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Epigenetics in Alzheimer's Disease: Perspective of DNA Methylation. Mol Neurobiol 2017; 55:1026-1044. [PMID: 28092081 DOI: 10.1007/s12035-016-0357-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/28/2016] [Indexed: 12/12/2022]
Abstract
Research over the years has shown that causes of Alzheimer's disease are not well understood, but over the past years, the involvement of epigenetic mechanisms in the developing memory formation either under pathological or physiological conditions has become clear. The term epigenetics represents the heredity of changes in phenotype that are independent of altered DNA sequences. Different studies validated that cytosine methylation of genomic DNA decreases with age in different tissues of mammals, and therefore, the role of epigenetic factors in developing neurological disorders in aging has been under focus. In this review, we summarized and reviewed the involvement of different epigenetic mechanisms especially the DNA methylation in Alzheimer's disease (AD), late-onset Alzheimer's disease (LOAD), familial Alzheimer's disease (FAD), and autosomal dominant Alzheimer's disease (ADAD). Down to the minutest of details, we tried to discuss the methylation patterns like mitochondrial DNA methylation and ribosomal DNA (rDNA) methylation. Additionally, we mentioned some therapeutic approaches related to epigenetics, which could provide a potential cure for AD. Moreover, we reviewed some recent studies that validate DNA methylation as a potential biomarker and its role in AD. We hope that this review will provide new insights into the understanding of AD pathogenesis from the epigenetic perspective especially from the perspective of DNA methylation.
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Vryer R, Saffery R. What's in a name? Context-dependent significance of 'global' methylation measures in human health and disease. Clin Epigenetics 2017; 9:2. [PMID: 28149330 PMCID: PMC5270354 DOI: 10.1186/s13148-017-0311-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/04/2017] [Indexed: 12/20/2022] Open
Abstract
The study of DNA methylation in development and disease has 'exploded' as a field in recent years, with three major classes of measurement now routine. These encompass (i) locus-specific, (ii) genome-scale/wide and (iii) 'global' methylation approaches. Measures of global methylation refer to the level of 5-methylcytosine (5mC) content in a sample relative to total cytosine. Despite this, several other measures are often referred to as 'global', with the underlying assumption that they accurately reflect 5mC content. The two most common surrogate, or proxy, measures include generating a mean or median methylation value from (i) the average measure in thousands of highly repetitive genomic elements and (ii) many thousands to several million primarily unique CpG sites throughout the genome. Numerous lines of evidence suggest the underlying assumption of equivalence of these measures is flawed, with considerable variation in the regulation of different 'flavours' of DNA methylation throughout the genome depending on cell type, differentiation and disease state. As such, the regulation of methylation 'types' is often uncoupled. The emerging picture suggests that no approach can accurately detect all biologically important differences in 5mC variation and distribution in all instances, with this needing to be ascertained on a case-by-case basis. Thus, it is important to clearly elaborate the genomic context and content of DNA methylation being analysed, the sample and developmental stage in which it is being examined and to remember that in most instances, the most common measures are not a true representation of 'global' 5mC content as orginally defined.
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Affiliation(s)
- Regan Vryer
- Murdoch Childrens Research Institute, 50 Flemington Rd, Parkville, Victoria 3052 Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria Australia
| | - Richard Saffery
- Murdoch Childrens Research Institute, 50 Flemington Rd, Parkville, Victoria 3052 Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria Australia
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103
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Shen J, Song R, Wan J, Huff C, Fang S, Lee JE, Zhao H. Global methylation of blood leukocyte DNA and risk of melanoma. Int J Cancer 2017; 140:1503-1509. [PMID: 28006848 DOI: 10.1002/ijc.30577] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/10/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022]
Abstract
Global DNA methylation, possibly influenced by lifestyle and environmental factors, has been suggested to play an active role in carcinogenesis. However, its role in melanoma has rarely been explored. The aims of this study were to evaluate the relationship between melanoma risk and levels of 5-methylcytosine (5-mC), a marker for global DNA methylation, in blood leukocyte DNA, and to determine whether this 5-mC level is influenced by pigmentation and sun exposure. This case-control study included 540 melanoma cases and 540 healthy controls. Overall, melanoma cases had significantly lower levels of 5-mC% than healthy controls (median: 3.24 vs. 3.91, p < 0.001). The significant difference between two groups did not differ by pigmentation or sun exposure. Among healthy controls, however, those who had fair skin color (p = 0.041) or light or no tanning after prolonged sun exposure (p = 0.031) or used a sunlamp (p = 0.028) had lower levels of 5-mC% than their counterparts. In addition, those with an intermediate or high phenotypic index, an indicator of cutaneous cancer susceptibility, had 2.58-fold greater likelihood of having a low level of 5-mC% [odds ratio (OR): 2.58; 95% confidence interval (CI): 1.72, 3.96] than those with a low phenotypic index. Lower levels of 5-mC% were associated with a 1.25-fold greater risk of melanoma (OR: 1.25; 95% CI: 1.08, 1.37). A significant dose-response relationship was observed in quartile analysis (p = 0.001). Our results suggest that global hypomethylation in blood leukocyte DNA is associated with increased risk of melanoma and that the level of methylation is influenced by pigmentation and sun exposure.
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Affiliation(s)
- Jie Shen
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Renduo Song
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Jie Wan
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Chad Huff
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Shenying Fang
- Departments of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Jeffrey E Lee
- Departments of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
| | - Hua Zhao
- Departments of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030
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104
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Vaiman D. Genes, epigenetics and miRNA regulation in the placenta. Placenta 2016; 52:127-133. [PMID: 28043658 DOI: 10.1016/j.placenta.2016.12.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 10/24/2016] [Accepted: 12/23/2016] [Indexed: 12/19/2022]
Abstract
This text reviews briefly the context in which epigenetics regulate gene expression in trophoblast development and function. It is an attempt to focus on a limited number of recent papers that, according to the author, shed new light on placental development, and constitute possible trails for improving knowledge and women follow-up in pathological pregnancies.
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Affiliation(s)
- Daniel Vaiman
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris-Descartes, 24, rue du Faubourg St-Jacques, 75014, Paris, France.
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105
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Placental expression of DNA methyltransferase 1 (DNMT1): Gender-specific relation with human placental growth. Placenta 2016; 48:119-125. [DOI: 10.1016/j.placenta.2016.09.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/16/2016] [Accepted: 09/22/2016] [Indexed: 01/31/2023]
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106
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Kim CH, Lee EK, Choi YJ, An HJ, Jeong HO, Park D, Kim BC, Yu BP, Bhak J, Chung HY. Short-term calorie restriction ameliorates genomewide, age-related alterations in DNA methylation. Aging Cell 2016; 15:1074-1081. [PMID: 27561685 PMCID: PMC6398531 DOI: 10.1111/acel.12513] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2016] [Indexed: 01/14/2023] Open
Abstract
DNA methylation plays major roles in many biological processes, including aging, carcinogenesis, and development. Analyses of DNA methylation using next-generation sequencing offer a new way to profile and compare methylomes across the genome in the context of aging. We explored genomewide DNA methylation and the effects of short-term calorie restriction (CR) on the methylome of aged rat kidney. Whole-genome methylation of kidney in young (6 months old), old (25 months old), and OCR (old with 4-week, short-term CR) rats was analyzed by methylated DNA immunoprecipitation and next-generation sequencing (MeDIP-Seq). CpG islands and repetitive regions were hypomethylated, but 5'-UTR, exon, and 3'-UTR hypermethylated in old and OCR rats. The methylation in the promoter and intron regions was decreased in old rats, but increased in OCR rats. Pathway enrichment analysis showed that the hypermethylated promoters in old rats were associated with degenerative phenotypes such as cancer and diabetes. The hypomethylated promoters in old rats related significantly to the chemokine signaling pathway. However, the pathways significantly enriched in old rats were not observed from the differentially methylated promoters in OCR rats. Thus, these findings suggest that short-term CR could partially ameliorate age-related methylation changes in promoters in old rats. From the epigenomic data, we propose that the hypermethylation found in the promoter regions of disease-related genes during aging may indicate increases in susceptibility to age-related diseases. Therefore, the CR-induced epigenetic changes that ameliorate age-dependent aberrant methylation may be important to CR's health- and life-prolonging effects.
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Affiliation(s)
| | - Eun Kyeong Lee
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Yeon Ja Choi
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Hye Jin An
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Hyeong Oh Jeong
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Daeui Park
- Department of Predictive Toxicology Korea Institute of Toxicology Daejeon Korea
| | - Byoung Chul Kim
- Department of Predictive Toxicology Korea Institute of Toxicology Daejeon Korea
| | - Byung Pal Yu
- Department of Physiology University of Texas Health Science Center San Antonio TX USA
| | - Jong Bhak
- Biomedical Engineering Ulsan National Institute of Sciences and Technology Ulsan Korea
| | - Hae Yung Chung
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
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Marzi C, Holdt LM, Fiorito G, Tsai PC, Kretschmer A, Wahl S, Guarrera S, Teupser D, Spector TD, Iacoviello L, Sacerdote C, Strauch K, Lee S, Thasler WE, Peters A, Thorand B, Wolf P, Prokisch H, Tumino R, Gieger C, Krogh V, Panico S, Bell JT, Matullo G, Waldenberger M, Grallert H, Koenig W. Epigenetic Signatures at AQP3 and SOCS3 Engage in Low-Grade Inflammation across Different Tissues. PLoS One 2016; 11:e0166015. [PMID: 27824951 PMCID: PMC5100881 DOI: 10.1371/journal.pone.0166015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/21/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Elevated levels of C-reactive protein (CRP, determined by a high-sensitivity assay) indicate low-grade inflammation which is implicated in many age-related disorders. Epigenetic studies on CRP might discover molecular mechanisms underlying CRP regulation. We aimed to identify DNA methylation sites related to CRP concentrations in cells and tissues regulating low-grade inflammation. RESULTS Genome-wide DNA methylation was measured in peripheral blood in 1,741 participants of the KORA F4 study using Illumina HumanMethylation450 BeadChip arrays. Four CpG sites (located at BCL3, AQP3, SOCS3, and cg19821297 intergenic at chromosome 19p13.2, P ≤ 1.01E-07) were significantly hypomethylated at high CRP concentrations independent of various confounders including age, sex, BMI, smoking, and white blood cell composition. Findings were not sex-specific. CRP-related top genes were enriched in JAK/STAT pathways (Benjamini-Hochberg corrected P < 0.05). Results were followed-up in three studies using DNA from peripheral blood (EPICOR, n = 503) and adipose tissue (TwinsUK, n = 368) measured as described above and from liver tissue (LMU liver cohort, n = 286) measured by MALDI-TOF mass spectrometry using EpiTYPER. CpG sites at the AQP3 locus (significant p-values in peripheral blood = 1.72E-03 and liver tissue = 1.51E-03) and the SOCS3 locus (p-values in liver < 2.82E-05) were associated with CRP in the validation panels. CONCLUSIONS Epigenetic modifications seem to engage in low-grade inflammation, possibly via JAK/STAT mediated pathways. Results suggest a shared relevance across different tissues at the AQP3 locus and highlight a role of DNA methylation for CRP regulation at the SOCS3 locus.
