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Juvinao-Quintero DL, Hivert MF, Sharp GC, Relton CL, Elliott HR. DNA Methylation and Type 2 Diabetes: the Use of Mendelian Randomization to Assess Causality. CURRENT GENETIC MEDICINE REPORTS 2019; 7:191-207. [PMID: 32274260 PMCID: PMC7145450 DOI: 10.1007/s40142-019-00176-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Purpose of Review This review summarises recent advances in the field of epigenetics in order to understand the aetiology of type 2 diabetes (T2D). Recent Findings DNA methylation at a number of loci has been shown to be robustly associated with T2D, including TXNIP, ABCG1, CPT1A, and SREBF1. However, due to the cross-sectional nature of many epidemiological studies and predominant analysis in samples derived from blood rather than disease relevant tissues, inferring causality is difficult. We therefore outline the use of Mendelian randomisation (MR) as one method able to assess causality in epigenetic studies of T2D. Summary Epidemiological studies have been fruitful in identifying epigenetic markers of T2D. Triangulation of evidence including utilisation of MR is essential to delineate causal from non-causal biomarkers of disease. Understanding the causality of epigenetic markers in T2D more fully will aid prioritisation of CpG sites as early biomarkers to detect disease or in drug development to target epigenetic mechanisms in order to treat patients.
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Affiliation(s)
- Diana L Juvinao-Quintero
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, USA
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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52
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Bianchi M, Alisi A, Fabrizi M, Vallone C, Ravà L, Giannico R, Vernocchi P, Signore F, Manco M. Maternal Intake of n-3 Polyunsaturated Fatty Acids During Pregnancy Is Associated With Differential Methylation Profiles in Cord Blood White Cells. Front Genet 2019; 10:1050. [PMID: 31708974 PMCID: PMC6824245 DOI: 10.3389/fgene.2019.01050] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/30/2019] [Indexed: 12/14/2022] Open
Abstract
A healthy diet during pregnancy is pivotal for the offspring health at birth and later in life. N-3 polyunsaturated fatty acids (n-3 PUFAs) are not endogenously produced in humans and are exclusively derived from the diet. They are pivotal for the fetus growth and neuronal development and seem beneficial in reducing the risk of cardiometabolic diseases and preventing later allergic disorders in the offspring by modulating the inflammatory immune response. In the present study, we investigated the association between maternal intakes of n-3PUFAs, profiled on maternal erythrocyte membranes at pregnancy term, and offspring DNA methylation on cord blood mononuclear cells in a sample of 118 mother–newborn pairs randomly drawn from the “Feeding fetus’ low-grade inflammation and insulin-resistance” study cohort. N-3 PUFA content on erythrocyte membranes is a validated biomarker to measure objectively medium term intake of n-3 PUFAs. Based on distribution of n-3 PUFA in the whole cohort of mothers, we identified mothers with low (n-3 PUFA concentration <25th percentile), medium (n-3 PUFAs between 25th and 75th percentiles), and high n-3 PUFA content (>75th percentile). The HumanMethylation450 BeadChip (Illumina) was used for the epigenome-wide association study using the Infinium Methylation Assay. The overall DNA methylation level was not different between the three groups while there was significant difference in methylation levels at certain sites. Indeed, 8,503 sites had significantly different methylations between low and high n-3 PUFA groups, 12,716 between low and medium n-3 PUFA groups, and 18,148 between high and medium n-3 PUFA groups. We found differentially methylated genes that belong prevalently to pathways of signal transduction, metabolism, downstream signaling of G protein-coupled receptors, and gene expression. Within these pathways, we identified four differentially methylated genes, namely, MSTN, IFNA13, ATP8B3, and GABBR2, that are involved in the onset of insulin resistance and adiposity, innate immune response, phospholipid translocation across cell membranes, and mechanisms of addiction to high fat diet, alcohol, and sweet taste. In conclusion, findings of this preliminary investigation suggest that maternal intake of n-3 PUFAs during pregnancy has potential to influence the offspring DNA methylation. Validation of results in a larger cohort and investigation of biological significance and impact on the phenotype are warranted.
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Affiliation(s)
- Marzia Bianchi
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Anna Alisi
- Research Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marta Fabrizi
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cristina Vallone
- Department of Obstetrics and Gynecology, Misericordia Hospital, Grosseto, Italy
| | - Lucilla Ravà
- Clinical Epidemiology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Riccardo Giannico
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fabrizio Signore
- Department of Obstetrics and Gynecology, Misericordia Hospital, Grosseto, Italy
| | - Melania Manco
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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53
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Fernandez-Twinn DS, Hjort L, Novakovic B, Ozanne SE, Saffery R. Intrauterine programming of obesity and type 2 diabetes. Diabetologia 2019; 62:1789-1801. [PMID: 31451874 PMCID: PMC6731191 DOI: 10.1007/s00125-019-4951-9] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/05/2019] [Indexed: 12/16/2022]
Abstract
The type 2 diabetes epidemic and one of its predisposing factors, obesity, are major influences on global health and economic burden. It is accepted that genetics and the current environment contribute to this epidemic; however, in the last two decades, both human and animal studies have consolidated considerable evidence supporting the 'developmental programming' of these conditions, specifically by the intrauterine environment. Here, we review the various in utero exposures that are linked to offspring obesity and diabetes in later life, including epidemiological insights gained from natural historical events, such as the Dutch Hunger Winter, the Chinese famine and the more recent Quebec Ice Storm. We also describe the effects of gestational exposure to endocrine disruptors, maternal infection and smoking to the fetus in relation to metabolic programming. Causal evidence from animal studies, motivated by human observations, is also discussed, as well as some of the proposed underlying molecular mechanisms for developmental programming of obesity and type 2 diabetes, including epigenetics (e.g. DNA methylation and histone modifications) and microRNA interactions. Finally, we examine the effects of non-pharmacological interventions, such as improving maternal dietary habits and/or increasing physical activity, on the offspring epigenome and metabolic outcomes.
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Affiliation(s)
- Denise S Fernandez-Twinn
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Level 4, Box 289, Addenbrooke's Treatment Centre, Cambridge, CB2 0QQ, UK
| | - Line Hjort
- Department of Endocrinology, the Diabetes and Bone-metabolic Research Unit, Rigshospitalet, Copenhagen, Denmark
- Department of Obstetrics, Center for Pregnant Women with Diabetes, Rigshospitalet, Copenhagen, Denmark
| | - Boris Novakovic
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Susan E Ozanne
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Level 4, Box 289, Addenbrooke's Treatment Centre, Cambridge, CB2 0QQ, UK.
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia.
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54
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de Lombares C, Heude E, Alfama G, Fontaine A, Hassouna R, Vernochet C, de Chaumont F, Olivo-Marin C, Ey E, Parnaudeau S, Tronche F, Bourgeron T, Luquet S, Levi G, Narboux-Nême N. Dlx5 and Dlx6 expression in GABAergic neurons controls behavior, metabolism, healthy aging and lifespan. Aging (Albany NY) 2019; 11:6638-6656. [PMID: 31514171 PMCID: PMC6756896 DOI: 10.18632/aging.102141] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/30/2019] [Indexed: 12/18/2022]
Abstract
Dlx5 and Dlx6 encode two homeobox transcription factors expressed by developing and mature GABAergic interneurons. During development, Dlx5/6 play a role in the differentiation of certain GABAergic subclasses. Here we address the question of the functional role of Dlx5/6 in the mature central nervous system. First, we demonstrate that Dlx5 and Dlx6 are expressed by all subclasses of adult cortical GABAergic neurons. Then we analyze VgatΔDlx5-6 mice in which Dlx5 and Dlx6 are simultaneously inactivated in all GABAergic interneurons. VgatΔDlx5-6 mice present a behavioral pattern suggesting reduction of anxiety-like behavior and obsessive-compulsive activities, and a lower interest in nest building. Twenty-month-old VgatΔDlx5-6 animals have the same size as their normal littermates, but present a 25% body weight reduction associated with a marked decline in white and brown adipose tissue. Remarkably, both VgatΔDlx5-6/+ and VgatΔDlx5-6 mice present a 33% longer median survival. Hallmarks of biological aging such as motility, adiposity and coat conditions are improved in mutant animals. Our data imply that GABAergic interneurons can regulate healthspan and lifespan through Dlx5/6-dependent mechanisms. Understanding these regulations can be an entry point to unravel the processes through which the brain affects body homeostasis and, ultimately, longevity and healthy aging.
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Affiliation(s)
- Camille de Lombares
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Muséum National d’Histoire Naturelle, Département AVIV, Paris, France
| | - Eglantine Heude
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Muséum National d’Histoire Naturelle, Département AVIV, Paris, France
| | - Gladys Alfama
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Muséum National d’Histoire Naturelle, Département AVIV, Paris, France
| | - Anastasia Fontaine
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Muséum National d’Histoire Naturelle, Département AVIV, Paris, France
| | - Rim Hassouna
- Unité de Biologie Fonctionnelle et Adaptative (BFA), Université Paris Diderot, Sorbonne Paris Cité, CNRS UMR 8251, Paris, France
| | - Cécile Vernochet
- Team "Gene Regulation and Adaptive Behaviors", Neurosciences Paris Seine, INSERM U 1130, CNRS UMR 8246, Paris, France
| | | | | | - Elodie Ey
- Human Genetics and Cognitive Functions, Institute Pasteur, CNRS UMR 3571, Paris, France
| | - Sébastien Parnaudeau
- Team "Gene Regulation and Adaptive Behaviors", Neurosciences Paris Seine, INSERM U 1130, CNRS UMR 8246, Paris, France
| | - François Tronche
- Team "Gene Regulation and Adaptive Behaviors", Neurosciences Paris Seine, INSERM U 1130, CNRS UMR 8246, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institute Pasteur, CNRS UMR 3571, Paris, France
| | - Serge Luquet
- Unité de Biologie Fonctionnelle et Adaptative (BFA), Université Paris Diderot, Sorbonne Paris Cité, CNRS UMR 8251, Paris, France
| | - Giovanni Levi
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Muséum National d’Histoire Naturelle, Département AVIV, Paris, France
| | - Nicolas Narboux-Nême
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Muséum National d’Histoire Naturelle, Département AVIV, Paris, France
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55
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Jansen RJ, Tong L, Argos M, Jasmine F, Rakibuz-Zaman M, Sarwar G, Islam MT, Shahriar H, Islam T, Rahman M, Yunus M, Kibriya MG, Baron JA, Ahsan H, Pierce BL. The effect of age on DNA methylation in whole blood among Bangladeshi men and women. BMC Genomics 2019; 20:704. [PMID: 31506065 PMCID: PMC6734473 DOI: 10.1186/s12864-019-6039-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/16/2019] [Indexed: 12/15/2022] Open
Abstract
Background It is well-known that methylation changes occur as humans age, however, understanding how age-related changes in DNA methylation vary by sex is lacking. In this study, we characterize the effect of age on DNA methylation in a sex-specific manner and determine if these effects vary by genomic context. We used the Illumina HumanMethylation 450 K array and DNA derived from whole blood for 400 adult participants (189 males and 211 females) from Bangladesh to identify age-associated CpG sites and regions and characterize the location of these age-associated sites with respect to CpG islands (vs. shore, shelf, or open sea) and gene regions (vs. intergenic). We conducted a genome-wide search for age-associated CpG sites (among 423,604 sites) using a reference-free approach to adjust for cell type composition (the R package RefFreeEWAS) and performed an independent replication analysis of age-associated CpGs. Results The number of age-associated CpGs (p < 5 x 10− 8) were 986 among men and 3479 among women of which 2027(63.8%) and 572 (64.1%) replicated (using Bonferroni adjusted p < 1.2 × 10− 5). For both sexes, age-associated CpG sites were more likely to be hyper-methylated with increasing age (compared to hypo-methylated) and were enriched in CpG islands and promoter regions compared with other locations and all CpGs on the array. Although we observed strong correlation between chronological age and previously-developed epigenetic age models (r ≈ 0.8), among our top (based on lowest p-value) age-associated CpG sites only 12 for males and 44 for females are included in these prediction models, and the median chronological age compared to predicted age was 44 vs. 51.7 in males and 45 vs. 52.1 in females. Conclusions Our results describe genome-wide features of age-related changes in DNA methylation. The observed associations between age and methylation were generally consistent for both sexes, although the associations tended to be stronger among women. Our population may have unique age-related methylation changes that are not captured in the established methylation-based age prediction model we used, which was developed to be non-tissue-specific. Electronic supplementary material The online version of this article (10.1186/s12864-019-6039-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rick J Jansen
- Department of Public Health, North Dakota State University, Fargo, ND, USA.,Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA.,Biostatistics Core Facility, North Dakota State University, Fargo, ND, USA
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA
| | - Maria Argos
- Divison of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA
| | | | - Golam Sarwar
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh
| | | | - Hasan Shahriar
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh
| | - Tariqul Islam
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh
| | - Mahfuzar Rahman
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh.,Research and Evaluation Division BRAC, Mohakhali, Dhaka, 1212, Bangladesh
| | - Md Yunus
- International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, 1000, Bangladesh
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA
| | - John A Baron
- Department of Epidemiology, Gillings School of Global Public Health, University of North Caroline, Chapel Hill, NC, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA. .,Department of Medicine, The University of Chicago, Chicago, IL, USA. .,Department of Human Genetics and Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA.
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA. .,Department of Human Genetics and Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA.
