
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Perkins E, Murphy SK, Murtha AP, Schildkraut J, Jirtle RL, Demark-Wahnefried W, Forman MR, Kurtzberg J, Overcash F, Huang Z, Hoyo C. Insulin-like growth factor 2/H19 methylation at birth and risk of overweight and obesity in children. J Pediatr 2012; 161:31-9. [PMID: 22341586 PMCID: PMC3360130 DOI: 10.1016/j.jpeds.2012.01.015] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 11/28/2011] [Accepted: 01/06/2012] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To determine whether aberrant DNA methylation at differentially methylated regions (DMRs) regulating insulin-like growth factor 2 (IGF2) expression in umbilical cord blood is associated with overweight or obesity in a multiethnic cohort. STUDY DESIGN Umbilical cord blood leukocytes of 204 infants born between 2005 and 2009 in Durham, North Carolina, were analyzed for DNA methylation at two IGF2 DMRs by using pyrosequencing. Anthropometric and feeding data were collected at age 1 year. Methylation differences were compared between children >85th percentile of the Centers for Disease Control and Prevention growth charts weight-for-age (WFA) and children ≤ 85th percentile of WFA at 1 year by using generalized linear models, adjusting for post-natal caloric intake, maternal cigarette smoking, and race/ethnicity. RESULTS The methylation percentages at the H19 imprint center DMR was higher in infants with WFA >85th percentile (62.7%; 95% CI, 59.9%-65.5%) than in infants with WFA ≤ 85th percentile (59.3%; 95% CI, 58.2%-60.3%; P = .02). At the intragenic IGF2 DMR, methylation levels were comparable between infants with WFA ≤ 85th percentile and infants with WFA >85th percentile. CONCLUSIONS Our findings suggest that IGF2 plasticity may be mechanistically important in early childhood overweight or obese status. If confirmed in larger studies, these findings suggest aberrant DNA methylation at sequences regulating imprinted genes may be useful identifiers of children at risk for the development of early obesity.
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Affiliation(s)
- Ellen Perkins
- Department of Community and Family Medicine, Duke University, Durham, NC 27710, USA
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190
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Cortessis VK, Thomas DC, Levine AJ, Breton CV, Mack TM, Siegmund KD, Haile RW, Laird PW. Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet 2012; 131:1565-89. [PMID: 22740325 PMCID: PMC3432200 DOI: 10.1007/s00439-012-1189-8] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 06/07/2012] [Indexed: 12/15/2022]
Abstract
Changes in epigenetic marks such as DNA methylation and histone acetylation are associated with a broad range of disease traits, including cancer, asthma, metabolic disorders, and various reproductive conditions. It seems plausible that changes in epigenetic state may be induced by environmental exposures such as malnutrition, tobacco smoke, air pollutants, metals, organic chemicals, other sources of oxidative stress, and the microbiome, particularly if the exposure occurs during key periods of development. Thus, epigenetic changes could represent an important pathway by which environmental factors influence disease risks, both within individuals and across generations. We discuss some of the challenges in studying epigenetic mediation of pathogenesis and describe some unique opportunities for exploring these phenomena.
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Affiliation(s)
- Victoria K. Cortessis
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, CA 90089 USA
| | - Duncan C. Thomas
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2001 N. Soto St., SSB-202F, Los Angeles, CA 90089-9234 USA
| | - A. Joan Levine
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, CA 90089 USA
| | - Carrie V. Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2001 N. Soto St., Los Angeles, CA 90089-9234 USA
| | - Thomas M. Mack
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, CA 90089 USA
| | - Kimberly D. Siegmund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 2001 N. Soto St., Los Angeles, CA 90089-9234 USA
| | - Robert W. Haile
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, USC Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, CA 90089 USA
| | - Peter W. Laird
- Departments of Surgery, Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, USC Norris Comprehensive Cancer Center, Epigenome Center, 1441 Eastlake Avenue, Los Angeles, CA 90089-9601 USA
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191
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LINE-1 methylation status and its association with tetralogy of fallot in infants. BMC Med Genomics 2012; 5:20. [PMID: 22672592 PMCID: PMC3408368 DOI: 10.1186/1755-8794-5-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 06/06/2012] [Indexed: 12/15/2022] Open
Abstract