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Affiliation(s)
- Carola Marzi
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- * E-mail:
| | - Lesca M Holdt
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Giovanni Fiorito
- Human Genetics Foundation (HuGeF)–Torino, Turin, Italy
- Medical Sciences Department, University of Turin, Turin, Italy
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Anja Kretschmer
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg, Germany
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Simonetta Guarrera
- Human Genetics Foundation (HuGeF)–Torino, Turin, Italy
- Medical Sciences Department, University of Turin, Turin, Italy
| | - Daniel Teupser
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Licia Iacoviello
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli (IS), Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Citta' della Salute e della Scienza Hospital-University of Turin and Center for Cancer Prevention (CPO), Torino, Italy
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Serene Lee
- Department of Surgery, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang E. Thasler
- Department of Surgery, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Barbara Thorand
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Petra Wolf
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technical University Munich, München, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technical University Munich, München, Germany
| | - Rosario Tumino
- Cancer Registry and Histopathology Unit, “Civile–M.P. Arezzo” Hospital, ASP 7, Ragusa, Italy
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg, Germany
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCSS Istituto Nazionale Tumori, Milan, Italy
| | - Salvatore Panico
- Department of Clinical and Medicine and Surgery, Federico II University, Naples, Italy
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Giuseppe Matullo
- Human Genetics Foundation (HuGeF)–Torino, Turin, Italy
- Medical Sciences Department, University of Turin, Turin, Italy
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Wolfgang Koenig
- Department of Internal Medicine II-Cardiology, University of Ulm Medical Center, Ulm, Germany
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
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108
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Kaz AM, Wong CJ, Varadan V, Willis JE, Chak A, Grady WM. Global DNA methylation patterns in Barrett's esophagus, dysplastic Barrett's, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use. Clin Epigenetics 2016; 8:111. [PMID: 27795744 PMCID: PMC5082363 DOI: 10.1186/s13148-016-0273-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/29/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The risk of developing Barrett's esophagus (BE) and/or esophageal adenocarcinoma (EAC) is associated with specific demographic and behavioral factors, including gender, obesity/elevated body mass index (BMI), and tobacco use. Alterations in DNA methylation, an epigenetic modification that can affect gene expression and that can be influenced by environmental factors, is frequently present in both BE and EAC and is believed to play a role in the formation of BE and its progression to EAC. It is currently unknown whether obesity or tobacco smoking influences the risk of developing BE/EAC via the induction of alterations in DNA methylation. To investigate this possibility, we assessed the genome-wide methylation status of 81 esophageal tissues, including BE, dysplastic BE, and EAC epithelia using HumanMethylation450 BeadChips (Illumina). RESULTS We found numerous differentially methylated loci in the esophagus tissues when comparing males to females, obese to lean individuals, and smokers to nonsmokers. Differences in DNA methylation between these groups were seen in a variety of functional genomic regions and both within and outside of CpG islands. Several cancer-related pathways were found to have differentially methylated genes between these comparison groups. CONCLUSIONS Our findings suggest obesity and tobacco smoking may influence DNA methylation in the esophagus and raise the possibility that these risk factors affect the development of BE, dysplastic BE, and EAC through influencing the epigenetic status of specific loci that have a biologically plausible role in cancer formation.
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Affiliation(s)
- Andrew M. Kaz
- Gastroenterology Section, VA Puget Sound Health Care System, Seattle, WA 98108 USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195 USA
| | - Chao-Jen Wong
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Vinay Varadan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Joseph E. Willis
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Amitabh Chak
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106 USA
- Division of Gastroenterology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195 USA
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109
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Heo HJ, Tozour JN, Delahaye F, Zhao Y, Cui L, Barzilai N, Einstein FH. Advanced aging phenotype is revealed by epigenetic modifications in rat liver after in utero malnutrition. Aging Cell 2016; 15:964-72. [PMID: 27470058 PMCID: PMC5013021 DOI: 10.1111/acel.12505] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2016] [Indexed: 02/06/2023] Open
Abstract
Adverse environmental exposures of mothers during fetal period predispose offspring to a range of age-related diseases earlier in life. Here, we set to determine whether a deregulated epigenetic pattern is similar in young animals whose mothers' nutrition was modulated during fetal growth to that acquired during normal aging in animals. Using a rodent model of maternal undernutrition (UN) or overnutrition (ON), we examined cytosine methylation profiles of liver from young female offspring and compared them to age-matched young controls and aged (20-month-old) animals. HELP-tagging, a genomewide restriction enzyme and sequencing assay demonstrates that fetal exposure to two different maternal diets is associated with nonrandom dysregulation of methylation levels with profiles similar to those seen in normal aging animals and occur in regions mapped to genes relevant to metabolic diseases and aging. Functional consequences were assessed by gene expression at 9 weeks old with more significant changes at 6 months of age. Early developmental exposures to unfavorable maternal diets result in altered methylation profiles and transcriptional dysregulation in Prkcb, Pc, Ncor2, and Smad3 that is also seen with normal aging. These Notch pathway and lipogenesis genes may be useful for prediction of later susceptibility to chronic disease.
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Affiliation(s)
- Hye J. Heo
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Jessica N. Tozour
- Department of Genetics Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Fabien Delahaye
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
- Department of Genetics Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Yongmei Zhao
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Lingguang Cui
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Nir Barzilai
- Department of Genetics Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
- Department of Medicine Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
| | - Francine Hughes Einstein
- Department of Obstetrics & Gynecology and Women's Health Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
- Department of Medicine Albert Einstein College of Medicine 1300 Morris Park Ave Bronx NY 10461 USA
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110
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DNA methylation: conducting the orchestra from exposure to phenotype? Clin Epigenetics 2016; 8:92. [PMID: 27602172 PMCID: PMC5012062 DOI: 10.1186/s13148-016-0256-8] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/22/2016] [Indexed: 01/02/2023] Open
Abstract
DNA methylation, through 5-methyl- and 5-hydroxymethylcytosine (5mC and 5hmC), is considered to be one of the principal interfaces between the genome and our environment, and it helps explain phenotypic variations in human populations. Initial reports of large differences in methylation level in genomic regulatory regions, coupled with clear gene expression data in both imprinted genes and malignant diseases, provided easily dissected molecular mechanisms for switching genes on or off. However, a more subtle process is becoming evident, where small (<10 %) changes to intermediate methylation levels are associated with complex disease phenotypes. This has resulted in two clear methylation paradigms. The latter “subtle change” paradigm is rapidly becoming the epigenetic hallmark of complex disease phenotypes, although we are currently hampered by a lack of data addressing the true biological significance and meaning of these small differences. Our initial expectation of rapidly identifying mechanisms linking environmental exposure to a disease phenotype led to numerous observational/association studies being performed. Although this expectation remains unmet, there is now a growing body of literature on specific genes, suggesting wide ranging transcriptional and translational consequences of such subtle methylation changes. Data from the glucocorticoid receptor (NR3C1) has shown that a complex interplay between DNA methylation, extensive 5′UTR splicing, and microvariability gives rise to the overall level and relative distribution of total and N-terminal protein isoforms generated. Additionally, the presence of multiple AUG translation initiation codons throughout the complete, processed mRNA enables translation variability, hereby enhancing the translational isoforms and the resulting protein isoform diversity, providing a clear link between small changes in DNA methylation and significant changes in protein isoforms and cellular locations. Methylation changes in the NR3C1 CpG island alters the NR3C1 transcription and eventually protein isoforms in the tissues, resulting in subtle but visible physiological variability. This review addresses the current pathophysiological and clinical associations of such characteristically small DNA methylation changes, the ever-growing roles of DNA methylation and the evidence available, particularly from the glucocorticoid receptor of the cascade of events initiated by such subtle methylation changes, as well as addressing the underlying question as to what represents a genuine biologically significant difference in methylation.
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111
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Deibel SH, Zelinski EL, Keeley RJ, Kovalchuk O, McDonald RJ. Epigenetic alterations in the suprachiasmatic nucleus and hippocampus contribute to age-related cognitive decline. Oncotarget 2016; 6:23181-203. [PMID: 26252151 PMCID: PMC4695111 DOI: 10.18632/oncotarget.4036] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 12/31/1969] [Indexed: 12/16/2022] Open
Abstract
Circadian rhythm dysfunction and cognitive decline, specifically memory loss, frequently accompany natural aging. Circadian rhythms and memory are intertwined, as circadian rhythms influence memory formation and recall in young and old rodents. Although, the precise relationship between circadian rhythms and memory is still largely unknown, it is hypothesized that circadian rhythm disruption, which occurs during aging, contributes to age-associated cognitive decline, specifically memory loss. While there are a variety of mechanisms that could mediate this effect, changes in the epigenome that occur during aging has been proposed as a potential candidate. Interestingly, epigenetic mechanisms, such as DNA methylation and sirtuin1 (SIRT1) are necessary for both circadian rhythms and memory. During aging, similar alterations of epigenetic mechanisms occur in the suprachiasmatic nucleus (SCN) and hippocampus, which are necessary for circadian rhythm generation and memory, respectively. Recently, circadian rhythms have been linked to epigenetic function in the hippocampus, as some of these epigenetic mechanisms oscillate in the hippocampus and are disrupted by clock gene deletion. The current paper will review how circadian rhythms and memory change with age, and will suggest how epigenetic changes in these processes might contribute to age-related cognitive decline.
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Affiliation(s)
- Scott H Deibel
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Erin L Zelinski
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Robin J Keeley
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Robert J McDonald
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
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112
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Buscarlet M, Tessier A, Provost S, Mollica L, Busque L. Human blood cell levels of 5-hydroxymethylcytosine (5hmC) decline with age, partly related to acquired mutations in TET2. Exp Hematol 2016; 44:1072-1084. [PMID: 27475703 DOI: 10.1016/j.exphem.2016.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/08/2016] [Accepted: 07/14/2016] [Indexed: 12/15/2022]
Abstract
Epigenetic alteration may play a role in age-associated dysfunction of stem cells and predispose to the development of hematological cancers. We analyzed global levels of hematopoietic 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) in a cross-sectional study comprising 198 unrelated individuals from four age categories (neonates, 25-30, 70-75, and >90 years old) by liquid chromatography-electrospray ionization-tandem mass spectrometry with multiple reaction monitoring. X-chromosome inactivation (XCI) ratios and telomere length (TL) were measured in all individuals by polymerase chain reaction. Sequencing of epigenetic regulator genes (including TET2, DNMT3A, ASXL1, IDH1, IDH2, and WT1) was performed in the two older subcohorts. We found that global 5hmC levels declined with age in human blood cells (27.5% reduction from birth to old age, p < 0.0005). The levels of 5mC underwent a more modest reduction (2.4% drop) between newborns and the elderly (p < 0.0005). Low 5hmC was associated with increased skewing of XCI (age-adjusted p = 0.0304) and reduced TL (age-adjusted p = 0.0354), both surrogate markers of clonal dominance. Of the 100 individuals over the age of 70, 16 had somatic mutations in TET2, 14 in DNMT3A, and none in IDH1, IDH2, or WT1. Individuals with TET2 mutations had significantly lower 5hmC (relative to unmutated individuals), whereas DNMT3A-mutated subjects did not. However, mutations in TET2 cannot account solely for the decline in 5hmC levels observed with aging because unmutated older individuals also had lower 5hmC levels compared with younger individuals. This suggests that the age-associated decline in 5hmC is multifactorial. Larger prospective studies are needed to determine whether 5hmC reduction is a biomarker of hematological cancer development.
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Affiliation(s)
| | - Alain Tessier
- Centre for Biological Applications of Mass Spectrometry, Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
| | - Sylvie Provost
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute Research Centre, Montreal, Canada
| | - Luigina Mollica
- Research Centre, Montreal, Canada; Department of Hematology, Installation Hôpital Maisonneuve-Rosemont, Montreal, Canada; Université de Montréal, Montreal, Canada
| | - Lambert Busque
- Research Centre, Montreal, Canada; Department of Hematology, Installation Hôpital Maisonneuve-Rosemont, Montreal, Canada; Université de Montréal, Montreal, Canada.