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56
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Sherwood WB, Bion V, Lockett GA, Ziyab AH, Soto-Ramírez N, Mukherjee N, Kurukulaaratchy RJ, Ewart S, Zhang H, Arshad SH, Karmaus W, Holloway JW, Rezwan FI. Duration of breastfeeding is associated with leptin (LEP) DNA methylation profiles and BMI in 10-year-old children. Clin Epigenetics 2019; 11:128. [PMID: 31464656 PMCID: PMC6716837 DOI: 10.1186/s13148-019-0727-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023] Open
Abstract
Background Breastfeeding is protective against many long-term diseases, yet the mechanisms involved are unknown. Leptin gene (LEP) is reported to be associated with body mass index (BMI). On the other hand, breastfeeding duration has been found to be associated with DNA methylation (DNAm) of the LEP gene. Therefore, epigenetic regulation of LEP may represent the mechanism underlying the protective effect of breastfeeding duration against obesity. Methods In the Isle of Wight Birth Cohort, peripheral blood DNAm at 23 cytosine-phosphate-guanine sites (CpGs) in the LEP locus in 10-year-old (n = 297) samples and 16 CpGs in 18-year-old (n = 305) samples, were generated using the Illumina Infinium MethylationEPIC and HumanMethylation450 Beadchips respectively and tested for association with breastfeeding duration (total and exclusive) using linear regression. To explore the association between breastfeeding durations and genome-wide DNAm, epigenome-wide association studies (EWASs) and differential methylation region (DMR) analyses were performed. BMI trajectories spanning the first 18 years of life were used as the outcome to test the association with breastfeeding duration (exposure) using multi-nominal logistic regression. Mediation analysis was performed for significant CpG sites. Results Both total and exclusive breastfeeding duration were associated with DNAm at four LEP CpG sites at 10 years (P value < 0.05), and not at 18 years. Though no association was observed between breastfeeding duration and genome-wide DNAm, DMR analyses identified five significant differentially methylated regions (Sidak adjusted P value < 0.05). Breastfeeding duration was also associated with the early transient overweight trajectory. Furthermore, DNAm of LEP was associated with this trajectory at one CpG site and early persistent obesity at another, though mediation analysis was not significant. Conclusions Breastfeeding duration is associated with LEP methylation at age 10 years and BMI trajectory. LEP DNAm is also significantly associated with BMI trajectories throughout childhood, though sample sizes were small. However, mediation analysis did not demonstrate that DNAm of LEP explained the protective effect of breastfeeding against childhood obesity. Electronic supplementary material The online version of this article (10.1186/s13148-019-0727-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William B Sherwood
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, University of Southampton, Duthie Building, MP808, Tremona Road, Southampton, Hampshire, SO16 6YD, UK
| | - Victoria Bion
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, University of Southampton, Duthie Building, MP808, Tremona Road, Southampton, Hampshire, SO16 6YD, UK
| | - Gabrielle A Lockett
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, University of Southampton, Duthie Building, MP808, Tremona Road, Southampton, Hampshire, SO16 6YD, UK
| | - Ali H Ziyab
- Department of Community Medicine and Behavioral Sciences, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | | | - Nandini Mukherjee
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN, 38152, USA
| | - Ramesh J Kurukulaaratchy
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN, 38152, USA
| | - S Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN, 38152, USA
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, University of Southampton, Duthie Building, MP808, Tremona Road, Southampton, Hampshire, SO16 6YD, UK.,Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, University of Southampton, Duthie Building, MP808, Tremona Road, Southampton, Hampshire, SO16 6YD, UK.
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57
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Gillberg L, Rönn T, Jørgensen SW, Perfilyev A, Hjort L, Nilsson E, Brøns C, Vaag A, Ling C. Fasting unmasks differential fat and muscle transcriptional regulation of metabolic gene sets in low versus normal birth weight men. EBioMedicine 2019; 47:341-351. [PMID: 31439477 PMCID: PMC6796584 DOI: 10.1016/j.ebiom.2019.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/19/2019] [Accepted: 08/06/2019] [Indexed: 12/17/2022] Open
Abstract
Background Individuals born with low birth weight (LBW) have an increased risk of metabolic diseases when exposed to diets rich in calories and fat but may respond to fasting in a metabolically preferential manner. We hypothesized that impaired foetal growth is associated with differential regulation of gene expression and epigenetics in metabolic tissues in response to fasting in young adulthood. Methods Genome-wide expression and DNA methylation were analysed in subcutaneous adipose tissue (SAT) and skeletal muscle from LBW and normal birth weight (NBW) men after 36 h fasting and after an isocaloric control study using microarrays. Findings Transcriptome analyses revealed that expression of genes involved in oxidative phosphorylation (OXPHOS) and other key metabolic pathways were lower in SAT from LBW vs NBW men after the control study, but paradoxically higher in LBW vs NBW men after 36 h fasting. Thus, fasting was associated with downregulated OXPHOS and metabolic gene sets in NBW men only. Likewise, in skeletal muscle only NBW men downregulated OXPHOS genes with fasting. Few epigenetic changes were observed in SAT and muscle between the groups. Interpretation Our results provide insights into the molecular mechanisms in muscle and adipose tissue governing a differential metabolic response in subjects with impaired foetal growth when exposed to fasting in adulthood. The results support the concept of developmental programming of metabolic diseases including type 2 diabetes. Fund The Swedish Research Council, the Danish Council for Strategic Research, the Novo Nordisk foundation, the Swedish Foundation for Strategic Research, The European Foundation for the Study of Diabetes, The EU 6th Framework EXGENESIS grant and Rigshospitalet.
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Affiliation(s)
- Linn Gillberg
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Tina Rönn
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | | | - Alexander Perfilyev
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Line Hjort
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Emma Nilsson
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Charlotte Brøns
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Allan Vaag
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular, Renal and Metabolism (CVRM), Translational Medical Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden
| | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden.
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58
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Mansell T, Ponsonby AL, Januar V, Novakovic B, Collier F, Burgner D, Vuillermin P, Ryan J, Saffery R. Early-life determinants of hypoxia-inducible factor 3A gene (HIF3A) methylation: a birth cohort study. Clin Epigenetics 2019; 11:96. [PMID: 31262346 PMCID: PMC6604333 DOI: 10.1186/s13148-019-0687-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/27/2019] [Indexed: 12/17/2022] Open
Abstract
Background Methylation of the hypoxia-inducible factor 3α gene (HIF3A) has been linked to pregnancy exposures, infant adiposity and later BMI. Genetic variation influences HIF3A methylation levels and may modify these relationships. However, data in very early life are limited, particularly in association with adverse pregnancy outcomes. We investigated the relationship between maternal and gestational factors, infant anthropometry, genetic variation and HIF3A DNA methylation in the Barwon Infant Study, a population-based birth cohort. Methylation of two previously studied regions of HIF3A were tested in the cord blood mononuclear cells of 938 infants. Results No compelling evidence was found of an association between birth weight, adiposity or maternal gestational diabetes with methylation at the most widely studied HIF3A region. Male sex (− 4.3%, p < 0.001) and pre-eclampsia (− 5.4%, p = 0.02) negatively associated with methylation at a second region of HIF3A; while positive associations were identified for gestational diabetes (4.8%, p = 0.01) and gestational age (1.2% increase per week, p < 0.001). HIF3A genetic variation also associated strongly with methylation at this region (p < 0.001). Conclusions Pre- and perinatal factors impact HIF3A methylation, including pre-eclampsia. This provides evidence that specific pregnancy complications, previously linked to adverse outcomes for both mother and child, impact the infant epigenome in a molecular pathway critical to several vascular and metabolic conditions. Further work is required to understand the mechanisms and clinical relevance, particularly the differing effects of in utero exposure to gestational diabetes or pre-eclampsia. Electronic supplementary material The online version of this article (10.1186/s13148-019-0687-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Toby Mansell
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Anne-Louise Ponsonby
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Vania Januar
- Murdoch Children's Research Institute, Parkville, Australia
| | - Boris Novakovic
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Fiona Collier
- Murdoch Children's Research Institute, Parkville, Australia.,School of Medicine, Deakin University, Geelong, Australia.,Child Health Research Unit, Barwon Health, Geelong, Australia
| | - David Burgner
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,Department of Paediatrics, Monash University, Clayton, Australia
| | - Peter Vuillermin
- Murdoch Children's Research Institute, Parkville, Australia.,School of Medicine, Deakin University, Geelong, Australia.,Child Health Research Unit, Barwon Health, Geelong, Australia
| | - Joanne Ryan
- Murdoch Children's Research Institute, Parkville, Australia.,School of Public Health & Preventive Medicine, Monash University, Melbourne, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Parkville, Australia. .,Department of Paediatrics, University of Melbourne, Parkville, Australia.
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59
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Potabattula R, Dittrich M, Schorsch M, Hahn T, Haaf T, El Hajj N. Male obesity effects on sperm and next-generation cord blood DNA methylation. PLoS One 2019; 14:e0218615. [PMID: 31246962 PMCID: PMC6597061 DOI: 10.1371/journal.pone.0218615] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022] Open
Abstract
The prevalence of metabolic disorders, in particular obesity has dramatically increased worldwide. Genetic variants explain only a minor part of the obesity epidemic induced by physical inactivity and over-nutrition. Epidemiological studies in humans and animal models indicate that epigenetic changes associated with adverse parental and/or intrauterine factors may contribute to the missing heritability of metabolic disorders. Possible adverse paternal effects are likely transmitted by sperm to the next-generation. To investigate this hypothesis, we have systematically analyzed the effects of male body mass index (BMI) on sperm epigenome and its association with next-generation fetal cord blood (FCB) DNA methylation. Methylation levels of maternally imprinted (PEG1, PEG4, PEG5, and PEG10), paternally imprinted (H19-IG DMR, IGF2-DMR0, and MEG3-IG DMR) regions, and obesity-related non-imprinted HIF3A gene were quantified by bisulphite pyrosequencing in sperm samples of 294 human donors undergoing in vitro fertilization or intracytoplasmic sperm injection, and in 113 FCBs of the resulting offspring. Multivariable regression analyses revealed that MEG3 intergenic differentially methylated region (IG DMR) showed positive correlation between sperm methylation and donor’s BMI. A gender-specific correlation between paternal BMI and FCB methylation was observed for MEG3-IG DMR, HIF3A, and IGF2-DMR0. The former two genes displayed same directional nominal association (as sperm) between paternal BMI and FCB methylation in male offspring. Hypomethylation of IGF2-DMR0 with increased paternal BMI was observed in FCBs from female offsprings. Our results suggest that male obesity is nominally associated with modification of sperm DNA methylome in humans, which may affect the epigenome of the next-generation. Nevertheless, it is important to note that none of the associated p-values survived multiple testing adjustments. Future work should test the effect of associated methylation aberrations in the offspring as DNA methylation was shown to control expression and/or imprint establishment across the studied genes.
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Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- * E-mail: (RP); , (NEH)
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
- * E-mail: (RP); , (NEH)
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60
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Abstract
PURPOSE OF REVIEW The influence of environmental factors on type 2 diabetes (T2D) risk is now well recognized and highlights the contribution of epigenetic mechanisms. This review will focus on the role of epigenetic factors in the risk and pathogenesis of T2D. RECENT FINDINGS Epigenetic dysregulation has emerged as a key mechanism underpinning the pathogenesis of T2D and its complications. Environmental variations, including alterations in lifestyle, nutrition, and metabolic demands during prenatal and postnatal life can induce epigenetic changes that may impact glucose homeostasis and the function of different metabolic organs. Accumulating data continues to uncover the specific pathways that are epigenetically dysregulated in T2D, providing an opportunity for therapeutic targeting. Environmental changes can disrupt specific epigenetic mechanisms underlying metabolic homeostasis, thus contributing to T2D pathogenesis. Such epigenetic changes can be transmitted to the next generation, contributing to the inheritance of T2D risk. Recent advances in epigenome-wide association studies and epigenetic editing tools present the attractive possibility of identifying epimutations associated with T2D, correcting specific epigenetic alterations, and designing novel epigenetic biomarkers and interventions for T2D.
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Affiliation(s)
- Sangeeta Dhawan
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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61
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Arpón A, Milagro FI, Ramos-Lopez O, Mansego ML, Riezu-Boj JI, Martínez JA. Methylome-Wide Association Study in Peripheral White Blood Cells Focusing on Central Obesity and Inflammation. Genes (Basel) 2019; 10:genes10060444. [PMID: 31212707 PMCID: PMC6627499 DOI: 10.3390/genes10060444] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/03/2019] [Accepted: 06/07/2019] [Indexed: 12/13/2022] Open
Abstract
Epigenetic signatures such as DNA methylation may be associated with specific obesity traits in different tissues. The onset and development of some obesity-related complications are often linked to visceral fat accumulation. The aim of this study was to explore DNA methylation levels in peripheral white blood cells to identify epigenetic methylation marks associated with waist circumference (WC). DNA methylation levels were assessed using Infinium Human Methylation 450K and MethylationEPIC beadchip (Illumina) to search for putative associations with WC values of 473 participants from the Methyl Epigenome Network Association (MENA) project. Statistical analysis and Ingenuity Pathway Analysis (IPA) were employed for assessing the relationship between methylation and WC. A total of 669 CpGs were statistically associated with WC (FDR < 0.05, slope ≥ |0.1|). From these CpGs, 375 CpGs evidenced a differential methylation pattern between females with WC ≤ 88 and > 88 cm, and 95 CpGs between males with WC ≤ 102 and > 102 cm. These differentially methylated CpGs are located in genes related to inflammation and obesity according to IPA. Receiver operating characteristic (ROC) curves of the top four significant differentially methylated CpGs separated by sex discriminated individuals with presence or absence of abdominal fat. ROC curves of all the CpGs from females and one CpG from males were validated in an independent sample (n = 161). These methylation results add further insights about the relationships between obesity, adiposity-associated comorbidities, and DNA methylation where inflammation processes may be involved.