Background Methylation levels of long interspersed nucleotide elements (LINE-1) are representative of genome-wide methylation status and play an important role in maintaining genomic stability and gene expression. To derive insight into the association between genome-wide methylation status and tetralogy of fallot (TOF), we compared the methylation status of LINE-1 element between TOF patients and controls. The methylation of the NKX 2–5, HAND 1, and TBX 20 promoter regions was also evaluated. Methods Genomic DNA from right ventricular tissue samples was obtained from 32 patients with TOF and 15 control subjects. Sequenom MassARRAY platform was performed to examine the methylation levels of LINE-1, NKX2-5, HAND1 and TBX20. Mann–Whitney U test was used to compare differences in methylation levels between two groups. Results The methylation level of LINE-1 was significantly lower in patients with TOF, with a median of 57.95% (interquartile range [IQR]: 56.10%–60.04%), as opposed to 59.70% in controls (IQR: 59.00%–61.30%; P = 0.0021). The highest LINE-1 methylation level was 61.3%. The risk of TOF increased in subjects with the lowest methylation levels (less than or equal to 59.0%; OR = 14.7, 95% CI: 1.8–117.7, P = 0.014) and in those with medium methylation levels (59.0%–61.3%; OR = 2.0, 95% CI: 0.3–14.2, P = 0.65). An ROC curve analysis showed a relatively high accuracy of using the LINE-1 methylation level in predicting the presence of TOF (AUC = 0.78, 95% CI: 0.65–0.91; P = 0.002). The association of the LINE-1 methylation level with TOF was only observed in males (P = 0.006) and not in females (P = 0.25). Neither age nor gender was found to be associated with the LINE-1 methylation level in patients or controls. Higher methylation levels of NKX2-5 and HAND1 and lower methylation levels of TBX20 were also observed in patients with TOF than in controls. No association was found between the methylation levels of NKX2-5, HAND1 and TBX 20 with the LINE-1 methylation level. Conclusions Lower LINE-1 methylation levels are associated with increased risk of TOF and may provide important clues for the development of TOF.
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192
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Wang D, Liu X, Zhou Y, Xie H, Hong X, Tsai HJ, Wang G, Liu R, Wang X. Individual variation and longitudinal pattern of genome-wide DNA methylation from birth to the first two years of life. Epigenetics 2012; 7:594-605. [PMID: 22522910 DOI: 10.4161/epi.20117] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Prenatal development and early childhood are critical periods for establishing the tissue-specific epigenome, and may have a profound impact on health and disease in later life. However, epigenomic profiles at birth and in early childhood remain largely unexplored. The focus of this report is to examine the individual variation and longitudinal pattern of genome-wide DNA methylation levels from birth through the first two years of life in 105 Black children (59 males and 46 females) enrolled at the Boston Medical Center. We performed epigenomic mapping of cord blood at birth and venous blood samples from the same set of children within the first two years of life using Illumina Infinium Humanmethylation27 BeadChip. We observed a wide range of inter-individual variations in genome-wide methylation at each time point including lower levels at CpG islands, TSS200, 5'UTR and 1st Exon locations, but significantly higher levels in CpG shores, shelves, TSS1500, gene body and 3'UTR. We identified CpG sites with significant intra-individual longitudinal changes in the first two years of life throughout the genome. Specifically, we identified 159 CpG sites in males and 149 CpG sites in females with significant longitudinal changes defined by both statistical significance and magnitude of changes. These significant CpG sites appeared to be located within genes with important biological functions including immunity and inflammation. Further studies are needed to replicate our findings, including analysis by specific cell types, and link those individual variations and longitudinal changes with specific health outcomes in early childhood and later life.
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Affiliation(s)
- Deli Wang
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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193
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Abstract
The ongoing revolution in molecular genetics has led many to speculate that one day we will be able to change the expression or phenotype of numerous complex traits to improve ourselves in many different ways. The prospect of genetic enhancements has generated heated controversy, with proponents advocating research and implementation, with caution advised for concerns about justice, and critics tending to see the prospect of genetic enhancements as an assault on human freedom and human nature. Both camps base their arguments on the unquestioned assumption that the science will realize either their dreams or nightmares. In this paper, I show that their beliefs are based upon two fundamental mistakes. First, they are based upon an unwarranted reliance in a genetic determinism that takes for granted that the traits that we might most want to enhance, like intelligence, aggression, shyness, and even athletic ability, can be causally directed by specific genes. In so doing, character descriptions are reified to be concrete and discrete entities, in this case, genes. Second, they have accepted on faith that there is, or will be, a science to translate their hopes or worries into reality when, in fact, that is unlikely to occur because of the irreducible complexity of phenotypic expression.
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Affiliation(s)
- Philip M Rosoff
- Department of Pediatrics, Duke University Medical Center, 108 Seeley G. Mudd Building, Box 3040, Durham, NC 27710, USA.