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113
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Reichetzeder C, Dwi Putra SE, Pfab T, Slowinski T, Neuber C, Kleuser B, Hocher B. Increased global placental DNA methylation levels are associated with gestational diabetes. Clin Epigenetics 2016; 8:82. [PMID: 27462376 PMCID: PMC4960714 DOI: 10.1186/s13148-016-0247-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/11/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Gestational diabetes mellitus (GDM) is associated with adverse pregnancy outcomes. It is known that GDM is associated with an altered placental function and changes in placental gene regulation. More recent studies demonstrated an involvement of epigenetic mechanisms. So far, the focus regarding placental epigenetic changes in GDM was set on gene-specific DNA methylation analyses. Studies that robustly investigated placental global DNA methylation are lacking. However, several studies showed that tissue-specific alterations in global DNA methylation are independently associated with type 2 diabetes. Thus, the aim of this study was to characterize global placental DNA methylation by robustly measuring placental DNA 5-methylcytosine (5mC) content and to examine whether differences in placental global DNA methylation are associated with GDM. METHODS Global DNA methylation was quantified by the current gold standard method, LC-MS/MS. In total, 1030 placental samples were analyzed in this single-center birth cohort study. RESULTS Mothers with GDM displayed a significantly increased global placental DNA methylation (3.22 ± 0.63 vs. 3.00 ± 0.46 %; p = 0.013; ±SD). Bivariate logistic regression showed a highly significant positive correlation between global placental DNA methylation and the presence of GDM (p = 0.0009). Quintile stratification according to placental DNA 5mC levels revealed that the frequency of GDM was evenly distributed in quintiles 1-4 (2.9-5.3 %), whereas the frequency in the fifth quintile was significantly higher (10.7 %; p = 0.003). Bivariate logistic models adjusted for maternal age, BMI, ethnicity, recurrent miscarriages, and familiar diabetes predisposition clearly demonstrated an independent association between global placental DNA hypermethylation and GDM. Furthermore, an ANCOVA model considering known predictors of DNA methylation substantiated an independent association between GDM and placental DNA methylation. CONCLUSIONS This is the first study that employed a robust quantitative assessment of placental global DNA methylation in over a thousand placental samples. The study provides large scale evidence that placental global DNA hypermethylation is associated with GDM, independent of established risk factors.
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Affiliation(s)
- C. Reichetzeder
- Department of Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
- Center for Cardiovascular Research (CCR), Campus Charité Mitte, University Hospital Charité, Berlin, Germany
| | - S. E. Dwi Putra
- Department of Experimental Nutritional Medicine, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, Nuthetal, Potsdam 14558 Germany
- Faculty of Biotechnology, University of Surabaya, Surabaya, Indonesia
| | - T. Pfab
- Center for Cardiovascular Research (CCR), Campus Charité Mitte, University Hospital Charité, Berlin, Germany
- Diaverum Deutschland, Potsdam, Germany
| | - T. Slowinski
- Department of Nephrology, Campus Charité Mitte, University Hospital Charité, Berlin, Germany
| | - C. Neuber
- Department of Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - B. Kleuser
- Department of Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - B. Hocher
- Department of Experimental Nutritional Medicine, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, Nuthetal, Potsdam 14558 Germany
- Institut für Laboratoriumsmedizin, Berlin, Germany
- Department of Basic Medicine, Medical College of Hunan Normal University, Changsha, China
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Placental Hypomethylation Is More Pronounced in Genomic Loci Devoid of Retroelements. G3-GENES GENOMES GENETICS 2016; 6:1911-21. [PMID: 27172225 PMCID: PMC4938645 DOI: 10.1534/g3.116.030379] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The human placenta is hypomethylated compared to somatic tissues. However, the degree and specificity of placental hypomethylation across the genome is unclear. We assessed genome-wide methylation of the human placenta and compared it to that of the neutrophil, a representative homogeneous somatic cell. We observed global hypomethylation in placenta (relative reduction of 22%) compared to neutrophils. Placental hypomethylation was pronounced in intergenic regions and gene bodies, while the unmethylated state of the promoter remained conserved in both tissues. For every class of repeat elements, the placenta showed lower methylation but the degree of hypomethylation differed substantially between these classes. However, some retroelements, especially the evolutionarily younger Alu elements, retained high levels of placental methylation. Surprisingly, nonretrotransposon-containing sequences showed a greater degree of placental hypomethylation than retrotransposons in every genomic element (intergenic, introns, and exons) except promoters. The differentially methylated fragments (DMFs) in placenta and neutrophils were enriched in gene-poor and CpG-poor regions. The placentally hypomethylated DMFs were enriched in genomic regions that are usually inactive, whereas hypermethylated DMFs were enriched in active regions. Hypomethylation of the human placenta is not specific to retroelements, indicating that the evolutionary advantages of placental hypomethylation go beyond those provided by expression of retrotransposons and retrogenes.
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115
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Gao J, Qiu X, Wang X, Peng C, Zheng F. Associations of ChREBP and Global DNA Methylation with Genetic and Environmental Factors in Chinese Healthy Adults. PLoS One 2016; 11:e0157128. [PMID: 27281235 PMCID: PMC4900669 DOI: 10.1371/journal.pone.0157128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 05/25/2016] [Indexed: 12/26/2022] Open
Abstract
Age, gender, diet, gene and lifestyle have been reported to affect metabolic status and disease susceptibility through epigenetic pathway. But it remains indistinct that which factors account for certain epigenetic modifications. Our aim was to identify the influencing factors on inter-individual DNA methylation variations of carbohydrate response element binding protein (ChREBP) and global genome in peripheral blood leucocytes (PBLs). ChREBP DNA methylation was determined by bisulfite sequencing, and genomic 5mdC contents were quantified by capillary hydrophilic-interaction liquid chromatography/ in-source fragmentation/ tandem mass spectrometry system in about 300 healthy individuals. Eleven single nucleotide polymorphisms (SNPs) spanning ChREBP and DNA methyltransferase 1 (DNMT1) were genotyped by high resolution melting or PCR-restriction fragment length polymorphism. DNMT1 mRNA expression was analyzed by quantitative PCR. We found ChREBP DNA methylation levels were statistically associated with age (Beta (B) = 0.028, p = 0.006) and serum total cholesterol concentrations (TC) (B = 0.815, p = 0.010), independent of sex, concentrations of triglyceride, high density lipoprotein cholesterol, low density lipoprotein cholesterol (LDL-C), fasting blood glucose and systolic blood pressure, diastolic blood pressure, PBLs counts and classifications. The DNMT1 haplotypes were related to ChREBP (odds ratio (OR) = 0.668, p = 0.029) and global (OR = 0.450, p = 0.015) DNA methylation as well as LDL-C, but not DNMT1 expression. However, only the relation to LDL-C was robust to correction for multiple testing (ORFDR = 1.593, pFDR = 0.013). These results indicated that the age and TC were independent influential factors of ChREBP methylation and DNMT1 variants could probably influence LDL-C to further modify ChREBP DNA methylation. Certainly, sequential comprehensive analysis of the interactions between genetic variants and blood lipid levels on ChREBP and global DNA methylation was required.
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Affiliation(s)
- Jiajia Gao
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xueping Qiu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xuebin Wang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chunyan Peng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fang Zheng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
- * E-mail:
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116
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Lendvai Á, Deutsch MJ, Plösch T, Ensenauer R. The peroxisome proliferator-activated receptors under epigenetic control in placental metabolism and fetal development. Am J Physiol Endocrinol Metab 2016; 310:E797-810. [PMID: 26860983 DOI: 10.1152/ajpendo.00372.2015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/02/2016] [Indexed: 01/09/2023]
Abstract
The placental metabolism can adapt to the environment throughout pregnancy to both the demands of the fetus and the signals from the mother. Such adaption processes include epigenetic mechanisms, which alter gene expression and may influence the offspring's health. These mechanisms are linked to the diversity of prenatal environmental exposures, including maternal under- or overnutrition or gestational diabetes. The peroxisome proliferator-activated receptors (PPARs) are nuclear receptors that contribute to the developmental plasticity of the placenta by regulating lipid and glucose metabolism pathways, including lipogenesis, steroidogenesis, glucose transporters, and placental signaling pathways, thus representing a link between energy metabolism and reproduction. Among the PPAR isoforms, PPARγ appears to be the main modulator of mammalian placentation. Certain fatty acids and lipid-derived moieties are the natural activating PPAR ligands. By controlling the amounts of maternal nutrients that go across to the fetus, the PPARs play an important regulatory role in placenta metabolism, thereby adapting to the maternal nutritional status. As demonstrated in animal studies, maternal nutrition during gestation can exert long-term influences on the PPAR methylation pattern in offspring organs. This review underlines the current state of knowledge on the relationship between environmental factors and the epigenetic regulation of the PPARs in placenta metabolism and offspring development.
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Affiliation(s)
- Ágnes Lendvai
- Center for Liver, Digestive, and Metabolic Diseases, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Manuel J Deutsch
- Research Center, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Torsten Plösch
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands;
| | - Regina Ensenauer
- Research Center, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; Experimental Pediatrics, Department of General Pediatrics, Pediatric Cardiology, and Neonatology, Heinrich-Heine-University Düsseldorf, Dusseldorf, Germany
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117
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Oh G, Ebrahimi S, Wang SC, Cortese R, Kaminsky ZA, Gottesman II, Burke JR, Plassman BL, Petronis A. Epigenetic assimilation in the aging human brain. Genome Biol 2016; 17:76. [PMID: 27122015 PMCID: PMC4848814 DOI: 10.1186/s13059-016-0946-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 04/11/2016] [Indexed: 12/22/2022] Open
Abstract
Background Epigenetic drift progressively increases variation in DNA modification profiles of aging cells, but the finale of such divergence remains elusive. In this study, we explored the dynamics of DNA modification and transcription in the later stages of human life. Results We find that brain tissues of older individuals (>75 years) become more similar to each other, both epigenetically and transcriptionally, compared with younger individuals. Inter-individual epigenetic assimilation is concurrent with increasing similarity between the cerebral cortex and the cerebellum, which points to potential brain cell dedifferentiation. DNA modification analysis of twins affected with Alzheimer’s disease reveals a potential for accelerated epigenetic assimilation in neurodegenerative disease. We also observe loss of boundaries and merging of neighboring DNA modification and transcriptomic domains over time. Conclusions Age-dependent epigenetic divergence, paradoxically, changes to convergence in the later stages of life. The newly described phenomena of epigenetic assimilation and tissue dedifferentiation may help us better understand the molecular mechanisms of aging and the origins of diseases for which age is a risk factor. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0946-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriel Oh
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St. R130, Toronto, Ontario, M5T 1R8, Canada
| | - Sasha Ebrahimi
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St. R130, Toronto, Ontario, M5T 1R8, Canada
| | - Sun-Chong Wang
- Institute of Systems Biology and Bioinformatics, National Central University, Chungli, 320, Taiwan
| | - Rene Cortese
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St. R130, Toronto, Ontario, M5T 1R8, Canada.,Department of Pediatrics, University of Chicago, Chicago, Illinois, 60637, USA
| | - Zachary A Kaminsky
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, Maryland, 21287, USA
| | - Irving I Gottesman
- Departments of Psychology and Psychiatry, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - James R Burke
- Duke University Medical Center, Duke University, Box 2900, Durham, North Carolina, 27701, USA
| | - Brenda L Plassman
- Duke University Medical Center, Duke University, Box 41, Durham, North Carolina, 27701, USA
| | - Art Petronis
- Krembil Family Epigenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St. R130, Toronto, Ontario, M5T 1R8, Canada.