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Affiliation(s)
- Ana Arpón
- Department of Nutrition, Food Sciences and Physiology, University of Navarra, Irunlarrea 1,31008 Pamplona, Spain.
- Centre for Nutrition Research, University of Navarra, Irunlarrea 1, 31008, Pamplona, Spain.
| | - Fermín I Milagro
- Department of Nutrition, Food Sciences and Physiology, University of Navarra, Irunlarrea 1,31008 Pamplona, Spain.
- Centre for Nutrition Research, University of Navarra, Irunlarrea 1, 31008, Pamplona, Spain.
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, 28029, Madrid, Spain.
- Navarra Institute for Health Research (IdiSNa), 31008, Pamplona, Spain.
| | - Omar Ramos-Lopez
- Department of Nutrition, Food Sciences and Physiology, University of Navarra, Irunlarrea 1,31008 Pamplona, Spain.
- Centre for Nutrition Research, University of Navarra, Irunlarrea 1, 31008, Pamplona, Spain.
| | - Maria L Mansego
- Department of Bioinformatics, Making Genetics S.L., 31002, Pamplona, Spain.
| | - José-Ignacio Riezu-Boj
- Department of Nutrition, Food Sciences and Physiology, University of Navarra, Irunlarrea 1,31008 Pamplona, Spain.
- Centre for Nutrition Research, University of Navarra, Irunlarrea 1, 31008, Pamplona, Spain.
- Navarra Institute for Health Research (IdiSNa), 31008, Pamplona, Spain.
| | - J Alfredo Martínez
- Department of Nutrition, Food Sciences and Physiology, University of Navarra, Irunlarrea 1,31008 Pamplona, Spain.
- Centre for Nutrition Research, University of Navarra, Irunlarrea 1, 31008, Pamplona, Spain.
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, 28029, Madrid, Spain.
- Navarra Institute for Health Research (IdiSNa), 31008, Pamplona, Spain.
- Precision Nutrition and Cardiometabolic Health Program, Madrid Institute for Advanced Studies (IMDEA), IMDEA Food, 28049, Madrid, Spain.
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62
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Nicoletti CF, Pinhel MAS, Diaz-Lagares A, Casanueva FF, Jácome A, Pinhanelli VC, de Oliveira BAP, Crujeiras AB, Nonino CB. DNA methylation screening after roux-en Y gastric bypass reveals the epigenetic signature stems from genes related to the surgery per se. BMC Med Genomics 2019; 12:72. [PMID: 31133015 PMCID: PMC6537208 DOI: 10.1186/s12920-019-0522-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
Background/objectives Obesity has been associated with gene methylation regulation. Recent studies have shown that epigenetic signature plays a role in metabolic homeostasis after Roux-en Y gastric bypass (RYGB). To conduct a genome-wide epigenetic analysis in peripheral blood to investigate whether epigenetic changes following RYGB stem from weight loss or the surgical procedure per se. Subjects/methods By means of the Infinium Human Methylation 450 BeadChip array, global methylation was analyzed in blood of 24 severely obese women before and 6 months after RYGB and in 24 normal-weight women (controls). Results In blood cells, nine DMCpG sites showed low methylation levels before surgery, methylation levels increased after RYGB and neared the levels measured in the controls. Additionally, 44 CpG sites associated with the Wnt and p53 signaling pathways were always differently methylated in the severely obese patients as compared to the controls and were not influenced by RYGB. Finally, 1638 CpG sites related to inflammation, angiogenesis, and apoptosis presented distinct methylation in the post-surgery patients as compared to the controls. Conclusion Bariatric surgery per se acts on CpGs related to inflammation, angiogenesis, and endothelin-signaling. However, the gene cluster associated with obesity remains unchanged, suggesting that weight loss 6 months after RYGB surgery cannot promote this effect. Graphical abstract ![]()
Electronic supplementary material The online version of this article (10.1186/s12920-019-0522-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C F Nicoletti
- Laboratory of Nutrigenomics Studies, Department of Internal Medicine, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - M A S Pinhel
- Laboratory of Nutrigenomics Studies, Department of Internal Medicine, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - A Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - F F Casanueva
- Epigenomics in Endocrinology and Nutrition, Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain.,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - A Jácome
- Department of Mathematics, MODES group, CITIC, Universidade da Coruña, Faculty of Science, A Coruña, Spain
| | - V C Pinhanelli
- Laboratory of Nutrigenomics Studies, Department of Internal Medicine, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - B A P de Oliveira
- Laboratory of Nutrigenomics Studies, Department of Internal Medicine, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - A B Crujeiras
- Epigenomics in Endocrinology and Nutrition, Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain. .,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain.
| | - C B Nonino
- Laboratory of Nutrigenomics Studies, Department of Internal Medicine, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil.
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63
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Ling C, Rönn T. Epigenetics in Human Obesity and Type 2 Diabetes. Cell Metab 2019; 29:1028-1044. [PMID: 30982733 PMCID: PMC6509280 DOI: 10.1016/j.cmet.2019.03.009] [Citation(s) in RCA: 452] [Impact Index Per Article: 90.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/05/2019] [Accepted: 03/18/2019] [Indexed: 12/16/2022]
Abstract
Epigenetic mechanisms control gene activity and the development of an organism. The epigenome includes DNA methylation, histone modifications, and RNA-mediated processes, and disruption of this balance may cause several pathologies and contribute to obesity and type 2 diabetes (T2D). This Review summarizes epigenetic signatures obtained from human tissues of relevance for metabolism-i.e., adipose tissue, skeletal muscle, pancreatic islets, liver, and blood-in relation to obesity and T2D. Although this research field is still young, these comprehensive data support not only a role for epigenetics in disease development, but also epigenetic alterations as a response to disease. Genetic predisposition, as well as aging, contribute to epigenetic variability, and several environmental factors, including exercise and diet, further interact with the human epigenome. The reversible nature of epigenetic modifications holds promise for future therapeutic strategies in obesity and T2D.
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Affiliation(s)
- Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden.
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
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64
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Abstract
The twin epidemics of obesity and type 2 diabetes (T2D) are a serious health, social, and economic issue. The dysregulation of adipose tissue biology is central to the development of these two metabolic disorders, as adipose tissue plays a pivotal role in regulating whole-body metabolism and energy homeostasis (1). Accumulating evidence indicates that multiple aspects of adipose biology are regulated, in part, by epigenetic mechanisms. The precise and comprehensive understanding of the epigenetic control of adipose tissue biology is crucial to identifying novel therapeutic interventions that target epigenetic issues. Here, we review the recent findings on DNA methylation events and machinery in regulating the developmental processes and metabolic function of adipocytes. We highlight the following points: 1) DNA methylation is a key epigenetic regulator of adipose development and gene regulation, 2) emerging evidence suggests that DNA methylation is involved in the transgenerational passage of obesity and other metabolic disorders, 3) DNA methylation is involved in regulating the altered transcriptional landscape of dysfunctional adipose tissue, 4) genome-wide studies reveal specific DNA methylation events that associate with obesity and T2D, and 5) the enzymatic effectors of DNA methylation have physiological functions in adipose development and metabolic function.
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Affiliation(s)
- Xiang Ma
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA
| | - Sona Kang
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA
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65
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Samblas M, Milagro FI, Martínez A. DNA methylation markers in obesity, metabolic syndrome, and weight loss. Epigenetics 2019; 14:421-444. [PMID: 30915894 DOI: 10.1080/15592294.2019.1595297] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The fact that not all individuals exposed to the same environmental risk factors develop obesity supports the hypothesis of the existence of underlying genetic and epigenetic elements. There is suggestive evidence that environmental stimuli, such as dietary pattern, particularly during pregnancy and early life, but also in adult life, can induce changes in DNA methylation predisposing to obesity and related comorbidities. In this context, the DNA methylation marks of each individual have emerged not only as a promising tool for the prediction, screening, diagnosis, and prognosis of obesity and metabolic syndrome features, but also for the improvement of weight loss therapies in the context of precision nutrition. The main objectives in this field are to understand the mechanisms involved in transgenerational epigenetic inheritance, and featuring the nutritional and lifestyle factors implicated in the epigenetic modifications. Likewise, DNA methylation modulation caused by diet and environment may be a target for newer therapeutic strategies concerning the prevention and treatment of metabolic diseases.
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Affiliation(s)
- Mirian Samblas
- a Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research , University of Navarra , Pamplona , Spain
| | - Fermín I Milagro
- a Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research , University of Navarra , Pamplona , Spain.,b CIBERobn, CIBER Fisiopatología de la Obesidad y Nutrición , Instituto de Salud Carlos III. Madrid , Spain.,c IdiSNA, Instituto de Investigación Sanitaria de Navarra (IdiSNA) , Pamplona , Spain
| | - Alfredo Martínez
- a Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research , University of Navarra , Pamplona , Spain.,b CIBERobn, CIBER Fisiopatología de la Obesidad y Nutrición , Instituto de Salud Carlos III. Madrid , Spain.,c IdiSNA, Instituto de Investigación Sanitaria de Navarra (IdiSNA) , Pamplona , Spain.,d IMDEA, Research Institute on Food & Health Sciences , Madrid , Spain
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66
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Arpón A, Milagro FI, Ramos-Lopez O, Mansego ML, Santos JL, Riezu-Boj JI, Martínez JA. Epigenome-wide association study in peripheral white blood cells involving insulin resistance. Sci Rep 2019; 9:2445. [PMID: 30792424 PMCID: PMC6385280 DOI: 10.1038/s41598-019-38980-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/11/2019] [Indexed: 02/06/2023] Open
Abstract
Insulin resistance (IR) is a hallmark of type 2 diabetes, metabolic syndrome and cardiometabolic risk. An epigenetic phenomena such as DNA methylation might be involved in the onset and development of systemic IR. The aim of this study was to explore the genetic DNA methylation levels in peripheral white blood cells with the objective of identifying epigenetic signatures associated with IR measured by the Homeostatic Model Assessment of IR (HOMA-IR) following an epigenome-wide association study approach. DNA methylation levels were assessed using Infinium Methylation Assay (Illumina), and were associated with HOMA-IR values of participants from the Methyl Epigenome Network Association (MENA) project, finding statistical associations for at least 798 CpGs. A stringent statistical analysis revealed that 478 of them showed a differential methylation pattern between individuals with HOMA-IR ≤ 3 and > 3. ROC curves of top four CpGs out of 478 allowed differentiating individuals between both groups (AUC≈0.88). This study demonstrated the association between DNA methylation in some specific CpGs and HOMA-IR values that will help to the understanding and in the development of new strategies for personalized approaches to predict and prevent IR-associated diseases.
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Affiliation(s)
- Ana Arpón
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - Fermín I Milagro
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain.,Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, Madrid, Spain
| | - Omar Ramos-Lopez
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - M Luisa Mansego
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - José Luis Santos
- Department of Nutrition, Diabetes and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José-Ignacio Riezu-Boj
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain. .,Navarra Institute for Health Research (IdiSNa), Pamplona, Spain.
| | - J Alfredo Martínez
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain.,Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, Madrid, Spain.,Navarra Institute for Health Research (IdiSNa), Pamplona, Spain.,Madrid Institute for Advanced Studies (IMDEA), IMDEA Food, Madrid, Spain
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67
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Dai W, Liu H, Xu X, Ge J, Luo S, Zhu D, Amos CI, Fang S, Lee JE, Li X, Nan H, Li C, Wei Q. Genetic variants in ELOVL2 and HSD17B12 predict melanoma-specific survival. Int J Cancer 2019; 145:2619-2628. [PMID: 30734280 DOI: 10.1002/ijc.32194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 01/11/2019] [Indexed: 11/06/2022]
Abstract
Fatty acids play a key role in cellular bioenergetics, membrane biosynthesis and intracellular signaling processes and thus may be involved in cancer development and progression. In the present study, we comprehensively assessed associations of 14,522 common single-nucleotide polymorphisms (SNPs) in 149 genes of the fatty-acid synthesis pathway with cutaneous melanoma disease-specific survival (CMSS). The dataset of 858 cutaneous melanoma (CM) patients from a published genome-wide association study (GWAS) by The University of Texas M.D. Anderson Cancer Center was used as the discovery dataset, and the identified significant SNPs were validated by a dataset of 409 CM patients from another GWAS from the Nurses' Health and Health Professionals Follow-up Studies. We found 40 noteworthy SNPs to be associated with CMSS in both discovery and validation datasets after multiple comparison correction by the false positive report probability method, because more than 85% of the SNPs were imputed. By performing functional prediction, linkage disequilibrium analysis, and stepwise Cox regression selection, we identified two independent SNPs of ELOVL2 rs3734398 T>C and HSD17B12 rs11037684 A>G that predicted CMSS, with an allelic hazards ratio of 0.66 (95% confidence interval = 0.51-0.84 and p = 8.34 × 10-4 ) and 2.29 (1.55-3.39 and p = 3.61 × 10-5 ), respectively. Finally, the ELOVL2 rs3734398 variant CC genotype was found to be associated with a significantly increased mRNA expression level. These SNPs may be potential markers for CM prognosis, if validated by additional larger and mechanistic studies.