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194
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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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195
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Dickins TE, Rahman Q. The extended evolutionary synthesis and the role of soft inheritance in evolution. Proc Biol Sci 2012; 279:2913-21. [PMID: 22593110 DOI: 10.1098/rspb.2012.0273] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In recent years, a number of researchers have advocated extending the modern synthesis in evolutionary biology. One of the core arguments made in favour of an extension comes from work on soft inheritance systems, including transgenerational epigenetic effects, cultural transmission and niche construction. In this study, we outline this claim and then take issue with it. We argue that the focus on soft inheritance has led to a conflation of proximate and ultimate causation, which has in turn obscured key questions about biological organization and calibration across the life span to maximize average lifetime inclusive fitness. We illustrate this by presenting hypotheses that we believe incorporate the core phenomena of soft inheritance and will aid in understanding them.
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Affiliation(s)
- Thomas E Dickins
- School of Psychology, University of East London, , London E15 4LZ, UK.
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196
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Umstad MP, Short RV, Wilson M, Craig JM. Chimaeric twins: Why monochorionicity does not guarantee monozygosity. Aust N Z J Obstet Gynaecol 2012; 52:305-7. [PMID: 22563999 DOI: 10.1111/j.1479-828x.2012.01445.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 03/29/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Mark P. Umstad
- Department of Obstetrics and Gynaecology; University of Melbourne; The Royal Women's Hospital; Parkville; Victoria; Australia
| | - Roger V. Short
- Faculty of Medicine, Dentistry and Health Sciences; University of Melbourne; Melbourne; Victoria; Australia
| | - Matthew Wilson
- Sydney West Area Health Service; Castle Hill; New South Wales; Australia
| | - Jeffrey M. Craig
- Murdoch Childrens Research Institute; Department of Paediatrics; University of Melbourne; The Royal Children's Hospital; Parkville; Victoria; Australia
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197
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Ollikainen M, Craig JM. Epigenetic discordance at imprinting control regions in twins. Epigenomics 2012; 3:295-306. [PMID: 22122339 DOI: 10.2217/epi.11.18] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Imprinting control regions are differentially methylated in a parent-of-origin-dependent manner and this methylation state is inherited through the germline. These regions control parent-specific monoallelic expression of their target genes. Genetically identical organisms show considerable variation in their epigenomes owing to environmental and stochastic influences creating fluctuations in phenotype. Monozygotic twin pairs discordant for imprinting disorders due to epigenetic changes at imprinting control regions are an example of phenotypic variation caused by extreme variations of the epigenome. Here, we discuss the within-pair epigenetic discordance at imprinted loci, both in phenotypically concordant and discordant monozygotic twin pairs.
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Affiliation(s)
- Miina Ollikainen
- Murdoch Childrens Research Institute & Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.
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McKay JA, Groom A, Potter C, Coneyworth LJ, Ford D, Mathers JC, Relton CL. Genetic and non-genetic influences during pregnancy on infant global and site specific DNA methylation: role for folate gene variants and vitamin B12. PLoS One 2012; 7:e33290. [PMID: 22479380 PMCID: PMC3316565 DOI: 10.1371/journal.pone.0033290] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 02/06/2012] [Indexed: 01/17/2023] Open
Abstract
Inter-individual variation in patterns of DNA methylation at birth can be explained by the influence of environmental, genetic and stochastic factors. This study investigates the genetic and non-genetic determinants of variation in DNA methylation in human infants. Given its central role in provision of methyl groups for DNA methylation, this study focuses on aspects of folate metabolism. Global (LUMA) and gene specific (IGF2, ZNT5, IGFBP3) DNA methylation were quantified in 430 infants by Pyrosequencing®. Seven polymorphisms in 6 genes (MTHFR, MTRR, FOLH1, CβS, RFC1, SHMT) involved in folate absorption and metabolism were analysed in DNA from both infants and mothers. Red blood cell folate and serum vitamin B12 concentrations were measured as indices of vitamin status. Relationships between DNA methylation patterns and several covariates viz. sex, gestation length, maternal and infant red cell folate, maternal and infant serum vitamin B12, maternal age, smoking and genotype were tested. Length of gestation correlated positively with IGF2 methylation (rho = 0.11, p = 0.032) and inversely with ZNT5 methylation (rho = −0.13, p = 0.017). Methylation of the IGFBP3 locus correlated inversely with infant vitamin B12 concentration (rho = −0.16, p = 0.007), whilst global DNA methylation correlated inversely with maternal vitamin B12 concentrations (rho = 0.18, p = 0.044). Analysis of common genetic variants in folate pathway genes highlighted several associations including infant MTRR 66G>A genotype with DNA methylation (χ2 = 8.82, p = 0.003) and maternal MTHFR 677C>T genotype with IGF2 methylation (χ2 = 2.77, p = 0.006). These data support the hypothesis that both environmental and genetic factors involved in one-carbon metabolism influence DNA methylation in infants. Specifically, the findings highlight the importance of vitamin B12 status, infant MTRR genotype and maternal MTHFR genotype, all of which may influence the supply of methyl groups for DNA methylation. In addition, gestational length appears to be an important determinant of infant DNA methylation patterns.