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118
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Bianco-Miotto T, Mayne BT, Buckberry S, Breen J, Rodriguez Lopez CM, Roberts CT. Recent progress towards understanding the role of DNA methylation in human placental development. Reproduction 2016; 152:R23-30. [PMID: 27026712 PMCID: PMC5064761 DOI: 10.1530/rep-16-0014] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/29/2016] [Indexed: 12/20/2022]
Abstract
Epigenetic modifications, and particularly DNA methylation, have been studied in many tissues, both healthy and diseased, and across numerous developmental stages. The placenta is the only organ that has a transient life of 9 months and undergoes rapid growth and dynamic structural and functional changes across gestation. Additionally, the placenta is unique because although developing within the mother, its genome is identical to that of the foetus. Given these distinctive characteristics, it is not surprising that the epigenetic landscape affecting placental gene expression may be different to that in other healthy tissues. However, the role of epigenetic modifications, and particularly DNA methylation, in placental development remains largely unknown. Of particular interest is the fact that the placenta is the most hypomethylated human tissue and is characterized by the presence of large partially methylated domains (PMDs) containing silenced genes. Moreover, how and why the placenta is hypomethylated and what role DNA methylation plays in regulating placental gene expression across gestation are poorly understood. We review genome-wide DNA methylation studies in the human placenta and highlight that the different cell types that make up the placenta have very different DNA methylation profiles. Summarizing studies on DNA methylation in the placenta and its relationship with pregnancy complications are difficult due to the limited number of studies available for comparison. To understand the key steps in placental development and hence what may be perturbed in pregnancy complications requires large-scale genome-wide DNA methylation studies coupled with transcriptome analyses.
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Affiliation(s)
- Tina Bianco-Miotto
- School of Agriculture, Food and WineUniversity of Adelaide, Adelaide, South Australia, Australia Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Benjamin T Mayne
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia School of MedicineUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical ResearchThe University of Western Australia, Crawley, Western Australia, Australia Plant Energy BiologyARC Centre of Excellence, The University of Western Australia, Crawley, Western Australia, Australia
| | - James Breen
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia Bioinformatics HubUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Carlos M Rodriguez Lopez
- School of Agriculture, Food and WineUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Claire T Roberts
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia School of MedicineUniversity of Adelaide, Adelaide, South Australia, Australia
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Macaulay EC, Bloomfield FH. Unravelling the Link Between the Placental Epigenome and Pregnancy Outcomes. Biol Reprod 2016; 94:82. [PMID: 26962116 DOI: 10.1095/biolreprod.116.139915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Erin C Macaulay
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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120
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Nilsen FM, Parrott BB, Bowden JA, Kassim BL, Somerville SE, Bryan TA, Bryan CE, Lange TR, Delaney JP, Brunell AM, Long SE, Guillette LJ. Global DNA methylation loss associated with mercury contamination and aging in the American alligator (Alligator mississippiensis). THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 545-546:389-97. [PMID: 26748003 PMCID: PMC4972023 DOI: 10.1016/j.scitotenv.2015.12.059] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 12/10/2015] [Accepted: 12/13/2015] [Indexed: 04/13/2023]
Abstract
Mercury is a widespread environmental contaminant with exposures eliciting a well-documented catalog of adverse effects. Yet, knowledge regarding the underlying mechanisms by which mercury exposures are translated into biological effects remains incomplete. DNA methylation is an epigenetic modification that is sensitive to environmental cues, and alterations in DNA methylation at the global level are associated with a variety of diseases. Using a liquid chromatography tandem mass spectrometry-based (LC-MS/MS) approach, global DNA methylation levels were measured in red blood cells of 144 wild American alligators (Alligator mississippiensis) from 6 sites with variable levels of mercury contamination across Florida's north-south axis. Variation in mercury concentrations measured in whole blood was highly associated with location, allowing the comparison of global DNA methylation levels across different "treatments" of mercury. Global DNA methylation in alligators across all locations was weakly associated with increased mercury exposure. However, a much more robust relationship was observed in those animals sampled from locations more highly contaminated with mercury. Also, similar to other vertebrates, global DNA methylation appears to decline with age in alligators. The relationship between age-associated loss of global DNA methylation and varying mercury exposures was examined to reveal a potential interaction. These findings demonstrate that global DNA methylation levels are associated with mercury exposure, and give insights into interactions between contaminants, aging, and epigenetics.
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Affiliation(s)
- Frances M Nilsen
- National Institute of Standards and Technology, Chemical Sciences Division, Environmental Chemical Sciences Group, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States; Medical University of South Carolina, Marine Biomedicine and Environmental Sciences, 221 Fort Johnson Road, Charleston, SC 29412, United States; Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States.
| | - Benjamin B Parrott
- Medical University of South Carolina, Marine Biomedicine and Environmental Sciences, 221 Fort Johnson Road, Charleston, SC 29412, United States; Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, SC 29403, United States; Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States
| | - John A Bowden
- National Institute of Standards and Technology, Chemical Sciences Division, Environmental Chemical Sciences Group, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States; Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States
| | - Brittany L Kassim
- National Institute of Standards and Technology, Chemical Sciences Division, Environmental Chemical Sciences Group, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States; Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States
| | - Stephen E Somerville
- Medical University of South Carolina, Marine Biomedicine and Environmental Sciences, 221 Fort Johnson Road, Charleston, SC 29412, United States; Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, SC 29403, United States; Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States
| | - Teresa A Bryan
- Medical University of South Carolina, Marine Biomedicine and Environmental Sciences, 221 Fort Johnson Road, Charleston, SC 29412, United States; Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, SC 29403, United States; Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States
| | - Colleen E Bryan
- National Institute of Standards and Technology, Chemical Sciences Division, Environmental Chemical Sciences Group, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States; Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States
| | - Ted R Lange
- Florida Fish and Wildlife Conservation Commission, 601 W. Woodward Ave, Eustis, FL 32726, United States
| | - J Patrick Delaney
- Deseret Ranches- 13754 Deseret Lane, St. Cloud, Florida 34773-9381, United States
| | - Arnold M Brunell
- Florida Fish and Wildlife Conservation Commission, 601 W. Woodward Ave, Eustis, FL 32726, United States
| | - Stephen E Long
- National Institute of Standards and Technology, Chemical Sciences Division, Environmental Chemical Sciences Group, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States; Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States
| | - Louis J Guillette
- Medical University of South Carolina, Marine Biomedicine and Environmental Sciences, 221 Fort Johnson Road, Charleston, SC 29412, United States; Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, SC 29403, United States; Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States
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Li-Tempel T, Larra MF, Sandt E, Mériaux SB, Schote AB, Schächinger H, Muller CP, Turner JD. The cardiovascular and hypothalamus-pituitary-adrenal axis response to stress is controlled by glucocorticoid receptor sequence variants and promoter methylation. Clin Epigenetics 2016; 8:12. [PMID: 26823689 PMCID: PMC4730588 DOI: 10.1186/s13148-016-0180-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/20/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Gender, genetic makeup, and prior experience interact to determine physiological responses to an external perceived stressor. Here, we investigated the contribution of both genetic variants and promoter methylation of the NR3C1 (glucocorticoid receptor) gene to the cardiovascular and hypothalamus-pituitary-adrenal (HPA) axis response to the socially evaluated cold pressor test (seCPT). RESULTS Two hundred thirty-two healthy participants were recruited and underwent the experiment. They were randomly assigned to either the seCPT group (cold water) or a control group (warm water). The seCPT group had a clear stress reaction; salivary cortisol levels and peak systolic and diastolic blood pressure all increased significantly compared to the control group. GR genotype (TthIIII, NR3C1-I, 1H, E22E, R23K, BclI and 9beta) and methylation data were obtained from 218 participants. Haplotypes were built from the GR genotypes, and haplotype 2 (minor allele of BclI) carriers had a higher cortisol response to the seCPT in comparison to non-carriers (20.77 ± 13.22; 14.99 ± 8.42; p = 0.034), as well as independently of the experimental manipulation, higher baseline heart rate (72.44 ± 10.99; 68.74 ± 9.79; p = 0.022) and blood pressure (115.81 ± 10.47; 111.61 ± 10.74; p = 0.048). Average methylation levels throughout promoter 1F and 1H were low (2.76 and 1.69 %, respectively), but there was a strong correlation between individual CpGs and the distance separating them (Pearson's correlation r = 0.725, p = 3.03 × 10(-26)). Higher promoter-wide methylation levels were associated with decreased baseline blood pressure, and when incorporated into a linear mixed effect model significantly predicted lower systolic and diastolic blood pressure evolution over time in response to the experimental manipulation. The underlying genotype significantly predicted methylation levels; particularly, the homozygous BclI minor allele was associated with higher methylation in promoter 1H (p = 0.042). CONCLUSIONS This is one of the first studies linking epigenetic modifications of the GR promoter, receptor genotype and physiological measures of the stress response. At baseline, there were clear genetic and epigenetic effects on blood pressure. The seCPT induced a strong cardiovascular and HPA axis response, and both systems were affected by the functional genetic variants, although methylation also predicted blood pressure reactivity. The return to baseline was predominantly influenced by the genomic sequence. Overall, the physiological response to the seCPT is controlled by an exquisite mix of genetic and epigenetic factors.
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Affiliation(s)
- Ting Li-Tempel
- Department of Neurobehavioral Genetics, Research Institute of Psychobiology, University of Trier, 54290 Trier, Germany
| | - Mauro F Larra
- Department of Clinical Physiology, Research Institute of Psychobiology, University of Trier, 54290 Trier, Germany
| | - Estelle Sandt
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, Esch-sur-Alzette, 4354 Grand-Duchy of Luxembourg
| | - Sophie B Mériaux
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, Esch-sur-Alzette, 4354 Grand-Duchy of Luxembourg
| | - Andrea B Schote
- Department of Neurobehavioral Genetics, Research Institute of Psychobiology, University of Trier, 54290 Trier, Germany
| | - Hartmut Schächinger
- Department of Clinical Physiology, Research Institute of Psychobiology, University of Trier, 54290 Trier, Germany
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, Esch-sur-Alzette, 4354 Grand-Duchy of Luxembourg ; Department of Immunology, Research Institute of Psychobiology, University of Trier, 54290 Trier, Germany
| | - Jonathan D Turner
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, Esch-sur-Alzette, 4354 Grand-Duchy of Luxembourg
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Matsha TE, Pheiffer C, Mutize T, Erasmus RT, Kengne AP. Glucose Tolerance, MTHFR C677T and NOS3 G894T Polymorphisms, and Global DNA Methylation in Mixed Ancestry African Individuals. J Diabetes Res 2016; 2016:8738072. [PMID: 27990443 PMCID: PMC5136398 DOI: 10.1155/2016/8738072] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/21/2016] [Accepted: 08/14/2016] [Indexed: 11/17/2022] Open
Abstract
The aim of this study is to quantify global DNA methylation and investigate the relationship with diabetes status and polymorphisms in MTHFR C677T and NOS3 G894T genes in mixed ancestry subjects from South Africa. Global DNA methylation was measured, and MTHFR rs1801133 and NOS3 rs1799983 polymorphisms were genotyped using high throughput real-time polymerase chain reaction and direct DNA sequencing. Of the 564 participants, 158 (28%) individuals had T2DM of which 97 (17.2%) were screen-detected cases. Another 119 (21.1%) had prediabetes, that is, impaired fasting glucose, impaired glucose tolerance, or the combination of both, and the remainder 287 (50.9%) had normal glucose tolerance. Global DNA methylation was significantly higher in prediabetes and screen-detected diabetes than in normal glucose tolerance (both p ≤ 0.033) and in screen-detected diabetes compared to known diabetes on treatment (p = 0.019). There was no difference in global DNA methylation between known diabetes on treatment and normal glucose tolerance (p > 0.999). In multivariable linear regression analysis, only NOS3 was associated with increasing global DNA methylation (β = 0.943; 95% CI: 0.286 to 1.560). The association of global DNA methylation with screen-detected diabetes but not treated diabetes suggests that glucose control agents to some extent may be reversing DNA methylation. The association between NOS3 rs1799983 polymorphisms and DNA methylation suggests gene-epigenetic mechanisms through which vascular diabetes complications develop despite adequate metabolic control.