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Affiliation(s)
- Wei Dai
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China.,Duke Cancer Institute, Duke University Medical Center, Durham, NC.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC
| | - Xinyuan Xu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC
| | - Jie Ge
- Duke Cancer Institute, Duke University Medical Center, Durham, NC.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC
| | - Dakai Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Xin Li
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, Indianapolis, IN.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Hongmei Nan
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, Indianapolis, IN.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Chunying Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC.,Department of Medicine, Duke University School of Medicine, Durham, NC
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68
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Coppedè F, Seghieri M, Stoccoro A, Santini E, Giannini L, Rossi C, Migliore L, Solini A. DNA methylation of genes regulating appetite and prediction of weight loss after bariatric surgery in obese individuals. J Endocrinol Invest 2019; 42:37-44. [PMID: 29603098 DOI: 10.1007/s40618-018-0881-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/25/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE Epigenetic traits are influenced by clinical variables; interaction between DNA methylation (DNAmeth) and bariatric surgery-induced weight loss has been scarcely explored. We investigated whether DNAmeth of genes encoding for molecules/hormones regulating appetite, food intake or obesity could predict successful weight outcome following Roux-en-Y gastric bypass (RYGB). METHODS Forty-five obese individuals with no known comorbidities were stratified accordingly to weight decrease one-year after RYGB (excess weight loss, EWL ≥ 50%: good responders, GR; EWL < 50%: worse responders, WR). DNAmeth of leptin (LEP), ghrelin (GHRL), ghrelin receptor (GHSR) and insulin-growth factor-2 (IGF2) was assessed before intervention. Single nucleotide polymorphisms of genes affecting DNAmeth, DNMT3A and DNMT3B, were also determined. RESULTS At baseline, type 2 diabetes was diagnosed by OGTT in 13 patients. Post-operatively, GR (n = 23) and WR (n = 22) achieved an EWL of 67.7 ± 9.6 vs 38.2 ± 9.0%, respectively. Baseline DNAmeth did not differ between GR and WR for any tested genes, even when the analysis was restricted to subjects with no diabetes. A relationship between GHRL and LEP methylation profiles emerged (r = 0.47, p = 0.001). Searching for correlation between DNAmeth of the studied genes with demographic characteristics and baseline biochemical parameters of the studied population, we observed a correlation between IGF2 methylation and folate (r = 0.44, p = 0.003). Rs11683424 for DNMT3A and rs2424913 for DNMT3B did not correlate with DNAmeth of the studied genes. CONCLUSIONS In severely obese subjects, the degree of DNAmeth of some genes affecting obesity and related conditions does not work as predictor of successful response to RYGB.
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Affiliation(s)
- F Coppedè
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - M Seghieri
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - A Stoccoro
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - E Santini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - L Giannini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - C Rossi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - L Migliore
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - A Solini
- Department of Surgical, Medical, Molecular and Critical Area Pathology, University of Pisa, Via Roma 67, 56126, Pisa, Italy.
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69
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Malousi A, Andreou AZ, Georgiou E, Tzimagiorgis G, Kovatsi L, Kouidou S. Age-dependent methylation in epigenetic clock CpGs is associated with G-quadruplex, co-transcriptionally formed RNA structures and tentative splice sites. Epigenetics 2018; 13:808-821. [PMID: 30270726 PMCID: PMC6224212 DOI: 10.1080/15592294.2018.1514232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Horvath's epigenetic clock consists of 353 CpGs whose methylation levels can accurately predict the age of individuals. Using bioinformatics analysis, we investigated the conformation, energy characteristics and presence of tentative splice sites of the sequences surrounding the epigenetic clock CpGs, in relation to the median methylation changes in different ages, the presence of CpG islands and their position in genes. Common characteristics in the 100 nt sequences surrounding the epigenetic clock CpGs are G-quadruplexes and/or tentative splice site motifs. Median methylation increases significantly in sequences which adopt less stable structures during transcription. Methylation is higher when CpGs overlap with G-quadruplexes than when they precede them. Median methylation in epigenetic clock CpGs is higher in sequences expressed as single products rather than in multiple products and those containing single donors and multiple acceptors. Age-related methylation variation is significant in sequences without G-quadruplexes, particularly those producing low stability nascent RNA and those with splice sites. CpGs in sequences close to transcription start sites and those which are possibly never expressed (hypothetical proteins) undergo similar extent of age-related median methylation decrease and increase. Preservation of methylation is observed in CpG islands without G-quadruplexes, contrary to CpGs far from CpG islands (open sea). Sequences containing G-quadruplexes and RNA pseudoknots, determining the recognition by H3K27 histone methyltransferase, are hypomethylated. The presented structural DNA and co-transcriptional RNA analysis of epigenetic clock sequences, foreshadows the association of age-related methylation changes with the principle biological processes of DNA and histone methylation, splicing and chromatin silencing.
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Affiliation(s)
- Andigoni Malousi
- a Laboratory of Biological Chemistry , Medical School, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | | | - Elisavet Georgiou
- a Laboratory of Biological Chemistry , Medical School, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - Georgios Tzimagiorgis
- a Laboratory of Biological Chemistry , Medical School, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - Leda Kovatsi
- c Laboratory of Forensic Medicine & Toxicology , Medical School, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - Sofia Kouidou
- a Laboratory of Biological Chemistry , Medical School, Aristotle University of Thessaloniki , Thessaloniki , Greece
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70
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Hjort L, Martino D, Grunnet LG, Naeem H, Maksimovic J, Olsson AH, Zhang C, Ling C, Olsen SF, Saffery R, Vaag AA. Gestational diabetes and maternal obesity are associated with epigenome-wide methylation changes in children. JCI Insight 2018; 3:122572. [PMID: 30185669 DOI: 10.1172/jci.insight.122572] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/31/2018] [Indexed: 12/15/2022] Open
Abstract
Offspring of women with gestational diabetes mellitus (GDM) are at increased risk of developing metabolic disease, potentially mediated by epigenetic mechanisms. We recruited 608 GDM and 626 control offspring from the Danish National Birth Cohort, aged between 9 and 16 years. DNA methylation profiles were measured in peripheral blood of 93 GDM offspring and 95 controls using the Illumina HumanMethylation450 BeadChip. Pyrosequencing was performed for validation/replication of putative GDM-associated, differentially methylated CpGs in additional 905 offspring (462 GDM, 444 control offspring). We identified 76 differentially methylated CpGs in GDM offspring compared with controls in the discovery cohort (FDR, P < 0.05). Adjusting for offspring BMI did not affect the association between methylation levels and GDM status for any of the 76 CpGs. Most of these epigenetic changes were due to confounding by maternal prepregnancy BMI; however, 13 methylation changes were independently associated with maternal GDM. Three prepregnancy BMI-associated CpGs (cg00992687 and cg09452568 of ESM1 and cg14328641 of MS4A3) were validated in the replication cohort, while cg09109411 (PDE6A) was found to be associated with GDM status. The identified methylation changes may reflect developmental programming of organ disease mechanisms and/or may serve as disease biomarkers.
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Affiliation(s)
- Line Hjort
- Department of Endocrinology (Diabetes and Metabolism), Rigshospitalet, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,The Danish Diabetes Academy, Odense, Denmark
| | - David Martino
- Centre for Food and Allergy Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Pediatrics, Melbourne University, Melbourne, Victoria, Australia
| | - Louise Groth Grunnet
- Department of Endocrinology (Diabetes and Metabolism), Rigshospitalet, Copenhagen, Denmark.,The Danish Diabetes Academy, Odense, Denmark
| | - Haroon Naeem
- Bioinformatics Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Monash Bioinformatics Platform, Monash University, Clayton, Victoria, Australia.,Department of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Jovana Maksimovic
- Department of Pediatrics, Melbourne University, Melbourne, Victoria, Australia.,Bioinformatics Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Anders Henrik Olsson
- Department of Endocrinology (Diabetes and Metabolism), Rigshospitalet, Copenhagen, Denmark
| | - Cuilin Zhang
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Rockville, Maryland, USA
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, CRC, Scania University Hospital, Malmö, Sweden
| | | | - Richard Saffery
- Department of Pediatrics, Melbourne University, Melbourne, Victoria, Australia.,Cancer and Disease Epigenetics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Allan Arthur Vaag
- Department of Endocrinology (Diabetes and Metabolism), Rigshospitalet, Copenhagen, Denmark.,Cardiovascular and Metabolic Disease (CVMD) Translational Medicine Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
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71
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Zhou Z, Sun B, Li X, Zhu C. DNA methylation landscapes in the pathogenesis of type 2 diabetes mellitus. Nutr Metab (Lond) 2018; 15:47. [PMID: 29988495 PMCID: PMC6025823 DOI: 10.1186/s12986-018-0283-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/18/2018] [Indexed: 01/22/2023] Open
Abstract
Although genetic variations and environmental factors are vital to the development and progression of type 2 diabetes mellitus (T2DM), emerging literature suggest that epigenetics, especially DNA methylation, play a key role in the pathogenesis of T2DM by affecting insulin secretion of pancreatic β cells and the body’s resistance to insulin. Previous studies have elucidated how DNA methylation interacted with various factors in T2DM pathogenesis. This review summarized the role of related methylation genes in insulin-sensitive organs, such as pancreatic islets, skeletal muscle, liver, brain and adipose tissue, as well as peripheral blood cells, comparing the tissue similarity and specificity of methylated genes, aiming at a better understanding of the pathogenesis of T2DM and providing new ideas for the personalized treatment of this metabolism-associated disease.
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Affiliation(s)
- Zheng Zhou
- 1Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Bao Sun
- 2Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410000 China.,3Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, 410000 China
| | - Xiaoping Li
- 1Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Chunsheng Zhu
- 1Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
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72
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Slieker RC, Relton CL, Gaunt TR, Slagboom PE, Heijmans BT. Age-related DNA methylation changes are tissue-specific with ELOVL2 promoter methylation as exception. Epigenetics Chromatin 2018; 11:25. [PMID: 29848354 PMCID: PMC5975493 DOI: 10.1186/s13072-018-0191-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/21/2018] [Indexed: 12/31/2022] Open
Abstract
Background The well-established association of chronological age with changes in DNA methylation is primarily founded on the analysis of large sets of blood samples, while conclusions regarding tissue-specificity are typically based on small number of samples, tissues and CpGs. Here, we systematically investigate the tissue-specific character of age-related DNA methylation changes at the level of the CpG, functional genomic region and nearest gene in a large dataset. Results We assembled a compendium of public data, encompassing genome-wide DNA methylation data (Illumina 450k array) on 8092 samples from 16 different tissues, including 7 tissues with moderate to high sample numbers (Dataset size range 96–1202, Ntotal = 2858). In the 7 tissues (brain, buccal, liver, kidney, subcutaneous fat, monocytes and T-helper cells), we identified 7850 differentially methylated positions that gained (gain-aDMPs; cut-offs: Pbonf ≤ 0.05, effect size ≥ 2%/10 years) and 4,287 that lost DNA methylation with age (loss-aDMPs), 92% of which had not previously been reported for whole blood. The majority of all aDMPs identified occurred in one tissue only (gain-aDMPs: 85.2%; loss-aDMPs: 97.4%), an effect independent of statistical power. This striking tissue-specificity extended to both the functional genomic regions (defined by chromatin state segmentation) and the nearest gene. However, aDMPs did accumulate in regions with the same functional annotation across tissues, namely polycomb-repressed CpG islands for gain-aDMPs and regions marked by active histone modifications for loss-aDMPs. Conclusion Our analysis shows that age-related DNA methylation changes are highly tissue-specific. These results may guide the development of improved tissue-specific markers of chronological and, perhaps, biological age. Electronic supplementary material The online version of this article (10.1186/s13072-018-0191-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roderick C Slieker
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN, UK
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
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73
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Cheng Y, Monteiro C, Matos A, You J, Fraga A, Pereira C, Catalán V, Rodríguez A, Gómez-Ambrosi J, Frühbeck G, Ribeiro R, Hu P. Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity-a pilot study. Clin Epigenetics 2018; 10:54. [PMID: 29692867 PMCID: PMC5904983 DOI: 10.1186/s13148-018-0490-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022] Open
Abstract
Background Periprostatic adipose tissue (PPAT) has been recognized to associate with prostate cancer (PCa) aggressiveness and progression. Here, we sought to investigate whether excess adiposity modulates the methylome of PPAT in PCa patients. DNA methylation profiling was performed in PPAT from obese/overweight (OB/OW, BMI > 25 kg m−2) and normal weight (NW, BMI < 25 kg m−2) PCa patients. Significant differences in methylated CpGs between OB/OW and NW groups were inferred by statistical modeling. Results Five thousand five hundred twenty-six differentially methylated CpGs were identified between OB/OW and NW PCa patients with 90.2% hypermethylated. Four hundred eighty-three of these CpGs were found to be located at both promoters and CpG islands, whereas the representing 412 genes were found to be involved in pluripotency of stem cells, fatty acid metabolism, and many other biological processes; 14 of these genes, particularly FADS1, MOGAT1, and PCYT2, with promoter hypermethylation presented with significantly decreased gene expression in matched samples. Additionally, 38 genes were correlated with antigen processing and presentation of endogenous antigen via MHC class I, which might result in fatty acid accumulation in PPAT and tumor immune evasion. Conclusions Results showed that the whole epigenome methylation profiles of PPAT were significantly different in OB/OW compared to normal weight PCa patients. The epigenetic variation associated with excess adiposity likely resulted in altered lipid metabolism and immune dysregulation, contributing towards unfavorable PCa microenvironment, thus warranting further validation studies in larger samples. Electronic supplementary material The online version of this article (10.1186/s13148-018-0490-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Cheng
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada.,2Experimental Center, Northwest University for Nationalities, Lanzhou, People's Republic of China
| | - Cátia Monteiro
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,Research Department, Portuguese League Against Cancer-North, Porto, Portugal
| | - Andreia Matos
- 5Laboratory of Genetics and Environmental Health Institute, Faculty of Medicine, University of Lisboa, Lisbon, Portugal.,6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal
| | - Jiaying You
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
| | - Avelino Fraga
- 6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal.,7Department of Urology, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Carina Pereira
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,8CINTESIS, Center for Health Technology and Services Research, Faculty of Medicine, e, University of Porto, Porto, Portugal
| | - Victoria Catalán
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Amaia Rodríguez
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Gómez-Ambrosi
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Frühbeck
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain.,11Department of Endocrinology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ricardo Ribeiro
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,5Laboratory of Genetics and Environmental Health Institute, Faculty of Medicine, University of Lisboa, Lisbon, Portugal.,6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal.,12Department of Clinical Pathology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,13i3S/INEB, Instituto de Investigação e Inovação em Saúde/Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Tumor & Microenvironment Interactions, Rua Alfredo Allen, 208 4200-135 Porto, Portugal
| | - Pingzhao Hu
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
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Small KS, Todorčević M, Civelek M, El-Sayed Moustafa JS, Wang X, Simon MM, Fernandez-Tajes J, Mahajan A, Horikoshi M, Hugill A, Glastonbury CA, Quaye L, Neville MJ, Sethi S, Yon M, Pan C, Che N, Viñuela A, Tsai PC, Nag A, Buil A, Thorleifsson G, Raghavan A, Ding Q, Morris AP, Bell JT, Thorsteinsdottir U, Stefansson K, Laakso M, Dahlman I, Arner P, Gloyn AL, Musunuru K, Lusis AJ, Cox RD, Karpe F, McCarthy MI. Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition. Nat Genet 2018; 50:572-580. [PMID: 29632379 PMCID: PMC5935235 DOI: 10.1038/s41588-018-0088-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 02/15/2018] [Indexed: 12/30/2022]
Abstract
Individual risk of type 2 diabetes (T2D) is modified by perturbations to the mass, distribution and function of adipose tissue. To investigate the mechanisms underlying these associations, we explored the molecular, cellular and whole-body effects of T2D-associated alleles near KLF14. We show that KLF14 diabetes-risk alleles act in adipose tissue to reduce KLF14 expression and modulate, in trans, the expression of 385 genes. We demonstrate, in human cellular studies, that reduced KLF14 expression increases pre-adipocyte proliferation but disrupts lipogenesis, and in mice, that adipose tissue-specific deletion of Klf14 partially recapitulates the human phenotype of insulin resistance, dyslipidemia and T2D. We show that carriers of the KLF14 T2D risk allele shift body fat from gynoid stores to abdominal stores and display a marked increase in adipocyte cell size, and that these effects on fat distribution, and the T2D association, are female specific. The metabolic risk associated with variation at this imprinted locus depends on the sex both of the subject and of the parent from whom the risk allele derives.