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Affiliation(s)
- Jill A McKay
- Institute for Ageing and Health, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, Tyne and Wear, United Kingdom.
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Peñaherrera MS, Jiang R, Avila L, Yuen RKC, Brown CJ, Robinson WP. Patterns of placental development evaluated by X chromosome inactivation profiling provide a basis to evaluate the origin of epigenetic variation. Hum Reprod 2012; 27:1745-53. [PMID: 22431562 PMCID: PMC3357192 DOI: 10.1093/humrep/des072] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Inactivation of the maternally or paternally derived X chromosome (XCI) initially occurs in a random manner in early development; however as tissues form, a ‘patchiness’ will occur in terms of which X is inactivated if cells positioned near each other are clonally descended from a common precursor. Determining the relationship between skewed XCI in different tissues and in different samples from the same tissue provides a molecular assessment of the developmental history of a particular tissue that can then be used to understand how genetic and epigenetic variation arises in development. METHODS XCI skewing was evaluated in and compared between amnion, chorion, trophoblast and mesenchyme using multiple sampling sites from 14 term placentae. XCI was also evaluated in chorionic villus samples obtained at multiple sites and depths from four additional term placentae. The pattern of variation was then compared with methylation variation associated with the H19/IGF2 imprinting control region (ICR); promoter regions of KISS1, PTPN6, CASP8 and APC; and LINE-1 elements. RESULTS Mean placental level of skewing for amnion and chorion are correlated, consistent with a common developmental origin of at least a component of these membranes from inner cell mass derivatives subsequent to XCI, while trophoblast appears to be derived independently, consistent with its origin from the trophectoderm. Villus samples taken from different depths spanning the fetal to maternal side of the placenta were highly clonally related. Comparing patterns of clonal growth identified through XCI to the distribution of epigenetic variation in other genomic regions suggests that some variation arises early in development (e.g. LINE-1 methylation), whereas other variation arises predominantly after villus tree formation (e.g. methylation at H19/IGF2 ICR). CONCLUSIONS The patterns of XCI skewing are consistent with a model whereby each biopsied site of chorionic villi represents one or a few individual villus trees, each of which is clonally derived from only one or a few precursor cells. Sampling of placentae to evaluate changes associated with clinical pathology should be done with consideration of the tree-to-tree differences. A limitation of this study is the small number of placentas used and therefore placental-specific differences in variation could not be assessed.
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Affiliation(s)
- M S Peñaherrera
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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Kasarskis A, Yang X, Schadt E. Integrative genomics strategies to elucidate the complexity of drug response. Pharmacogenomics 2012; 12:1695-715. [PMID: 22118053 DOI: 10.2217/pgs.11.115] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Pharmacogenomic investigation from both genome-wide association studies and experiments focused on candidate loci involved in drug mechanism and metabolism has yielded a substantial and increasing list of robust genetic effects on drug therapy in humans. At the same time, reasonably comprehensive molecular data such as gene expression, proteomic and metabolomic data are now available for collections of hundreds to thousands of individuals. If these data are structured in a statistically robust and computationally tractable way, such as a network model, they can aid in the analysis of new pharmacogenomics studies by suggesting novel hypotheses for the regulation of genes involved in drug metabolism and response. Similarly, hypotheses taken from these same models can direct genome-wide association studies by focusing the genome-wide association studies analysis on a number of specific hypotheses informed by the relationships customarily seen between a gene's expression or protein activity and genetic variation at a particular locus. Network models based on other sorts of systematic biological data such as cell-based surveys of drug effect on gene expression and mining of literature and electronic medical records for associations between clinical and molecular phenotypes also promise similar utility. Although surely primitive in comparison with what will be developed, these model-based approaches to leveraging the increasing volume of data generated in the course of patient care and medical research nevertheless suggest a huge opportunity to improve our understanding of biological systems involved in pharmacogenomics and apply them to questions of medical relevance.
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