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Affiliation(s)
- Tandi E. Matsha
- Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Cape Town, South Africa
- *Tandi E. Matsha: and
| | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa
- *Carmen Pheiffer:
| | - Tinashe Mutize
- Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Rajiv T. Erasmus
- Division of Chemical Pathology, Faculty of Medicine and Health Sciences, National Health Laboratory Service (NHLS) and University of Stellenbosch, Cape Town, South Africa
| | - Andre P. Kengne
- Non-Communicable Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
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123
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Hollar D. Epigenetic Significance of Chromatin Organization During Cellular Aging and Organismal Lifespan. EPIGENETICS, THE ENVIRONMENT, AND CHILDREN’S HEALTH ACROSS LIFESPANS 2016. [PMCID: PMC7153164 DOI: 10.1007/978-3-319-25325-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David Hollar
- Pfeiffer University, Morrisville, North Carolina USA
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Mendoza-Pérez J, Gu J, Herrera LA, Tannir NM, Matin SF, Karam JA, Huang M, Chang DW, Wood CG, Wu X. Genomic DNA Hypomethylation and Risk of Renal Cell Carcinoma: A Case-Control Study. Clin Cancer Res 2015; 22:2074-82. [PMID: 26655847 DOI: 10.1158/1078-0432.ccr-15-0977] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 11/22/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Genomic DNA hypomethylation is a hallmark of most cancer genomes, promoting genomic instability and cell transformation. In the present study, we sought to determine whether global DNA methylation in peripheral blood is associated with risk of renal cell carcinoma (RCC). EXPERIMENTAL DESIGN A retrospective case-control study consisting of 889 RCC cases and an equal number of age, gender, and ethnicity-matched controls was applied. Global DNA methylation was measured as 5-mC% content. Logistic regression was used to estimate odds ratio (OR) and 95% confidence interval (CI) for the association between DNA methylation level and the risk of RCC. RESULTS The median 5-mC% was significantly lower in cases than in healthy controls (P< 0.001). In multivariate logistic regression analysis, individuals in the lowest tertile (T1) of 5-mC% had higher risk of RCC with OR of 1.40 (95% CI, 1.06-1.84), compared with individuals in the highest tertile (T3;Pfor trend= 0.02). When stratified by RCC risk factors, associations between hypomethylation and increased RCC risk appeared to be stronger among males (OR, 1.61;Pfor trend= 0.01), younger age (OR, 1.47;Pfor trend= 0.03), never smokers (OR, 1.55;Pfor trend= 0.02), family history of other cancer (OR, 1.64;Pfor trend= 1.22E-03), and late stage (OR, 2.06,Pfor trend= 4.98E-04). Additionally, we observed significant interaction between gender and 5-mC% in elevating RCC risk (Pfor interaction= 0.03). CONCLUSIONS Our findings suggest an association between global DNA hypomethylation and RCC risk. To establish global DNA hypomethylation as a risk factor for RCC, future prospective studies are warranted. This study may provide further understanding of the etiology of RCC tumorigenesis.
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Affiliation(s)
- Julia Mendoza-Pérez
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Surena F Matin
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jose A Karam
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David W Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher G Wood
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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125
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Abstract
The process of aging results in a host of changes at the cellular and molecular levels, which include senescence, telomere shortening, and changes in gene expression. Epigenetic patterns also change over the lifespan, suggesting that epigenetic changes may constitute an important component of the aging process. The epigenetic mark that has been most highly studied is DNA methylation, the presence of methyl groups at CpG dinucleotides. These dinucleotides are often located near gene promoters and associate with gene expression levels. Early studies indicated that global levels of DNA methylation increase over the first few years of life and then decrease beginning in late adulthood. Recently, with the advent of microarray and next‐generation sequencing technologies, increases in variability of DNA methylation with age have been observed, and a number of site‐specific patterns have been identified. It has also been shown that certain CpG sites are highly associated with age, to the extent that prediction models using a small number of these sites can accurately predict the chronological age of the donor. Together, these observations point to the existence of two phenomena that both contribute to age‐related DNA methylation changes: epigenetic drift and the epigenetic clock. In this review, we focus on healthy human aging throughout the lifetime and discuss the dynamics of DNA methylation as well as how interactions between the genome, environment, and the epigenome influence aging rates. We also discuss the impact of determining ‘epigenetic age’ for human health and outline some important caveats to existing and future studies.
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Affiliation(s)
- Meaghan J. Jones
- Centre for Molecular Medicine and Therapeutics Child and Family Research InstituteUniversity of British Columbia Vancouver BC Canada
- Department of Medical Genetics University of British ColumbiaVancouver BC Canada
| | - Sarah J. Goodman
- Centre for Molecular Medicine and Therapeutics Child and Family Research InstituteUniversity of British Columbia Vancouver BC Canada
- Department of Medical Genetics University of British ColumbiaVancouver BC Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics Child and Family Research InstituteUniversity of British Columbia Vancouver BC Canada
- Department of Medical Genetics University of British ColumbiaVancouver BC Canada
- Human Early Learning Partnership School of Population and Public Health University of British Columbia Vancouver BC Canada
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126
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Yousefi P, Huen K, Davé V, Barcellos L, Eskenazi B, Holland N. Sex differences in DNA methylation assessed by 450 K BeadChip in newborns. BMC Genomics 2015; 16:911. [PMID: 26553366 PMCID: PMC4640166 DOI: 10.1186/s12864-015-2034-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/08/2015] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND DNA methylation is an important epigenetic mark that can potentially link early life exposures to adverse health outcomes later in life. Host factors like sex and age strongly influence biological variation of DNA methylation, but characterization of these relationships is still limited, particularly in young children. METHODS In a sample of 111 Mexican-American subjects (58 girls , 53 boys), we interrogated DNA methylation differences by sex at birth using the 450 K BeadChip in umbilical cord blood specimens, adjusting for cell composition. RESULTS We observed that ~3% of CpG sites were differentially methylated between girls and boys at birth (FDR P < 0.05). Of those CpGs, 3031 were located on autosomes, and 82.8% of those were hypermethylated in girls compared to boys. Beyond individual CpGs, we found 3604 sex-associated differentially methylated regions (DMRs) where the majority (75.8%) had higher methylation in girls. Using pathway analysis, we found that sex-associated autosomal CpGs were significantly enriched for gene ontology terms related to nervous system development and behavior. Among hits in our study, 35.9% had been previously reported as sex-associated CpG sites in other published human studies. Further, for replicated hits, the direction of the association with methylation was highly concordant (98.5-100%) with previous studies. CONCLUSIONS To our knowledge, this is the first reported epigenome-wide analysis by sex at birth that examined DMRs and adjusted for confounding by cell composition. We confirmed previously reported trends that methylation profiles are sex-specific even in autosomal genes, and also identified novel sex-associated CpGs in our methylome-wide analysis immediately after birth, a critical yet relatively unstudied developmental window.
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Affiliation(s)
- Paul Yousefi
- School of Public Health, University of California, 733 University Hall, School of Public Health, UC, Berkeley, CA, 94720-7360, USA
| | - Karen Huen
- School of Public Health, University of California, 733 University Hall, School of Public Health, UC, Berkeley, CA, 94720-7360, USA
| | - Veronica Davé
- School of Public Health, University of California, 733 University Hall, School of Public Health, UC, Berkeley, CA, 94720-7360, USA
| | - Lisa Barcellos
- School of Public Health, University of California, 733 University Hall, School of Public Health, UC, Berkeley, CA, 94720-7360, USA
| | - Brenda Eskenazi
- School of Public Health, University of California, 733 University Hall, School of Public Health, UC, Berkeley, CA, 94720-7360, USA
| | - Nina Holland
- School of Public Health, University of California, 733 University Hall, School of Public Health, UC, Berkeley, CA, 94720-7360, USA.
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127
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Singmann P, Shem-Tov D, Wahl S, Grallert H, Fiorito G, Shin SY, Schramm K, Wolf P, Kunze S, Baran Y, Guarrera S, Vineis P, Krogh V, Panico S, Tumino R, Kretschmer A, Gieger C, Peters A, Prokisch H, Relton CL, Matullo G, Illig T, Waldenberger M, Halperin E. Characterization of whole-genome autosomal differences of DNA methylation between men and women. Epigenetics Chromatin 2015; 8:43. [PMID: 26500701 PMCID: PMC4615866 DOI: 10.1186/s13072-015-0035-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/29/2015] [Indexed: 01/19/2023] Open
Abstract
Background Disease risk and incidence between males and females reveal differences, and sex is an important component of any investigation of the determinants of phenotypes or disease etiology. Further striking differences between men and women are known, for instance, at the metabolic level. The extent to which men and women vary at the level of the epigenome, however, is not well documented. DNA methylation is the best known epigenetic mechanism to date. Results In order to shed light on epigenetic differences, we compared autosomal DNA methylation levels between men and women in blood in a large prospective European cohort of 1799 subjects,
and replicated our findings in three independent European cohorts. We identified and validated 1184 CpG sites to be differentially methylated between men and women and observed that these CpG sites were distributed across all autosomes. We showed that some of the differentially methylated loci also exhibit differential gene expression between men and women. Finally, we found that the differentially methylated loci are enriched among imprinted genes, and that their genomic location in the genome is concentrated in CpG island shores. Conclusion Our epigenome-wide association study indicates that differences between men and women are so substantial that they should be considered in design and analyses of future studies. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0035-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paula Singmann
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Doron Shem-Tov
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Giovanni Fiorito
- Human Genetics Foundation-Torino, Turin, Italy ; Department of Medical Sciences, University of Torino, Turin, Italy
| | - So-Youn Shin
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK ; Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Katharina Schramm
- Institute of Human Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Petra Wolf
- Institute of Human Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Yael Baran
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Simonetta Guarrera
- Human Genetics Foundation-Torino, Turin, Italy ; Department of Medical Sciences, University of Torino, Turin, Italy
| | - Paolo Vineis
- Human Genetics Foundation-Torino, Turin, Italy ; Epidemiology and Public Health, Imperial College London, London, UK
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCSS Istituto Nazionale Tumori, Milan, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | - Rosario Tumino
- Cancer Registry and Histopathology Unit, "Civile-M.P. Arezzo" Hospital, ASP 7, Ragusa, Italy
| | - Anja Kretschmer
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK ; Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Giuseppe Matullo
- Human Genetics Foundation-Torino, Turin, Italy ; Department of Medical Sciences, University of Torino, Turin, Italy
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Hannover Unified Biobank, Hannover Medical School, Hannover, Germany ; Institute for Human Genetics, Hannover Medical School, Hannover, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Eran Halperin
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel ; Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Science, Tel-Aviv University, Tel-Aviv, Israel ; International Computer Science Institute, Berkeley, CA USA
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128
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Sarabi MM, Naghibalhossaini F. Association of DNA methyltransferases expression with global and gene-specific DNA methylation in colorectal cancer cells. Cell Biochem Funct 2015; 33:427-33. [PMID: 26416384 DOI: 10.1002/cbf.3126] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 12/14/2022]
Abstract
There are conflicting reports regarding the association between DNA methyltransferases (DNMTs) expression and global or gene-specific DNA methylation in colorectal cancer (CRC) cells. To correlate DNMTs expression with DNA methylation, we quantified DNMT1, DNMT3A and DNMT3B mRNA levels in five CRC cell lines (HCT116, LS180, HT29/219, Caco2 and SW742) by real-time reverse-transcriptase polymerase chain reaction (PCR) assay. In addition, we examined the global 5-methyl cytosine levels and the methylation patterns of 12 CpG islands in these CRC cells by enzyme-linked immunosorbent assay and methylation-specific PCR methods, respectively. The average expression levels of three DNMTs in HCT116, Caco2, HT29/219 and SW742, relative to the expression level in LS180 (taken to be 1), were 90.1, 31.6, 2.66 and 1.86. Our data indicated that overall about 1.45%, 1.03%, 0.98%, 0.86% and 0.85% of the cytosines were methylated in the genome of HCT116, Caco2, HT29/219, SW742 and LS180 cells, respectively. The 5-mC percentages were positively correlated with the relative cellular DNMTs expression in five CRC cell lines as verified by Pearson correlation test. However, we found no positive correlation between mRNA expression of DNMTs and gene promoter hypermethylation in these cells. Our results suggest that cellular DNMT expression is positively correlated with global DNA methylation level but not with regional DNA hypermethylation at each locus.