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Affiliation(s)
- Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Marijana Todorčević
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Mete Civelek
- Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Xiao Wang
- Cardiovascular Institute, Department of Medicine, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Michelle M Simon
- Biocomputing, Medical Research Council Harwell Institute, Oxford, UK
| | | | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Momoko Horikoshi
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alison Hugill
- Genetics of Type 2 Diabetes, Medical Research Council Harwell Institute, Oxford, UK
| | - Craig A Glastonbury
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Lydia Quaye
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Matt J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Siddharth Sethi
- Biocomputing, Medical Research Council Harwell Institute, Oxford, UK
| | - Marianne Yon
- Genetics of Type 2 Diabetes, Medical Research Council Harwell Institute, Oxford, UK
| | - Calvin Pan
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nam Che
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ana Viñuela
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | | | | | - Qiurong Ding
- CAS Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Ingrid Dahlman
- Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Peter Arner
- Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Kiran Musunuru
- Cardiovascular Institute, Department of Medicine, Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Aldons J Lusis
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Roger D Cox
- Genetics of Type 2 Diabetes, Medical Research Council Harwell Institute, Oxford, UK
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK.
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Fernández-Sanlés A, Sayols-Baixeras S, Curcio S, Subirana I, Marrugat J, Elosua R. DNA Methylation and Age-Independent Cardiovascular Risk, an Epigenome-Wide Approach: The REGICOR Study (REgistre GIroní del COR). Arterioscler Thromb Vasc Biol 2018; 38:645-652. [PMID: 29326313 PMCID: PMC5823770 DOI: 10.1161/atvbaha.117.310340] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/14/2017] [Indexed: 12/31/2022]
Abstract
OBJECTIVE The objectives of this study were to decipher whether age-independent cardiovascular risk is associated with DNA methylation at 5'-cytosine-phosphate-guanine-3' (CpG) level and to determine whether these differential methylation signatures are associated with the incidence of cardiovascular events. APPROACH AND RESULTS We designed a 2-stage, cross-sectional, epigenome-wide association study. Age-independent cardiovascular risk calculation was based on vascular age and on the residuals of the relationship between age and cardiovascular risk. Blood DNA methylomes from 2 independent populations were profiled using the Infinium HumanMethylation450 BeadChip. The discovery stage of these studies was performed in the REGICOR cohort (REgistre GIroní del COR; n=645). Next, we validated the initial findings in the Framingham Offspring Study (n=2542). Eight CpGs located in 4 genes (AHRR, CPT1A, PPIF, and SBNO2) and 3 intergenic regions showed differential methylation in association with age-independent cardiovascular risk (P≤1.17×10-7). These CpGs explained 12.01% to 15.16% of the variability of age-independent cardiovascular risk in REGICOR and 7.51% to 8.53% in Framingham Offspring Study. Four of them were only related to smoking, 3 were related to smoking and body mass index, and 1 to diabetes mellitus, triglycerides levels, and body mass index (P≤7.81×10-4). In addition, we developed methylation risk scores based on these CpGs and observed an association between these scores and cardiovascular disease incidence (hazard ratio=1.32; 95% confidence interval: 1.16-1.51). CONCLUSIONS Age-independent cardiovascular risk was related to different DNA methylation profiles, with 8 CpGs showing differential methylation patterns. Most of these CpGs were associated with smoking, and 3 of them were also related to body mass index. Risk scores based on these differential methylation patterns were associated with cardiovascular events and could be useful predictive indices.
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Affiliation(s)
- Alba Fernández-Sanlés
- From the Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain (A.F.-S., S.S.-B., I.S., J.M., R.E.); Universitat Pompeu Fabra, Barcelona, Spain (A.F.-S., S.S.-B.); CIBER Cardiovascular Diseases, Barcelona, Spain (S.S.-B., J.M., R.E.); CIBER Epidemiology and Public Health (CIBERESP), Barcelona, Spain (I.S.); Centro Universitario de Investigación, Innovación y Diagnóstico Arterial (CUiiDARTE), Physiology Department, School of Medicine, Republic University, Montevideo, Uruguay (S.C.); and Medical School, University of Vic-Central University of Catalonia, Barcelona, Spain (R.E.)
| | - Sergi Sayols-Baixeras
- From the Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain (A.F.-S., S.S.-B., I.S., J.M., R.E.); Universitat Pompeu Fabra, Barcelona, Spain (A.F.-S., S.S.-B.); CIBER Cardiovascular Diseases, Barcelona, Spain (S.S.-B., J.M., R.E.); CIBER Epidemiology and Public Health (CIBERESP), Barcelona, Spain (I.S.); Centro Universitario de Investigación, Innovación y Diagnóstico Arterial (CUiiDARTE), Physiology Department, School of Medicine, Republic University, Montevideo, Uruguay (S.C.); and Medical School, University of Vic-Central University of Catalonia, Barcelona, Spain (R.E.)
| | - Santiago Curcio
- From the Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain (A.F.-S., S.S.-B., I.S., J.M., R.E.); Universitat Pompeu Fabra, Barcelona, Spain (A.F.-S., S.S.-B.); CIBER Cardiovascular Diseases, Barcelona, Spain (S.S.-B., J.M., R.E.); CIBER Epidemiology and Public Health (CIBERESP), Barcelona, Spain (I.S.); Centro Universitario de Investigación, Innovación y Diagnóstico Arterial (CUiiDARTE), Physiology Department, School of Medicine, Republic University, Montevideo, Uruguay (S.C.); and Medical School, University of Vic-Central University of Catalonia, Barcelona, Spain (R.E.)
| | - Isaac Subirana
- From the Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain (A.F.-S., S.S.-B., I.S., J.M., R.E.); Universitat Pompeu Fabra, Barcelona, Spain (A.F.-S., S.S.-B.); CIBER Cardiovascular Diseases, Barcelona, Spain (S.S.-B., J.M., R.E.); CIBER Epidemiology and Public Health (CIBERESP), Barcelona, Spain (I.S.); Centro Universitario de Investigación, Innovación y Diagnóstico Arterial (CUiiDARTE), Physiology Department, School of Medicine, Republic University, Montevideo, Uruguay (S.C.); and Medical School, University of Vic-Central University of Catalonia, Barcelona, Spain (R.E.)
| | - Jaume Marrugat
- From the Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain (A.F.-S., S.S.-B., I.S., J.M., R.E.); Universitat Pompeu Fabra, Barcelona, Spain (A.F.-S., S.S.-B.); CIBER Cardiovascular Diseases, Barcelona, Spain (S.S.-B., J.M., R.E.); CIBER Epidemiology and Public Health (CIBERESP), Barcelona, Spain (I.S.); Centro Universitario de Investigación, Innovación y Diagnóstico Arterial (CUiiDARTE), Physiology Department, School of Medicine, Republic University, Montevideo, Uruguay (S.C.); and Medical School, University of Vic-Central University of Catalonia, Barcelona, Spain (R.E.)
| | - Roberto Elosua
- From the Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain (A.F.-S., S.S.-B., I.S., J.M., R.E.); Universitat Pompeu Fabra, Barcelona, Spain (A.F.-S., S.S.-B.); CIBER Cardiovascular Diseases, Barcelona, Spain (S.S.-B., J.M., R.E.); CIBER Epidemiology and Public Health (CIBERESP), Barcelona, Spain (I.S.); Centro Universitario de Investigación, Innovación y Diagnóstico Arterial (CUiiDARTE), Physiology Department, School of Medicine, Republic University, Montevideo, Uruguay (S.C.); and Medical School, University of Vic-Central University of Catalonia, Barcelona, Spain (R.E.).
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Davegårdh C, García-Calzón S, Bacos K, Ling C. DNA methylation in the pathogenesis of type 2 diabetes in humans. Mol Metab 2018; 14:12-25. [PMID: 29496428 PMCID: PMC6034041 DOI: 10.1016/j.molmet.2018.01.022] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 02/08/2023] Open
Abstract
Background Type 2 diabetes (T2D) is a multifactorial, polygenic disease caused by impaired insulin secretion and insulin resistance. Genome-wide association studies (GWAS) were expected to resolve a large part of the genetic component of diabetes; yet, the single nucleotide polymorphisms identified by GWAS explain less than 20% of the estimated heritability for T2D. There was subsequently a need to look elsewhere to find disease-causing factors. Mechanisms mediating the interaction between environmental factors and the genome, such as epigenetics, may be of particular importance in the pathogenesis of T2D. Scope of Review This review summarizes knowledge of the impact of epigenetics on the pathogenesis of T2D in humans. In particular, the review will focus on alterations in DNA methylation in four human tissues of importance for the disease; pancreatic islets, skeletal muscle, adipose tissue, and the liver. Case–control studies and studies examining the impact of non-genetic and genetic risk factors on DNA methylation in humans will be considered. These studies identified epigenetic changes in tissues from subjects with T2D versus non-diabetic controls. They also demonstrate that non-genetic factors associated with T2D such as age, obesity, energy rich diets, physical activity and the intrauterine environment impact the epigenome in humans. Additionally, interactions between genetics and epigenetics seem to influence the pathogenesis of T2D. Conclusions Overall, previous studies by our group and others support a key role for epigenetics in the growing incidence of T2D.
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Affiliation(s)
- Cajsa Davegårdh
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden.
| | - Sonia García-Calzón
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden
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Walaszczyk E, Luijten M, Spijkerman AMW, Bonder MJ, Lutgers HL, Snieder H, Wolffenbuttel BHR, van Vliet-Ostaptchouk JV. DNA methylation markers associated with type 2 diabetes, fasting glucose and HbA 1c levels: a systematic review and replication in a case-control sample of the Lifelines study. Diabetologia 2018; 61:354-368. [PMID: 29164275 PMCID: PMC6448925 DOI: 10.1007/s00125-017-4497-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/13/2017] [Indexed: 12/21/2022]
Abstract
AIMS/HYPOTHESIS Epigenetic mechanisms may play an important role in the aetiology of type 2 diabetes. Recent epigenome-wide association studies (EWASs) identified several DNA methylation markers associated with type 2 diabetes, fasting glucose and HbA1c levels. Here we present a systematic review of these studies and attempt to replicate the CpG sites (CpGs) with the most significant associations from these EWASs in a case-control sample of the Lifelines study. METHODS We performed a systematic literature search in PubMed and EMBASE for EWASs to test the association between DNA methylation and type 2 diabetes and/or glycaemic traits and reviewed the search results. For replication purposes we selected 100 unique CpGs identified in peripheral blood, pancreas, adipose tissue and liver from 15 EWASs, using study-specific Bonferroni-corrected significance thresholds. Methylation data (Illumina 450K array) in whole blood from 100 type 2 diabetic individuals and 100 control individuals from the Lifelines study were available. Multivariate linear models were used to examine the associations of the specific CpGs with type 2 diabetes and glycaemic traits. RESULTS From the 52 CpGs identified in blood and selected for replication, 15 CpGs showed nominally significant associations with type 2 diabetes in the Lifelines sample (p < 0.05). The results for five CpGs (in ABCG1, LOXL2, TXNIP, SLC1A5 and SREBF1) remained significant after a stringent multiple-testing correction (changes in methylation from -3% up to 3.6%, p < 0.0009). All associations were directionally consistent with the original EWAS results. None of the selected CpGs from the tissue-specific EWASs were replicated in our methylation data from whole blood. We were also unable to replicate any of the CpGs associated with HbA1c levels in the healthy control individuals of our sample, while two CpGs (in ABCG1 and CCDC57) for fasting glucose were replicated at a nominal significance level (p < 0.05). CONCLUSIONS/INTERPRETATION A number of differentially methylated CpGs reported to be associated with type 2 diabetes in the EWAS literature were replicated in blood and show promise for clinical use as disease biomarkers. However, more prospective studies are needed to support the robustness of these findings.