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Affiliation(s)
- Mostafa Moradi Sarabi
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fakhraddin Naghibalhossaini
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Autoimmune Diseases Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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129
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Abstract
Constitutional epimutation, which is an aberration in gene expression due to an altered epigenotype that is widely distributed in normal tissues (albeit frequently mosaic), provides an alternative mechanism to genetic mutation for cancer predisposition. Observational studies in cancer-affected families have revealed intergenerational inheritance of constitutional epimutation, providing unique insights into the heritability of epigenetic traits in humans. In this Opinion article, the potential contribution of constitutional epimutation to the 'missing' causality and heritability of cancer is explored.
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Affiliation(s)
- Megan P Hitchins
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Grant Building S169, 1291 Welch Road, Stanford, California 94305, USA
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130
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Januar V, Desoye G, Novakovic B, Cvitic S, Saffery R. Epigenetic regulation of human placental function and pregnancy outcome: considerations for causal inference. Am J Obstet Gynecol 2015; 213:S182-96. [PMID: 26428498 DOI: 10.1016/j.ajog.2015.07.011] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/03/2015] [Accepted: 07/13/2015] [Indexed: 12/14/2022]
Abstract
Epigenetic mechanisms, often defined as regulating gene activity independently of underlying DNA sequence, are crucial for healthy development. The sum total of epigenetic marks within a cell or tissue (the epigenome) is sensitive to environmental influence, and disruption of the epigenome in utero has been associated with adverse pregnancy outcomes. Not surprisingly, given its multifaceted functions and important role in regulating pregnancy outcome, the placenta shows unique epigenetic features. Interestingly however, many of these are only otherwise seen in human malignancy (the pseudomalignant placental epigenome). Epigenetic variation in the placenta is now emerging as a candidate mediator of environmental influence on placental functioning and a key regulator of pregnancy outcome. However, replication of findings is generally lacking, most likely due to small sample sizes and a lack of standardization of analytical approaches. Defining DNA methylation "signatures" in the placenta associated with maternal and fetal outcomes offers tremendous potential to improve pregnancy outcomes, but care must be taken in interpretation of findings. Future placental epigenetic research would do well to address the issues present in epigenetic epidemiology more generally, including careful consideration of sample size, potentially confounding factors, issues of tissue heterogeneity, reverse causation, and the role of genetics in modulating epigenetic profile. The importance of animal or in vitro models in establishing a functional role of epigenetic variation identified in human beings, which is key to establishing causation, should not be underestimated.
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Affiliation(s)
- Vania Januar
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Gernot Desoye
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Boris Novakovic
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Silvija Cvitic
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Richard Saffery
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Department of Pediatrics, University of Melbourne, Parkville, Australia.
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131
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Herrera CL, Kim DY, Kumar SR, Bryan JN. Peroxisome proliferator activated receptor γ protein expression is asymmetrically distributed in primary lung tumor and metastatic to lung osteosarcoma samples and does not correlate with gene methylation. BMC Vet Res 2015; 11:230. [PMID: 26334880 PMCID: PMC4559327 DOI: 10.1186/s12917-015-0547-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/21/2015] [Indexed: 12/02/2022] Open
Abstract
Background Peroxisome proliferator activated receptor-γ (PPAR-γ) is a ligand-dependent transcription factor that plays important roles in cellular proliferation and differentiation. It has been implicated as a tumor suppressor in many solid tumors including human prostate, breast, colon, and lung cancer. The objective of this study was to determine the tissue distribution of PPAR-γ in normal canine lung, canine lung cancer, and metastatic to lung cancer, as well as determine the role, if any, of DNA methylation in epigenetic control of gene expression. The protein was studied using immunohistochemistry (IHC) and DNA methylation was studied using combined bisulfite restriction analysis (COBRA), and methylation-specific PCR (MSP). Results PPAR-γ is expressed in all large conducting airways, particularly in goblet cells and bronchial glands, in the canine lung. The protein is also expressed in interstitial macrophages. PPAR-γ is expressed in 33 % of canine non-small cell lung cancer (NSCLC) cases and 66 % of metastatic osteosarcoma (OSA) cases. There is a significant loss of 5′ PPAR-γ methylation from normal lung to primary lung cancer and metastatic OSA (p = 0.0002), however altered PPAR-γ promoter methylation at the interrogated locus does not appear to be associated with changes in protein expression. Conclusions PPAR-γ protein is expressed in normal canine lung tissue, canine primary lung cancer, and metastatic OSA. Confirmation of PPAR-γ protein expression in tumor-bearing dogs supports the investigation of PPAR-γ agonists in this subset of veterinary patients. These results are the first to describe epigenetic marks and protein localization of PPAR-γ among different lung pathologies in the dog.
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Affiliation(s)
- Chamisa L Herrera
- Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA. .,Current Address: BluePearl Seattle, 11536 Lake City Way NE, Seattle, WA 98125, USA.
| | - Dae Young Kim
- Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA.
| | - Senthil R Kumar
- Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA.
| | - Jeffrey N Bryan
- Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA.
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132
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Hartley JD, Ferguson BJ, Moffett A. The role of shed placental DNA in the systemic inflammatory syndrome of preeclampsia. Am J Obstet Gynecol 2015; 213:268-77. [PMID: 25794631 DOI: 10.1016/j.ajog.2015.03.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/02/2015] [Accepted: 03/12/2015] [Indexed: 10/23/2022]
Abstract
Preeclampsia is a syndrome occurring only in pregnancy characterized by systemic maternal inflammation and associated with the presence of the placenta. How these 2 aspects of the disease are linked has been the subject of numerous theories and ideas. Recently, there has been increasing interest in DNA shed from the placenta into the maternal circulation as a potential agent initiating the inflammatory response. This review will discuss the current evidence and future directions for placental DNA as the linking factor in preeclampsia in the context of other hypotheses.
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133
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Bekaert B, Kamalandua A, Zapico SC, Van de Voorde W, Decorte R. Improved age determination of blood and teeth samples using a selected set of DNA methylation markers. Epigenetics 2015; 10:922-30. [PMID: 26280308 DOI: 10.1080/15592294.2015.1080413] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Age estimation from DNA methylation markers has seen an exponential growth of interest, not in the least from forensic scientists. The current published assays, however, can still be improved by lowering the number of markers in the assay and by providing more accurate models to predict chronological age. From the published literature we selected 4 age-associated genes (ASPA, PDE4C, ELOVL2, and EDARADD) and determined CpG methylation levels from 206 blood samples of both deceased and living individuals (age range: 0-91 years). This data was subsequently used to compare prediction accuracy with both linear and non-linear regression models. A quadratic regression model in which the methylation levels of ELOVL2 were squared showed the highest accuracy with a Mean Absolute Deviation (MAD) between chronological age and predicted age of 3.75 years and an adjusted R(2) of 0.95. No difference in accuracy was observed for samples obtained either from living and deceased individuals or between the 2 genders. In addition, 29 teeth from different individuals (age range: 19-70 years) were analyzed using the same set of markers resulting in a MAD of 4.86 years and an adjusted R(2) of 0.74. Cross validation of the results obtained from blood samples demonstrated the robustness and reproducibility of the assay. In conclusion, the set of 4 CpG DNA methylation markers is capable of producing highly accurate age predictions for blood samples from deceased and living individuals.
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Affiliation(s)
- Bram Bekaert
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium.,b KU-Leuven - University of Leuven; University Hospitals Leuven; Department of Forensic Medicine; Laboratory of Forensic Genetics and Molecular Archeology ; Leuven , Belgium
| | - Aubeline Kamalandua
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium
| | - Sara C Zapico
- c Smithsonian Institution; NMNH; MRC112 ; Anthropology Department ; Washington, DC USA
| | - Wim Van de Voorde
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium.,b KU-Leuven - University of Leuven; University Hospitals Leuven; Department of Forensic Medicine; Laboratory of Forensic Genetics and Molecular Archeology ; Leuven , Belgium
| | - Ronny Decorte
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium.,b KU-Leuven - University of Leuven; University Hospitals Leuven; Department of Forensic Medicine; Laboratory of Forensic Genetics and Molecular Archeology ; Leuven , Belgium
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Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas. PLoS Genet 2015; 11:e1005442. [PMID: 26241857 PMCID: PMC4524645 DOI: 10.1371/journal.pgen.1005442] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/14/2015] [Indexed: 12/11/2022] Open
Abstract
Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylated domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. Higher relative gene body methylation was the conserved feature across all mammalian placentas, despite differences in PMD/HMDs and absolute methylation levels. Specifically, higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification was observed compared with the rest of the genome. As in human placenta, higher methylation is associated with higher gene expression and is predictive of genic location across species. Analysis of DNA methylation in oocytes and preimplantation embryos shows a conserved pattern of gene body methylation similar to the placenta. Intriguingly, mouse and cow oocytes and mouse early embryos have PMD/HMDs but their placentas do not, suggesting that PMD/HMDs are a feature of early preimplantation methylation patterns that become lost during placental development in some species and following implantation of the embryo.
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135
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Cho YH, Woo HD, Jang Y, Porter V, Christensen S, Hamilton RF, Chung HW. The Association of LINE-1 Hypomethylation with Age and Centromere Positive Micronuclei in Human Lymphocytes. PLoS One 2015. [PMID: 26196382 PMCID: PMC4510364 DOI: 10.1371/journal.pone.0133909] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Global hypomethylation in white blood cell (WBC) DNA has recently been proposed as a potential biomarker for determining cancer risk through genomic instability. However, the amplitude of the changes associated with age and the impacts of environmental factors on DNA methylation are unclear. In this study, we investigated the association of genomic hypomethylation with age, cigarette use, drinking status and the presence of centromere positive micronuclei (MNC+)-a biomarker for age-dependent genomic instability. Genomic hypomethylation of the repetitive element LINE-1 was measured in WBC DNA from 32 healthy male volunteers using the pyrosequencing assay. We also measured MNC+ with the micronucleus-centromere assay using a pan-centromeric probe. Possibly due to the small sample size and resulting low statistical power, smoking and drinking status had no significant effect on LINE-1 hypomethylation or the occurrence of MNC+. Consequently, we did not include them in further analyses. In contrast, LINE-1 hypomethylation and age significantly predicted MNC+; therefore, we examined whether LINE-1 hypomethylation plays a role in MNC+ formation by age, since genomic hypomethylation is associated with genomic instability. However, LINE-1 hypomethylation did not significantly mediate the effect of age on MNC+. Our data indicate that the repetitive element LINE-1 is demethylated with age and increasing MNC+ frequency, but additional studies are needed to fully understand the relation between genomic DNA hypomethylation, age and genomic instability.
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Affiliation(s)
- Yoon Hee Cho
- Center for Environmental Health Sciences, Department of Biomedical & Pharmaceutical Sciences, The University of Montana, Missoula, Montana, United States of America
- * E-mail:
| | - Hae Dong Woo
- Molecular Epidemiology Branch, Division of Cancer Epidemiology and Prevention, Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do, Korea
| | - Yoonhee Jang
- Department of Psychology, The University of Montana, Missoula, Montana, United States of America
| | - Virginia Porter
- Center for Environmental Health Sciences, Department of Biomedical & Pharmaceutical Sciences, The University of Montana, Missoula, Montana, United States of America
| | - Sonja Christensen
- Center for Environmental Health Sciences, Department of Biomedical & Pharmaceutical Sciences, The University of Montana, Missoula, Montana, United States of America
| | - Raymond F. Hamilton
- Center for Environmental Health Sciences, Department of Biomedical & Pharmaceutical Sciences, The University of Montana, Missoula, Montana, United States of America
| | - Hai Won Chung
- Department of Molecular Epidemiology, School of Public Health, Seoul National University, Gwanak-gu, Seoul, Korea
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Lévesque ML, Casey KF, Szyf M, Ismaylova E, Ly V, Verner MP, Suderman M, Brendgen M, Vitaro F, Dionne G, Boivin M, Tremblay RE, Booij L. Genome-wide DNA methylation variability in adolescent monozygotic twins followed since birth. Epigenetics 2015; 9:1410-21. [PMID: 25437055 DOI: 10.4161/15592294.2014.970060] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA methylation patterns are characterized by highly conserved developmental programs, but allow for divergent gene expression resulting from stochastic epigenetic drift or divergent environments. Genome-wide methylation studies in monozygotic (MZ) twins are providing insight into the extent of epigenetic variation that occurs, irrespective of genotype. However, little is known about the variability of DNA methylation patterns in adolescence, a period involving significant and rapid physical, emotional, social, and neurodevelopmental change. Here, we assessed genome-wide DNA methylation using the 450 K Illumina BeadChip in a sample of 37 MZ twin pairs followed longitudinally since birth to investigate: 1) the extent of variation in DNA methylation in identical genetic backgrounds in adolescence and; 2) whether these variations are randomly distributed or enriched in particular functional pathways. We also assessed stability of DNA methylation over 3-6 months to distinguish stable trait-like and variable state-like genes. A pathway analysis found high within-pair variability in genes associated with development, cellular mechanisms, tissue and cell morphology, and various disorders. Test-retest analyses performed in a sub-sample of 8 twin pairs demonstrated enrichment in gene pathways involved in organismal development, cellular growth and proliferation, cell signaling, and particular disorders. The variability found in functional gene pathways may plausibly underlie phenotypic differences in this adolescent MZ twin sample. Furthermore, we assessed stability of methylation over 3-6 months and found that some genes were stable while others were unstable, suggesting that the methylome remains dynamic in adolescence and that dynamic sites tend to be organized in certain gene pathways.
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137
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Cappetta M, Berdasco M, Hochmann J, Bonilla C, Sans M, Hidalgo PC, Artagaveytia N, Kittles R, Martínez M, Esteller M, Bertoni B. Effect of genetic ancestry on leukocyte global DNA methylation in cancer patients. BMC Cancer 2015; 15:434. [PMID: 26012346 PMCID: PMC4445803 DOI: 10.1186/s12885-015-1461-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 05/21/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The study of genetic variants alone is not enough to explain a complex disease like cancer. Alterations in DNA methylation patterns have been associated with different types of tumor. In order to detect markers of susceptibility for the development of cutaneous melanoma and breast cancer in the Uruguayan population, we integrated genetic and epigenetic information of patients and controls. METHODS We performed two case-control studies that included 49 individuals with sporadic cutaneous melanoma and 73 unaffected controls, and 179 women with sporadic breast cancer and 209 women controls. We determined the level of global leukocyte DNA methylation using relative quantification of 5mdC by HPLC, and we compared methylation levels between cases and controls with nonparametric statistical tests. Since the Uruguayan population is admixed and both melanoma and breast cancer have very high incidences in Uruguay compared to other populations, we examined whether individual ancestry influences global leucocyte DNA methylation status. We carried out a correlation analysis between the percentage of African, European and Native American individual ancestries, determined using 59 ancestry informative markers, and global DNA methylation in all participants. RESULTS We detected global DNA hypomethylation in leukocytes of melanoma and breast cancer patients compared with healthy controls (p < 0.001). Additionally, we found a negative correlation between African ancestry and global DNA methylation in cancer patients (p <0.005). CONCLUSIONS These results support the potential use of global DNA methylation as a biomarker for cancer risk. In addition, our findings suggest that the ancestral genome structure generated by the admixture process influences DNA methylation patterns, and underscore the importance of considering genetic ancestry as a modifying factor in epigenetic association studies in admixed populations such as Latino ones.
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Affiliation(s)
- Mónica Cappetta
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
| | - María Berdasco
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de LLobregat, Barcelona, Catalonia, Spain.
| | - Jimena Hochmann
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
| | - Carolina Bonilla
- School of Social and Community Medicine, University of Bristol, Bristol, UK.
| | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay.
| | - Pedro C Hidalgo
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay.
- Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay.
| | - Nora Artagaveytia
- Departamento Básico de Medicina, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
| | - Rick Kittles
- Department of Surgery and Public Health, University of Arizona, Tucson, USA.
| | - Miguel Martínez
- Cátedra de Dermatología, Hospital de Clínicas "Manuel Quintela", Universidad de la República, Montevideo, Uruguay.
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de LLobregat, Barcelona, Catalonia, Spain.
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain.
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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138
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Nahar MS, Liao C, Kannan K, Harris C, Dolinoy DC. In utero bisphenol A concentration, metabolism, and global DNA methylation across matched placenta, kidney, and liver in the human fetus. CHEMOSPHERE 2015; 124:54-60. [PMID: 25434263 PMCID: PMC4297568 DOI: 10.1016/j.chemosphere.2014.10.071] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 10/28/2014] [Accepted: 10/31/2014] [Indexed: 05/18/2023]
Abstract
While urine has been an easily accessible and feasible matrix for human biomonitoring, analytical measurements in internal tissues and organs can provide more accurate exposure assessments to understand disease etiology. This is especially important for the endocrine active compound, bisphenol A (BPA), where studies investigating internal doses at sensitive periods of human development are currently lacking. Herein, BPA concentrations, BPA-specific metabolizing enzyme gene expression, and global DNA methylation were characterized across three matched tissues from elective pregnancy terminations of 2nd trimester human fetuses: the placenta, liver, and kidney (N=12 each; N=36 total). Compared to liver (free: 0.54-50.5 ng g(-1)), BPA concentrations were lower in matched placenta (<0.05-25.4 ng g(-1)) and kidney (0.08-11.1 ng g(-1)) specimens. BPA-specific metabolism gene expression of GUSB, UGT2B15, STS, and SULT1A1 differed across each tissue type; however, conjugation and deconjugation expression patterns were similar across the fetus. Average LINE1 and CCGG global methylation were 58.3% and 59.2% in placenta, 79.5% and 66.4% in fetal liver, and 77.9% and 77.0% in fetal kidney, with significant tissue-specific DNA methylation differences in both LINE1 (p-value<0.001) and CCGG content (p-value<0.001). Total BPA concentrations were positively associated with global methylation for the placenta only using the LINE1 assay (p-value: 0.002), suggesting organ-specific biological effects after fetal exposure. Utilizing sensitive human clinical specimens, results are informative for BPA toxicokinetics and toxicodynamics assessment in the developing human fetus.
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Affiliation(s)
- Muna S Nahar
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Chunyang Liao
- Wadsworth Center, New York State Department of Health, Department of Environmental Health Sciences, State University of New York at Albany, Albany, NY, USA
| | - Kurunthachalam Kannan
- Wadsworth Center, New York State Department of Health, Department of Environmental Health Sciences, State University of New York at Albany, Albany, NY, USA; Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Craig Harris
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA.
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139
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Sidler C, Woycicki R, Kovalchuk I, Kovalchuk O. WI-38 senescence is associated with global and site-specific hypomethylation. Aging (Albany NY) 2015; 6:564-74. [PMID: 25063771 PMCID: PMC4153623 DOI: 10.18632/aging.100679] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Cellular senescence plays an important role in the age-dependent functional decline of organs and organ systems, as well as in age-related pathologies, such as cancer. Therefore, a better understanding of its underlying molecular mechanisms is crucial in the search for intervening measures. In this study, we considered the role of DNA methylation in senescence. We found that senescence is associated with global DNA hypomethylation, but also involves site-specific DNA hypo- and hypermethylation. In some cases, this differential methylation may affect gene expression and thereby modulate functional processes within cells. However, the majority of the CpG sites that were differentially methylated did not correspond with altered gene expression, suggesting that DNA methylation affects senescence by other means also, such as, for instance, genome stability.
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Affiliation(s)
- Corinne Sidler
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Rafal Woycicki
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
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140
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Masemola ML, van der Merwe L, Lombard Z, Viljoen D, Ramsay M. Reduced DNA methylation at the PEG3 DMR and KvDMR1 loci in children exposed to alcohol in utero: a South African Fetal Alcohol Syndrome cohort study. Front Genet 2015; 6:85. [PMID: 25806045 PMCID: PMC4354390 DOI: 10.3389/fgene.2015.00085] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 02/17/2015] [Indexed: 11/22/2022] Open
Abstract
Fetal alcohol syndrome (FAS) is a devastating developmental disorder resulting from alcohol exposure during fetal development. It is a considerable public health problem worldwide and is characterized by central nervous system abnormalities, dysmorphic facial features, and growth retardation. Imprinted genes are known to play an important role in growth and development and therefore four imprinting control regions (ICRs), H19 ICR, IG-DMR, KvDMR1 and PEG3 DMR were examined. It is proposed that DNA methylation changes may contribute to developmental abnormalities seen in FAS and which persist into adulthood. The participants included FAS children and controls from the Western and Northern Cape Provinces. DNA samples extracted from blood and buccal cells were bisulfite modified, the ICRs were amplified by PCR and pyrosequencing was used to derive a quantitative estimate of methylation at selected CpG dinucleotides: H19 ICR (six CpG sites; 50 controls and 73 cases); KvDMR1 (7, 55, and 86); IG-DMR (10, 56, and 84); and PEG3 DMR (7, 50, and 79). The most profound effects of alcohol exposure are on neuronal development. In this study we report on epigenetic effects observed in blood which may not directly reflect tissue-specific alterations in the developing brain. After adjusting for age and sex (known confounders for DNA methylation), there was a significant difference at KvDMR1 and PEG3 DMR, but not the H19 ICR, with only a small effect (0.84% lower in cases; p = 0.035) at IG-DMR. The two maternally imprinted loci, KvDMR1 and PEG3 DMR, showed lower average locus-wide methylation in the FAS cases (1.49%; p < 0.001 and 7.09%; p < 0.001, respectively). The largest effect was at the PEG3 DMR though the functional impact is uncertain. This study supports the role of epigenetic modulation as a mechanism for the teratogenic effects of alcohol by altering the methylation profiles of imprinted loci in a locus-specific manner.
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Affiliation(s)
- Matshane L Masemola
- Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa
| | - Lize van der Merwe
- Department of Statistics, Faculty of Natural Sciences, University of the Western Cape , Cape Town, South Africa ; Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa ; Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand , Johannesburg, South Africa ; School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand , Johannesburg, South Africa
| | - Denis Viljoen
- Foundation for Alcohol Related Research , Cape Town, South Africa
| | - Michèle Ramsay
- Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa ; Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand , Johannesburg, South Africa
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141
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Abstract
This review provides an overview of the unique features of DNA methylation in the human placenta. We discuss the importance of understanding placental development, structure, and function in the interpretation of DNA methylation data. Examples are given of how DNA methylation is important in regulating placental-specific gene expression, including monoallelic expression and X-chromosome inactivation in the placenta. We also discuss studies of global DNA methylation changes in the context of placental pathology and environmental exposures.
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Affiliation(s)
- Wendy P Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - E Magda Price
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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142
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Transcriptional activity of human endogenous retroviruses in human peripheral blood mononuclear cells. BIOMED RESEARCH INTERNATIONAL 2015; 2015:164529. [PMID: 25734056 PMCID: PMC4334862 DOI: 10.1155/2015/164529] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/30/2014] [Accepted: 01/10/2015] [Indexed: 01/09/2023]
Abstract
Human endogenous retroviruses (HERVs) have been implicated in human physiology and in human pathology. A better knowledge of the retroviral transcriptional activity in the general population and during the life span would greatly help the debate on its pathologic potential. The transcriptional activity of four HERV families (H, K, W, and E) was assessed, by qualitative and quantitative PCR, in PBMCs from 261 individuals aged from 1 to 80 years. Our results show that HERV-H, HERV-K, and HERV-W, but not HERV-E, are transcriptionally active in the test population already in the early childhood. In addition, the transcriptional levels of HERV-H, HERV-K, and HERV-W change significantly during the life span, albeit with distinct patterns. Our results, reinforce the hypothesis of a physiological correlation between HERVs activity and the different stages of life in humans. Studies aiming at identifying the factors, which are responsible for these changes during the individual's life, are still needed. Although the observed phenomena are presumably subjected to great variability, the basal transcriptional activity of each individual, also depending on the different ages of life, must be carefully considered in all the studies involving HERVs as causative agents of disease.