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Affiliation(s)
- Eliza Walaszczyk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Mirjam Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Marc J Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Helen L Lutgers
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, HPC AA31, P.O. Box 30001, 9700 RB, Groningen, the Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bruce H R Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, HPC AA31, P.O. Box 30001, 9700 RB, Groningen, the Netherlands
| | - Jana V van Vliet-Ostaptchouk
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, HPC AA31, P.O. Box 30001, 9700 RB, Groningen, the Netherlands.
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Gillman AS, Gardiner CK, Koljack CE, Bryan AD. Body mass index, diet, and exercise: testing possible linkages to breast cancer risk via DNA methylation. Breast Cancer Res Treat 2018; 168:241-248. [PMID: 29127590 PMCID: PMC5823732 DOI: 10.1007/s10549-017-4573-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Abstract
PURPOSE To examine DNA methylation as a mechanism linking diet, physical activity, weight status, and breast cancer risk. METHODS Insufficiently active women of varying weight status, without a history of cancer, completed a maximal exercise test, clinical measurement of height and weight, and a dietary intake measure. They also provided blood samples, which were analyzed to ascertain average methylation of candidate genes related to breast cancer (BRCA1, RUNX3, GALNT9, and PAX6) and inflammation (TLR4 and TLR6). RESULTS Elevated weight status (r = - .18, p < .05) and poorer aerobic fitness (r = .24, p < .01) were each associated with decreased methylation of inflammation genes. Methylation of inflammation genes statistically mediated the relationship between weight status and cancer gene methylation (standardized indirect effect = .12, p < .05) as well as between cardiorespiratory fitness and cancer gene methylation (standardized indirect effect = - .172, p < .01). However, recent dietary behavior was not associated with methylation of either inflammation or cancer genes. CONCLUSIONS Both weight status and cardiovascular fitness are associated with methylation of genes associated with both inflammation and cancer. Methylation of inflammatory genes might serve as a mechanistic link between lifestyle factors and methylation changes in genes that increase risk for breast cancer.
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Affiliation(s)
- Arielle S Gillman
- Department of Psychology& Neuroscience, University of Colorado Boulder, Muenzinger D244, 345 UCB, Boulder, CO, 80309-0345, USA.
| | - Casey K Gardiner
- Department of Psychology& Neuroscience, University of Colorado Boulder, Muenzinger D244, 345 UCB, Boulder, CO, 80309-0345, USA
| | - Claire E Koljack
- Department of Psychology& Neuroscience, University of Colorado Boulder, Muenzinger D244, 345 UCB, Boulder, CO, 80309-0345, USA
| | - Angela D Bryan
- Department of Psychology& Neuroscience, University of Colorado Boulder, Muenzinger D244, 345 UCB, Boulder, CO, 80309-0345, USA
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Kokosar M, Benrick A, Perfilyev A, Nilsson E, Källman T, Ohlsson C, Ling C, Stener-Victorin E. A Single Bout of Electroacupuncture Remodels Epigenetic and Transcriptional Changes in Adipose Tissue in Polycystic Ovary Syndrome. Sci Rep 2018; 8:1878. [PMID: 29382850 PMCID: PMC5790004 DOI: 10.1038/s41598-017-17919-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022] Open
Abstract
A single bout of electroacupuncture results in muscle contractions and increased whole body glucose uptake in women with polycystic ovary syndrome (PCOS). Women with PCOS have transcriptional and epigenetic alterations in the adipose tissue and we hypothesized that electroacupuncture induces epigenetic and transcriptional changes to restore metabolic alterations. Twenty-one women with PCOS received a single bout of electroacupuncture, which increased the whole body glucose uptake. In subcutaneous adipose tissue biopsies, we identified treatment-induced expression changes of 2369 genes (Q < 0.05) and DNA methylation changes of 7055 individual genes (Q = 0.11). The largest increase in expression was observed for FOSB (2405%), and the largest decrease for LOC100128899 (54%). The most enriched pathways included Acute phase response signaling and LXR/RXR activation. The DNA methylation changes ranged from 1-16%, and 407 methylation sites correlated with gene expression. Among genes known to be differentially expressed in PCOS, electroacupuncture reversed the expression of 80 genes, including PPARγ and ADIPOR2. Changes in the expression of Nr4a2 and Junb are reversed by adrenergic blockers in rats demonstrating that changes in gene expression, in part, is due to activation of the sympathetic nervous system. In conclusion, low-frequency electroacupuncture with muscle contractions remodels epigenetic and transcriptional changes that elicit metabolic improvement.
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Affiliation(s)
- Milana Kokosar
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Benrick
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- School of Health and Education, University of Skövde, Skövde, Sweden
| | - Alexander Perfilyev
- Epigenetics and Diabetes, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Clinical Research Centre, Scania University Hospital, Malmö, Sweden
| | - Emma Nilsson
- Epigenetics and Diabetes, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Clinical Research Centre, Scania University Hospital, Malmö, Sweden
| | - Thomas Källman
- Department of Medical Biochemistry and Microbiology, NBIS - National Bioinformatics Infrastructure Sweden, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Clinical Research Centre, Scania University Hospital, Malmö, Sweden
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Xu K, Zhang X, Wang Z, Hu Y, Sinha R. Epigenome-wide association analysis revealed that SOCS3 methylation influences the effect of cumulative stress on obesity. Biol Psychol 2018; 131:63-71. [PMID: 27826092 PMCID: PMC5419875 DOI: 10.1016/j.biopsycho.2016.11.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 10/03/2016] [Accepted: 11/03/2016] [Indexed: 12/20/2022]
Abstract
Chronic stress has a significant impact on obesity. However, how stress influences obesity remains unclear. We conducted an epigenome-wide DNA methylation association analysis of obesity (N=510) and examined whether cumulative stress influenced the DNA methylation on body weight. We identified 20 CpG sites associated with body mass index at the false discovery rate q<0.05, including a novel site, cg18181703, in suppressor of cytokine signaling 3 (SOCS3) gene (coefficient β=-0.0022, FDR q=4.94×10-5). The interaction between cg18181703 and cumulative adverse life stress contributed to variations in body weight (p=0.002). Individuals with at least five major life events and lower methylation of cg1818703 showed a 1.38-fold higher risk of being obese (95%CI: 1.17-1.76). Our findings suggest that aberrant in DNA methylation is associated with body weight and that methylation of SOCS3 moderates the effect of cumulative stress on obesity.
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Affiliation(s)
- Ke Xu
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT 06511, United States; Connecticut Veteran Health System, 950 Campbell Ave, Building 35, Room #43, West Haven, 06516, United States.
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT 06511, United States; Connecticut Veteran Health System, 950 Campbell Ave, Building 35, Room #43, West Haven, 06516, United States
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06511, United States
| | - Ying Hu
- Yale Stress Center, Yale University, 2 Church St S #209, New Haven, CT 06519, United States
| | - Rajita Sinha
- Department of Psychiatry, Yale School of Medicine, 300 George street, Suite 901, New Haven, CT 06511, United States; Center for Biomedical Informatics and Information Technology, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, United States
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81
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Keating ST, van Diepen JA, Riksen NP, El-Osta A. Epigenetics in diabetic nephropathy, immunity and metabolism. Diabetologia 2018; 61:6-20. [PMID: 29128937 PMCID: PMC6448927 DOI: 10.1007/s00125-017-4490-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/22/2017] [Indexed: 01/01/2023]
Abstract
When it comes to the epigenome, there is a fine line between clarity and confusion-walk that line and you will discover another fascinating level of transcription control. With the genetic code representing the cornerstone of rules for information that is encoded to proteins somewhere above the genome level there is a set of rules by which chemical information is also read. These epigenetic modifications show a different side of the genetic code that is diverse and regulated, hence modifying genetic transcription transiently, ranging from short- to long-term alterations. While this complexity brings exquisite control it also poses a formidable challenge to efforts to decode mechanisms underlying complex disease. Recent technological and computational advances have improved unbiased acquisition of epigenomic patterns to improve our understanding of the complex chromatin landscape. Key to resolving distinct chromatin signatures of diabetic complications is the identification of the true physiological targets of regulatory proteins, such as reader proteins that recognise, writer proteins that deposit and eraser proteins that remove specific chemical moieties. But how might a diverse group of proteins regulate the diabetic landscape from an epigenomic perspective? Drawing from an ever-expanding compendium of experimental and clinical studies, this review details the current state-of-play and provides a perspective of chromatin-dependent mechanisms implicated in diabetic complications, with a special focus on diabetic nephropathy. We hypothesise a codified signature of the diabetic epigenome and provide examples of prime candidates for chemical modification. As for the pharmacological control of epigenetic marks, we explore future strategies to expedite and refine the search for clinically relevant discoveries. We also consider the challenges associated with therapeutic strategies targeting epigenetic pathways.
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Affiliation(s)
- Samuel T Keating
- Department of Internal Medicine, Department of Internal Medicine (463), Radboud University Medical Center, Nijmegen, PO Box 9101, 6500 HB, Nijmegen, the Netherlands.
| | - Janna A van Diepen
- Department of Internal Medicine, Department of Internal Medicine (463), Radboud University Medical Center, Nijmegen, PO Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine, Department of Internal Medicine (463), Radboud University Medical Center, Nijmegen, PO Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Assam El-Osta
- Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC, 3004, Australia.
- Department of Pathology, The University of Melbourne, Parkville, VIC, Australia.
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, China.
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De Rosa S, Arcidiacono B, Chiefari E, Brunetti A, Indolfi C, Foti DP. Type 2 Diabetes Mellitus and Cardiovascular Disease: Genetic and Epigenetic Links. Front Endocrinol (Lausanne) 2018; 9:2. [PMID: 29387042 PMCID: PMC5776102 DOI: 10.3389/fendo.2018.00002] [Citation(s) in RCA: 187] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/03/2018] [Indexed: 12/14/2022] Open
Abstract
Type 2 diabetes mellitus (DM) is a common metabolic disorder predisposing to diabetic cardiomyopathy and atherosclerotic cardiovascular disease (CVD), which could lead to heart failure through a variety of mechanisms, including myocardial infarction and chronic pressure overload. Pathogenetic mechanisms, mainly linked to hyperglycemia and chronic sustained hyperinsulinemia, include changes in metabolic profiles, intracellular signaling pathways, energy production, redox status, increased susceptibility to ischemia, and extracellular matrix remodeling. The close relationship between type 2 DM and CVD has led to the common soil hypothesis, postulating that both conditions share common genetic and environmental factors influencing this association. However, although the common risk factors of both CVD and type 2 DM, such as obesity, insulin resistance, dyslipidemia, inflammation, and thrombophilia, can be identified in the majority of affected patients, less is known about how these factors influence both conditions, so that efforts are still needed for a more comprehensive understanding of this relationship. The genetic, epigenetic, and environmental backgrounds of both type 2 DM and CVD have been more recently studied and updated. However, the underlying pathogenetic mechanisms have seldom been investigated within the broader shared background, but rather studied in the specific context of type 2 DM or CVD, separately. As the precise pathophysiological links between type 2 DM and CVD are not entirely understood and many aspects still require elucidation, an integrated description of the genetic, epigenetic, and environmental influences involved in the concomitant development of both diseases is of paramount importance to shed new light on the interlinks between type 2 DM and CVD. This review addresses the current knowledge of overlapping genetic and epigenetic aspects in type 2 DM and CVD, including microRNAs and long non-coding RNAs, whose abnormal regulation has been implicated in both disease conditions, either etiologically or as cause for their progression. Understanding the links between these disorders may help to drive future research toward an integrated pathophysiological approach and to provide future directions in the field.
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Affiliation(s)
- Salvatore De Rosa
- Department of Medical and Surgical Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Biagio Arcidiacono
- Department of Health Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Eusebio Chiefari
- Department of Health Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Antonio Brunetti
- Department of Health Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Antonio Brunetti, ; Ciro Indolfi, ; Daniela P. Foti,
| | - Ciro Indolfi
- Department of Medical and Surgical Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Antonio Brunetti, ; Ciro Indolfi, ; Daniela P. Foti,
| | - Daniela P. Foti
- Department of Health Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Antonio Brunetti, ; Ciro Indolfi, ; Daniela P. Foti,
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83
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Zhang X, Hu Y, Justice AC, Li B, Wang Z, Zhao H, Krystal JH, Xu K. DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty. Nat Commun 2017; 8:2243. [PMID: 29269866 PMCID: PMC5740109 DOI: 10.1038/s41467-017-02326-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/20/2017] [Indexed: 01/13/2023] Open
Abstract
Intravenous illicit drug use (IDU) and hepatitis C infection (HCV) commonly co-occur among HIV-infected individuals. These co-occurring conditions may produce interacting epigenetic effects in white blood cells that influence immune function and health outcomes. Here, we report an epigenome-wide association analysis comparing IDU+/ HCV+ and IDU-/HCV- in 386 HIV-infected individuals as a discovery sample and in 412 individuals as a replication sample. We observe 6 significant CpGs in the promoters of 4 genes, NLRC5, TRIM69, CX3CR1, and BCL9, in the discovery sample and in meta-analysis. We identify 19 differentially methylated regions on chromosome 6 harboring MHC gene clusters. Importantly, a panel of IDU+/HCV+-associated CpGs discriminated HIV frailty based upon a validated index with an area under the curve of 79.3% for high frailty and 82.3% for low frailty. These findings suggest that IDU and HCV involve epigenetic programming and that their associated methylation signatures discriminate HIV pathophysiologic frailty.