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143
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McCarthy NS, Melton PE, Cadby G, Yazar S, Franchina M, Moses EK, Mackey DA, Hewitt AW. Meta-analysis of human methylation data for evidence of sex-specific autosomal patterns. BMC Genomics 2014; 15:981. [PMID: 25406947 PMCID: PMC4255932 DOI: 10.1186/1471-2164-15-981] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 10/08/2014] [Indexed: 11/21/2022] Open
Abstract
Background Several individual studies have suggested that autosomal CpG methylation differs by sex both in terms of individual CpG sites and global autosomal CpG methylation. However, these findings have been inconsistent and plagued by spurious associations due to the cross reactivity of CpG probes on commercial microarrays. We collectively analysed 76 published studies (n = 6,795) for sex-associated differences in both autosomal and sex chromosome CpG sites. Results Overall autosomal methylation profiles varied substantially by study, and we encountered substantial batch effects. We accounted for these by conducting random effects meta-analysis for individual autosomal CpG methylation associations. After excluding non-specific probes, we found 184 autosomal CpG sites differentially methylated by sex after correction for multiple testing. In line with previous studies, average beta differences were small. Many of the most significantly associated CpG probes were new. Of note was differential CpG methylation in the promoters of genes thought to be involved in spermatogenesis and male fertility, such as SLC9A2, SPESP1, CRISP2, and NUPL1. Pathway analysis revealed overrepresentation of genes differentially methylated by sex in several broad Gene Ontology biological processes, including RNA splicing and DNA repair. Conclusions This study represents a comprehensive analysis of sex-specific methylation patterns. We demonstrate the existence of sex-specific methylation profiles and report a large number of novel DNA methylation differences in autosomal CpG sites between sexes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-981) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nina S McCarthy
- Centre for the Genetic Origins of Health and Disease (GOHaD), University of Western Australia, Perth, Australia.
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144
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Age-related DNA methylation changes for forensic age-prediction. Int J Legal Med 2014; 129:237-44. [PMID: 25399049 DOI: 10.1007/s00414-014-1100-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/29/2014] [Indexed: 10/24/2022]
Abstract
There is no available method of age-prediction for biological samples. The accumulating evidences indicate that DNA methylation patterns change with age. Aging resembles a developmentally regulated process that is tightly controlled by specific epigenetic modifications and age-associated methylation changes exist in human genome. In this study, three age-related methylation fragments were isolated and identified in blood of 40 donors. Age-related methylation changes with each fragment was validated and replicated in a general population sample of 65 donors over a wide age range (11-72 years). Methylation of these fragments is linearly correlated with age over a range of six decades (r = 0.80-0.88). Using average methylation of CpG sites of three fragments, a regression model that explained 95 % of the variance in age was built and is able to predict an individual's age with great accuracy (R (2 )= 0.93). The predicted value is highly correlated with the observed age in the sample (r = 0.96) and has great accuracy of average 4 years difference between predicted age and true age. This study implicates that DNA methylation can be an available biological marker of age-prediction. Further measurement of relevant markers in the genome could be a tool in routine screening to predict age of forensic biological samples.
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145
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Stenz L, Zewdie S, Laforge-Escarra T, Prados J, La Harpe R, Dayer A, Paoloni-Giacobino A, Perroud N, Aubry JM. BDNF promoter I methylation correlates between post-mortem human peripheral and brain tissues. Neurosci Res 2014; 91:1-7. [PMID: 25450314 DOI: 10.1016/j.neures.2014.10.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/25/2014] [Accepted: 10/06/2014] [Indexed: 10/25/2022]
Abstract
Several psychiatric disorders have been associated with CpG methylation changes in CG rich promoters of the brain-derived neurotrophic factor (BDNF) mainly by extracting DNA from peripheral blood cells. Whether changes in peripheral DNA methylation can be used as a proxy for brain-specific alterations remains an open question. In this study we aimed to compare DNA methylation levels in BDNF promoter regions in human blood cells, muscle and brain regions using bisulfite-pyrosequencing. We found a significant correlation between the levels of BDNF promoter I methylation measured in quadriceps and vPFC tissues extracted from the same individuals (n = 98, Pearson, r = 0.48, p = 4.5 × 10(-7)). In the hippocampus, BDNF promoter I and IV methylation levels were strongly correlated (Pearson, n = 37, r = 0.74, p = 1.4 × 10(-7)). We found evidence for sex-dependent effect on BDNF promoter methylation levels in the various tissues and blood samples. Taken together, these data indicate a strong intra-individual correlation between peripheral and brain tissue. They also suggest that sex determines methylation patterns in BDNF promoter region across different types of tissue, including muscle, brain, and blood.
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Affiliation(s)
- Ludwig Stenz
- Department of Psychiatry, University of Geneva, Switzerland; Department of Basic Neurosciences, University of Geneva Medical School, Geneva, Switzerland.
| | - Seblewongel Zewdie
- Department of Psychiatry, University of Geneva, Switzerland; Department of Basic Neurosciences, University of Geneva Medical School, Geneva, Switzerland
| | - Térèse Laforge-Escarra
- Department of Genetic and Laboratory Medicine, Geneva University Hospital, 1211 Geneva 14, Switzerland
| | - Julien Prados
- Department of Psychiatry, University of Geneva, Switzerland; Department of Basic Neurosciences, University of Geneva Medical School, Geneva, Switzerland
| | - Romano La Harpe
- Institute of Forensic Medicine, University of Geneva, Switzerland
| | - Alexandre Dayer
- Department of Mental Health and Psychiatry, University Hospital of Geneva, Geneva, Switzerland; Department of Basic Neurosciences, University of Geneva Medical School, Geneva, Switzerland
| | - Ariane Paoloni-Giacobino
- Department of Genetic and Laboratory Medicine, Geneva University Hospital, 1211 Geneva 14, Switzerland
| | - Nader Perroud
- Department of Psychiatry, University of Geneva, Switzerland; Department of Mental Health and Psychiatry, University Hospital of Geneva, Geneva, Switzerland
| | - Jean-Michel Aubry
- Department of Psychiatry, University of Geneva, Switzerland; Department of Mental Health and Psychiatry, University Hospital of Geneva, Geneva, Switzerland
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146
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Ausió J, Paz AMD, Esteller M. MeCP2: the long trip from a chromatin protein to neurological disorders. Trends Mol Med 2014; 20:487-98. [DOI: 10.1016/j.molmed.2014.03.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/12/2014] [Accepted: 03/14/2014] [Indexed: 12/13/2022]
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147
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Dynamic Alu methylation during normal development, aging, and tumorigenesis. BIOMED RESEARCH INTERNATIONAL 2014; 2014:784706. [PMID: 25243180 PMCID: PMC4163490 DOI: 10.1155/2014/784706] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/16/2014] [Indexed: 12/15/2022]
Abstract
DNA methylation primarily occurs on CpG dinucleotides and plays an important role in transcriptional regulations during tissue development and cell differentiation. Over 25% of CpG dinucleotides in the human genome reside within Alu elements, the most abundant human repeats. The methylation of Alu elements is an important mechanism to suppress Alu transcription and subsequent retrotransposition. Decades of studies revealed that Alu methylation is highly dynamic during early development and aging. Recently, many environmental factors were shown to have a great impact on Alu methylation. In addition, aberrant Alu methylation has been documented to be an early event in many tumors and Alu methylation levels have been associated with tumor aggressiveness. The assessment of the Alu methylation has become an important approach for early diagnosis and/or prognosis of cancer. This review focuses on the dynamic Alu methylation during development, aging, and tumor genesis. The cause and consequence of Alu methylation changes will be discussed.
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148
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Iglesias T, Espina M, Montes-Bayón M, Sierra LM, Blanco-González E. Anion exchange chromatography for the determination of 5-methyl-2'-deoxycytidine: application to cisplatin-sensitive and cisplatin-resistant ovarian cancer cell lines. Anal Bioanal Chem 2014; 407:2423-31. [PMID: 25142048 DOI: 10.1007/s00216-014-8070-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/22/2014] [Accepted: 07/25/2014] [Indexed: 12/30/2022]
Abstract
Epigenetic alterations are increasingly implicated in the initiation and progression of cancer. Genome-wide (global) hypomethylation seems to occur in early neoplasia and is a feature of genomic DNA derived from solid tumour tissues like ovarian cancer. Thus, analytical methods that provide sensitive and quantitative information about cytosine methylation in DNA are currently required. In this work, we compare two different anion-exchange columns for the separation of methylated cytosine from the other DNA nucleotides: a silica-based (Tracer Extrasil SAX) column and a polystyrene/divinyl benzene-based (Mono-Q™) column. Under the optimised conditions, linearity range, precision and detection limits of the developed high-performance liquid chromatography (HPLC) method were evaluated and compared using conventional ultraviolet (UV) absorbance detection at 270 nm. Good separation of the five target nucleotides, including 5-methyl-2'-deoxycytidine monophosphate (5mdCMP) and 2'-deoxycytidine monophosphate (dCMP) was achieved on the Mono-Q™ column with a gradient elution of ammonium acetate buffer (1 M, pH 6.9) at a flow rate of 1 mL min(-1). The coupling of this column to inductively coupled plasma mass spectrometry (ICP-MS) permitted also phosphorous ((31)P) specific detection of the nucleotides. Both detection systems offered adequate analytical performance characteristics, with detection limits of 30 and 40 μg L(-1) for 5mdCMP by HPLC-UV and HPLC-ICP-MS, respectively. However, the latter method allowed the determination of the global DNA methylation level (%) without the need for external calibration. Different genomic DNA samples were analysed including calf thymus DNA and DNA from two human cancer cell lines (adenocarcinoma epithelial A549 and ovarian carcinoma A2780) using the proposed strategy. In the line A2780, the cisplatin-sensitive and cisplatin-resistant variants were analysed, finding no significant differences in the methylation percentage after treatment with cisplatin.
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Affiliation(s)
- Tamara Iglesias
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, C/ Julián Clavería 8, 33006, Oviedo, Spain
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149
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Epigenetics of hematopoietic stem cell aging and disease. Int J Hematol 2014; 100:326-34. [DOI: 10.1007/s12185-014-1647-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 02/07/2023]
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150
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Epigenetically modified nucleotides in chronic heroin and cocaine treated mice. Toxicol Lett 2014; 229:451-7. [PMID: 25064621 DOI: 10.1016/j.toxlet.2014.07.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 12/19/2022]
Abstract
Epigenetic changes include the addition of a methyl group to the 5' carbon of the cytosine ring, known as DNA methylation, which results in the generation of the fifth DNA base, namely 5-methylcytosine. During active or passive demethylation, an intermediate modified base is formed, 5-hydroxymethylcytosine. We have currently quantified 5-methylcytosine and 5-hydroxymethylcytosine in the liver and brain of mice treated with cocaine or heroin, using liquid chromatography/tandem mass spectrometry (LC-MS/MS). Our results show that global 5-methylcytosine levels are not affected by heroin or cocaine administration, neither in the liver nor in the brain. However, 5-hydroxymethylcytosine levels are reduced in the liver following cocaine administration, while they are not affected by cocaine in the brain or by heroin administration in the liver and the brain. Elucidation of the epigenetic phenomena that takes place with respect to drug abuse and addiction, via quantitative analysis of different modified bases, may enable a better understanding of the underlying mechanisms and may lead to more personalized and effective treatment options.
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