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Affiliation(s)
- Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Ying Hu
- National Cancer Institute Center for Biomedical Information & Information Technology, 9609 Medical Center Drive, Bethesda, MD, 20850, USA
| | - Amy C Justice
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA
- Yale University School of Medicine, New Haven Veterans Affairs Connecticut Healthcare System, New Haven, CT, 06516, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA.
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA.
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84
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Karlsson Linnér R, Marioni RE, Rietveld CA, Simpkin AJ, Davies NM, Watanabe K, Armstrong NJ, Auro K, Baumbach C, Jan Bonder M, Buchwald J, Fiorito G, Ismail K, Iurato S, Joensuu A, Karell P, Kasela S, Lahti J, McRae AF, Mandaviya PR, Seppälä I, Wang Y, Baglietto L, Binder EB, Harris SE, Hodge AM, Horvath S, Hurme M, Johannesson M, Latvala A, Mather KA, Medland SE, Metspalu A, Milani L, Milne RL, Pattie A, Pedersen NL, Peters A, Polidoro S, Räikkönen K, Severi G, Starr JM, Stolk L, Waldenberger M, Eriksson JG, Esko T, Franke L, Gieger C, Giles GG, Hägg S, Jousilahti P, Kaprio J, Kähönen M, Lehtimäki T, Martin NG, van Meurs JBC, Ollikainen M, Perola M, Posthuma D, Raitakari OT, Sachdev PS, Taskesen E, Uitterlinden AG, Vineis P, Wijmenga C, Wright MJ, Relton C, Davey Smith G, Deary IJ, Koellinger PD, Benjamin DJ. An epigenome-wide association study meta-analysis of educational attainment. Mol Psychiatry 2017; 22:1680-1690. [PMID: 29086770 PMCID: PMC6372242 DOI: 10.1038/mp.2017.210] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/16/2017] [Accepted: 08/21/2017] [Indexed: 01/29/2023]
Abstract
The epigenome is associated with biological factors, such as disease status, and environmental factors, such as smoking, alcohol consumption and body mass index. Although there is a widespread perception that environmental influences on the epigenome are pervasive and profound, there has been little evidence to date in humans with respect to environmental factors that are biologically distal. Here we provide evidence on the associations between epigenetic modifications-in our case, CpG methylation-and educational attainment (EA), a biologically distal environmental factor that is arguably among the most important life-shaping experiences for individuals. Specifically, we report the results of an epigenome-wide association study meta-analysis of EA based on data from 27 cohort studies with a total of 10 767 individuals. We find nine CpG probes significantly associated with EA. However, robustness analyses show that all nine probes have previously been found to be associated with smoking. Only two associations remain when we perform a sensitivity analysis in the subset of never-smokers, and these two probes are known to be strongly associated with maternal smoking during pregnancy, and thus their association with EA could be due to correlation between EA and maternal smoking. Moreover, the effect sizes of the associations with EA are far smaller than the known associations with the biologically proximal environmental factors alcohol consumption, body mass index, smoking and maternal smoking during pregnancy. Follow-up analyses that combine the effects of many probes also point to small methylation associations with EA that are highly correlated with the combined effects of smoking. If our findings regarding EA can be generalized to other biologically distal environmental factors, then they cast doubt on the hypothesis that such factors have large effects on the epigenome.
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Affiliation(s)
- Richard Karlsson Linnér
- Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, Center for Neurogenomics and Cognitive Research, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
- Institute for Behavior and Biology, Erasmus University Rotterdam, P.O. Box 1738, 3000 DR, Rotterdam, the Netherlands
| | - Riccardo E Marioni
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Cornelius A Rietveld
- Institute for Behavior and Biology, Erasmus University Rotterdam, P.O. Box 1738, 3000 DR, Rotterdam, the Netherlands
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, Burgemeester Oudlaan 50, Rotterdam, 3062 PA, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Andrew J Simpkin
- MRC Intergrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Barley House, Oakfield Grove, Bristol, BS28BN, United Kingdom
| | - Neil M Davies
- MRC Intergrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Barley House, Oakfield Grove, Bristol, BS28BN, United Kingdom
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, Center for Neurogenomics and Cognitive Research, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
| | - Nicola J Armstrong
- Mathematics and Statistics, Murdoch University, 90 South St., Murdoch, 6150, WA, Australia
| | - Kirsi Auro
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
- National Institute for Health and Welfare, Genomics and Biomarkers, PO Box 30, Helsinki, FI-00271, Finland
| | - Clemens Baumbach
- Research Unit of Molecular Epidemiology (AME), Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Munich, Germany, Neuherberg, 85764, Germany
| | - Marc Jan Bonder
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jadwiga Buchwald
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Giovanni Fiorito
- Molecular and genetic epidemiology unit, Human Genetics Foundation Torino (HuGeF), Via Nizza 52, Turin, 10126, Italy
- Department of Medical Sciences, University of Torino, Corso Dogliotti 14
| | - Khadeeja Ismail
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Stella Iurato
- Department Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany, Kraepelinstr. 2-10, Munich, 80804, Germany
| | - Anni Joensuu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
- National Institute for Health and Welfare, Genomics and Biomarkers, PO Box 30, Helsinki, FI-00271, Finland
| | - Pauliina Karell
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Silva Kasela
- Estonian Genome Center, University of Tartu, Riia 23B, Tartu, 51010, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu, 51010, Estonia
| | - Jari Lahti
- Institute of Behavioural Studies, Siltavuorenpenger 1A, University of Helsinki, Helsinki, FI-00014, Finland
- Collegium for Advanced Studies, University of Helsinki, Helsinki, FI-00014, Finland
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD
| | - Pooja R Mandaviya
- Department of Clinical Chemistry, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - Yunzhang Wang
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, Stockholm, 17177, Sweden
| | - Laura Baglietto
- Centre for Research in Epidemiology and Population Health, Inserm (Institut National de la Santé et de la Recherche Médicale), 114 rue Edouard Vaillant, Villejuif, 94805, France
| | - Elisabeth B Binder
- Department Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany, Kraepelinstr. 2-10, Munich, 80804, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, USA
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Allison M Hodge
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, 3004, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Level 3, 207 Bouverie Street, Carlton, Melbourne, 3010, Victoria, Australia
| | - Steve Horvath
- Human Genetics and Biostatistics, University of California Los Angeles, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
| | - Mikko Hurme
- Department of Microbiology and Immunology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
- Gerontology Research Center, University of Tampere, Tampere 33014, Finland
- Fimlab Laboratories, Tampere 33520, Finland
| | - Magnus Johannesson
- Department of Economics, Stockholm School of Economics, Box 6501, Stockholm, 11383, Sweden
| | - Antti Latvala
- Department of Public Health, University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Karen A Mather
- Centre for Healthy Brain Ageing, Psychiatry, UNSW Australia, High St., Sydney, NSW 2052, Australia
| | - Sarah E Medland
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Rd., Herston, QLD 4006, Australia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Riia 23B, Tartu, 51010, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu, 51010, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Riia 23B, Tartu, 51010, Estonia
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, 3004, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Level 3, 207 Bouverie Street, Carlton, Melbourne, 3010, Victoria, Australia
| | - Alison Pattie
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
| | - Nancy L Pedersen
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, Stockholm, 17177, Sweden
| | - Annette Peters
- Research Unit of Molecular Epidemiology (AME), Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Munich, Germany, Neuherberg, 85764, Germany
| | - Silvia Polidoro
- Molecular and genetic epidemiology unit, Human Genetics Foundation Torino (HuGeF), Via Nizza 52, Turin, 10126, Italy
| | - Katri Räikkönen
- Institute of Behavioural Studies, Siltavuorenpenger 1A, University of Helsinki, Helsinki, FI-00014, Finland
| | - Gianluca Severi
- Molecular and genetic epidemiology unit, Human Genetics Foundation Torino (HuGeF), Via Nizza 52, Turin, 10126, Italy
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, 3004, Victoria, Australia
- Centre for Research in Epidemiology and Population Health (CESP), Inserm (Institut National de la Santé et de la Recherche Médicale), 28 Rue Laennec, Lyon, 69373, France
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
| | - Lisette Stolk
- Department of Clinical Chemistry, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
- Netherlands Consortium for Healthy Ageing, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology (AME), Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Munich, Germany, Neuherberg, 85764, Germany
| | | | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Tukholmankatu 8 B, Helsinki, FI-00014, Finland
- National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Riia 23B, Tartu, 51010, Estonia
- Program in Medical and Population Genetics, Broad Institute, 415 Main St., Cambridge, MA 02142, USA
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Christian Gieger
- Research Unit of Molecular Epidemiology (AME), Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Munich, Germany, Neuherberg, 85764, Germany
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, 3004, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Level 3, 207 Bouverie Street, Carlton, Melbourne, 3010, Victoria, Australia
| | - Sara Hägg
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, Stockholm, 17177, Sweden
| | - Pekka Jousilahti
- National Institute for Health and Welfare, Genomics and Biomarkers, PO Box 30, Helsinki, FI-00271, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
- Department of Public Health, University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33521, Finland
- Department of Clinical Physiology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, QLD 4006, Australia
| | - Joyce B C van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
- Netherlands Consortium for Healthy Ageing, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
- Department of Public Health, University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
- National Institute for Health and Welfare, Genomics and Biomarkers, PO Box 30, Helsinki, FI-00271, Finland
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, Center for Neurogenomics and Cognitive Research, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20521, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20014, Finland
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, Psychiatry, UNSW Australia, High St., Sydney, NSW 2052, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, Barker St. Randwick
| | - Erdogan Taskesen
- Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, Center for Neurogenomics and Cognitive Research, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
- VU University Medical Center (VUMC), Alzheimer Center, Department of Neurology, Amsterdam, the Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
- Netherlands Consortium for Healthy Ageing, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
| | - Paolo Vineis
- Molecular and genetic epidemiology unit, Human Genetics Foundation Torino (HuGeF), Via Nizza 52, Turin, 10126, Italy
- MRC/PHE Centre for Environment and Health, School of Public Health, Imperial College London, St Mary’s Campus, Norfolk Place, London, W2 1PG, United Kingdom
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Margaret J Wright
- Queensland Brain Institute and Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Caroline Relton
- MRC Intergrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Barley House, Oakfield Grove, Bristol, BS28BN, United Kingdom
| | - George Davey Smith
- MRC Intergrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Barley House, Oakfield Grove, Bristol, BS28BN, United Kingdom
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
| | - Philipp D Koellinger
- Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, Center for Neurogenomics and Cognitive Research, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
- Institute for Behavior and Biology, Erasmus University Rotterdam, P.O. Box 1738, 3000 DR, Rotterdam, the Netherlands
| | - Daniel J Benjamin
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA 90089-3332, USA
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Sayols-Baixeras S, Subirana I, Fernández-Sanlés A, Sentí M, Lluís-Ganella C, Marrugat J, Elosua R. DNA methylation and obesity traits: An epigenome-wide association study. The REGICOR study. Epigenetics 2017; 12:909-916. [PMID: 29099282 DOI: 10.1080/15592294.2017.1363951] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Obesity is associated with increased risk of several diseases and has become epidemic. Obesity is highly heritable but the genetic variants identified by genome-wide association studies explain only limited variability. Epigenetics could contribute to explain the missing variability. The study aim was to discover differential methylation patterns related to obesity. We designed an epigenome-wide association study with a discovery phase in a subsample of 641 REGICOR study participants, validated by analysis of 2,515 participants in the Framingham Offspring Study. Blood DNA methylation was assessed using Illumina HumanMethylation450 BeadChip. Next, we meta-analyzed the data using the fixed effects method and performed a functional and pathway analysis using the Ingenuity Pathway Analysis software. We were able to validate 94 CpGs associated with body mass index (BMI) and 49 CpGs associated with waist circumference, located in 95 loci. In addition, we newly discovered 70 CpGs associated with BMI and 33 CpGs related to waist circumference. These CpGs explained 25.94% and 29.22% of the variability of BMI and waist circumference, respectively, in the REGICOR sample. We also evaluated 65 of the 95 validated loci in the GIANT genome-wide association data; 10 of them had Tag SNPs associated with BMI. The top-ranked diseases and functions identified in the functional and pathway analysis were neurologic, psychological, endocrine, and metabolic.
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Affiliation(s)
- Sergi Sayols-Baixeras
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain.,b Universitat Pompeu Fabra (UPF) , Barcelona , Catalonia , Spain.,c CIBER Cardiovascular diseases (CIBERCV) , Barcelona , Catalonia , Spain
| | - Isaac Subirana
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain.,d CIBER Epidemiology and Public Health (CIBERESP) , Barcelona , Catalonia , Spain
| | - Alba Fernández-Sanlés
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain.,b Universitat Pompeu Fabra (UPF) , Barcelona , Catalonia , Spain
| | - Mariano Sentí
- b Universitat Pompeu Fabra (UPF) , Barcelona , Catalonia , Spain.,c CIBER Cardiovascular diseases (CIBERCV) , Barcelona , Catalonia , Spain
| | - Carla Lluís-Ganella
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain
| | - Jaume Marrugat
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain.,c CIBER Cardiovascular diseases (CIBERCV) , Barcelona , Catalonia , Spain
| | - Roberto Elosua
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain.,c CIBER Cardiovascular diseases (CIBERCV) , Barcelona , Catalonia , Spain
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86
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Cheng Z, Zheng L, Almeida FA. Epigenetic reprogramming in metabolic disorders: nutritional factors and beyond. J Nutr Biochem 2017; 54:1-10. [PMID: 29154162 DOI: 10.1016/j.jnutbio.2017.10.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/26/2017] [Accepted: 10/10/2017] [Indexed: 12/13/2022]
Abstract
Environmental factors (e.g., malnutrition and physical inactivity) contribute largely to metabolic disorders including obesity, type 2 diabetes, cardiometabolic disease and nonalcoholic fatty liver diseases. The abnormalities in metabolic activity and pathways have been increasingly associated with altered DNA methylation, histone modification and noncoding RNAs, whereas lifestyle interventions targeting diet and physical activity can reverse the epigenetic and metabolic changes. Here we review recent evidence primarily from human studies that links DNA methylation reprogramming to metabolic derangements or improvements, with a focus on cross-tissue (e.g., the liver, skeletal muscle, pancreas, adipose tissue and blood samples) epigenetic markers, mechanistic mediators of the epigenetic reprogramming, and the potential of using epigenetic traits to predict disease risk and intervention response. The challenges in epigenetic studies addressing the mechanisms of metabolic diseases and future directions are also discussed and prospected.
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Affiliation(s)
- Zhiyong Cheng
- Department of Human Nutrition, Foods, and Exercise, Fralin Translational Obesity Research Center, College of Agriculture and Life Science, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Louise Zheng
- Department of Human Nutrition, Foods, and Exercise, Fralin Translational Obesity Research Center, College of Agriculture and Life Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Fabio A Almeida
- Department of Health Promotion, Social & Behavioral Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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87
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Nilsson E, Ling C. DNA methylation links genetics, fetal environment, and an unhealthy lifestyle to the development of type 2 diabetes. Clin Epigenetics 2017; 9:105. [PMID: 29026446 PMCID: PMC5627472 DOI: 10.1186/s13148-017-0399-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/29/2017] [Indexed: 01/09/2023] Open
Abstract
Type 2 diabetes is a complex trait with both environmental and hereditary factors contributing to the overall pathogenesis. One link between genes, environment, and disease is epigenetics influencing gene transcription and, consequently, organ function. Genome-wide studies have shown altered DNA methylation in tissues important for glucose homeostasis including pancreas, liver, skeletal muscle, and adipose tissue from subjects with type 2 diabetes compared with nondiabetic controls. Factors predisposing for type 2 diabetes including an adverse intrauterine environment, increasing age, overweight, physical inactivity, a family history of the disease, and an unhealthy diet have all shown to affect the DNA methylation pattern in target tissues for insulin resistance in humans. Epigenetics including DNA methylation may therefore improve our understanding of the type 2 diabetes pathogenesis, contribute to development of novel treatments, and be a useful tool to identify individuals at risk for developing the disease.
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Affiliation(s)
- Emma Nilsson
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Scania University Hospital, Jan Waldenströms gata 35, 205 02 Malmö, Sweden
| | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Scania University Hospital, Jan Waldenströms gata 35, 205 02 Malmö, Sweden
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88
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DNA methylation in blood from neonatal screening cards and the association with BMI and insulin sensitivity in early childhood. Int J Obes (Lond) 2017; 42:28-35. [PMID: 29064478 DOI: 10.1038/ijo.2017.228] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/13/2017] [Accepted: 08/27/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND/OBJECTIVES There is increasing evidence that metabolic diseases originate in early life, and epigenetic changes have been implicated as key drivers of this early life programming. This led to the hypothesis that epigenetic marks present at birth may predict an individual's future risk of obesity and type 2 diabetes. In this study, we assessed whether epigenetic marks in blood of newborn children were associated with body mass index (BMI) and insulin sensitivity later in childhood. SUBJECTS/METHODS DNA methylation was measured in neonatal blood spot samples of 438 children using the Illumina Infinium 450 k BeadChip. Associations were assessed between DNA methylation at birth and BMI z-scores, body fat mass, fasting plasma glucose, insulin and homeostatic model assessment of insulin resistance (HOMA-IR) at age 5 years, as well as birth weight, maternal BMI and smoking status. RESULTS No individual methylation sites at birth were associated with obesity or insulin sensitivity measures at 5 years. DNA methylation in 69 genomic regions at birth was associated with BMI z-scores at age 5 years, and in 63 regions with HOMA-IR. The methylation changes were generally small (<5%), except for a region near the non-coding RNA nc886 (VTRNA2-1) where a clear link between methylation status at birth and BMI in childhood was observed (P=0.001). Associations were also found between DNA methylation, maternal smoking and birth weight. CONCLUSIONS We identified a number of DNA methylation regions at birth that were associated with obesity or insulin sensitivity measurements in childhood. These findings support the mounting evidence on the role of epigenetics in programming of metabolic health. Whether many of these small changes in DNA methylation are causally related to the health outcomes, and of clinical relevance, remains to be determined, but the nc886 region represents a promising obesity risk marker that warrants further investigation.
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89
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Meeks KA, Henneman P, Venema A, Burr T, Galbete C, Danquah I, Schulze MB, Mockenhaupt FP, Owusu-Dabo E, Rotimi CN, Addo J, Smeeth L, Bahendeka S, Spranger J, Mannens MM, Zafarmand MH, Agyemang C, Adeyemo A. An epigenome-wide association study in whole blood of measures of adiposity among Ghanaians: the RODAM study. Clin Epigenetics 2017; 9:103. [PMID: 28947923 PMCID: PMC5609006 DOI: 10.1186/s13148-017-0403-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/05/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Epigenome-wide association studies (EWAS) have identified DNA methylation loci involved in adiposity. However, EWAS on adiposity in sub-Saharan Africans are lacking despite the high burden of adiposity among African populations. We undertook an EWAS for anthropometric indices of adiposity among Ghanaians aiming to identify DNA methylation loci that are significantly associated. METHODS The Illumina 450k DNA methylation array was used to profile DNA methylation in whole blood samples of 547 Ghanaians from the Research on Obesity and Diabetes among African Migrants (RODAM) study. Differentially methylated positions (DMPs) and differentially methylation regions (DMRs) were identified for BMI and obesity (BMI ≥ 30 kg/m2), as well as for waist circumference (WC) and abdominal obesity (WC ≥ 102 cm in men, ≥88 cm in women). All analyses were adjusted for age, sex, blood cell distribution estimates, technical covariates, recruitment site and population stratification. We also did a replication study of previously reported EWAS loci for anthropometric indices in other populations. RESULTS We identified 18 DMPs for BMI and 23 for WC. For obesity and abdominal obesity, we identified three and one DMP, respectively. Fourteen DMPs overlapped between BMI and WC. DMP cg00574958 annotated to gene CPT1A was the only DMP associated with all outcomes analysed, attributing to 6.1 and 5.6% of variance in obesity and abdominal obesity, respectively. DMP cg07839457 (NLRC5) and cg20399616 (BCAT1) were significantly associated with BMI, obesity and with WC and had not been reported by previous EWAS on adiposity. CONCLUSIONS This first EWAS for adiposity in Africans identified three epigenome-wide significant loci (CPT1A, NLRC5 and BCAT1) for both general adiposity and abdominal adiposity. The findings are a first step in understanding the role of DNA methylation in adiposity among sub-Saharan Africans. Studies on other sub-Saharan African populations as well as translational studies are needed to determine the role of these DNA methylation variants in the high burden of adiposity among sub-Saharan Africans.
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Affiliation(s)
- Karlijn A.C. Meeks
- Department of Public Health, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Tom Burr
- Source BioScience, 1 Orchard Place, Nottingham Business Park, Nottingham, NG8 6PX UK
| | - Cecilia Galbete
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Ina Danquah
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
- Institute for Social Medicine, Epidemiology and Health Economics, Charité – Universitaetsmedizin Berlin, Berlin, Germany
| | - Matthias B. Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Frank P. Mockenhaupt
- Institute of Tropical Medicine and International Health, Charité – University Medicine Berlin, Campus Virchow-Klinikum Augustenburger Platz 1, 13353 Berlin, Germany
| | - Ellis Owusu-Dabo
- Department of Global and International Health, School of Public Health; Kumasi Centre for collaborative Research, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti Region Ghana
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, MSC 5635, Bethesda, MD 20892-5635 USA
| | - Juliet Addo
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Liam Smeeth
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | | | - Joachim Spranger
- Department of Endocrinology and Metabolism, Charité – University Medicine Berlin, Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Berlin, Germany
- Center for Cardiovascular Research (CCR), Charité – University Medicine Berlin, Berlin, Germany
| | - Marcel M.A.M. Mannens
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Mohammad H. Zafarmand
- Department of Public Health, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public Health, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, MSC 5635, Bethesda, MD 20892-5635 USA
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90
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Bacalini MG, Deelen J, Pirazzini C, De Cecco M, Giuliani C, Lanzarini C, Ravaioli F, Marasco E, van Heemst D, Suchiman HED, Slieker R, Giampieri E, Recchioni R, Marcheselli F, Salvioli S, Vitale G, Olivieri F, Spijkerman AMW, Dollé MET, Sedivy JM, Castellani G, Franceschi C, Slagboom PE, Garagnani P. Systemic Age-Associated DNA Hypermethylation of ELOVL2 Gene: In Vivo and In Vitro Evidences of a Cell Replication Process. J Gerontol A Biol Sci Med Sci 2017; 72:1015-1023. [PMID: 27672102 DOI: 10.1093/gerona/glw185] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 08/26/2016] [Indexed: 12/17/2022] Open
Abstract
Epigenetic remodeling is one of the major features of the aging process. We recently demonstrated that DNA methylation of ELOVL2 and FHL2 CpG islands is highly correlated with age in whole blood. Here we investigated several aspects of age-associated hypermethylation of ELOVL2 and FHL2. We showed that ELOVL2 methylation is significantly different in primary dermal fibroblast cultures from donors of different ages. Using epigenomic data from public resources, we demonstrated that most of the tissues show ELOVL2 and FHL2 hypermethylation with age. Interestingly, ELOVL2 hypermethylation was not found in tissues with very low replication rate. We demonstrated that ELOVL2 hypermethylation is associated with in vitro cell replication rather than with senescence. We confirmed intra-individual hypermethylation of ELOVL2 and FHL2 in longitudinally assessed participants from the Doetinchem Cohort Study. Finally we showed that, although the methylation of the two loci is not associated with longevity/mortality in the Leiden Longevity Study, ELOVL2 methylation is associated with cytomegalovirus status in nonagenarians, which could be informative of a higher number of replication events in a fraction of whole-blood cells. Collectively, these results indicate that ELOVL2 methylation is a marker of cell divisions occurring during human aging.
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Affiliation(s)
- Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy.,Personal Genomics S.r.l., Verona, Italy
| | - Joris Deelen
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands.,Max Planck Institute for Biology of Ageing, Köln, Germany
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | - Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics, Brown University, Providence, Rhode Island
| | | | - Catia Lanzarini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | | | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine
| | - Diana van Heemst
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - H Eka D Suchiman
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - Roderick Slieker
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - Enrico Giampieri
- Department of Physics and Astronomy, University of Bologna, Italy
| | - Rina Recchioni
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
| | - Fiorella Marcheselli
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | - Giovanni Vitale
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Italy
| | - Fabiola Olivieri
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy.,Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | | | - Martijn E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics, Brown University, Providence, Rhode Island
| | | | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine.,Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy.,IRCCS Institute of Neurological Sciences, Bologna, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
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91
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Epigenetic Regulation of PLIN 1 in Obese Women and its Relation to Lipolysis. Sci Rep 2017; 7:10152. [PMID: 28860604 PMCID: PMC5578955 DOI: 10.1038/s41598-017-09232-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 07/17/2017] [Indexed: 02/08/2023] Open
Abstract
Increased adipocyte lipolysis links obesity to insulin resistance. The lipid droplet coating-protein Perilipin participates in regulation of lipolysis and is implicated in obesity. In the present study we investigate epigenetic regulation of the PLIN1 gene by correlating PLIN1 CpG methylation to gene expression and lipolysis, and functionally evaluating PLIN1 promoter methylation. PLIN1 CpG methylation in adipocytes and gene expression in white adipose tissue (WAT) was quantified in two cohorts by array. Basal lipolysis in WAT explants and adipocytes was quantified by measuring glycerol release. CpG-methylation of the PLIN1 promoter in adipocytes from obese women was higher as compared to never-obese women. PLIN1 promoter methylation was inversely correlated with PLIN1 mRNA expression and the lipolytic activity. Human mesenchymal stem cells (hMSCs) differentiated in vitro into adipocytes and harboring methylated PLIN1 promoter displayed decreased reporter gene activity as compared to hMSCs harboring unmethylated promoter. Treatment of hMSCs differentiated in vitro into adipocytes with a DNA methyltransferase inhibitor increased levels of PLIN1 mRNA and protein. In conclusion, the PLIN1 gene is epigenetically regulated and promoter methylation is inversely correlated with basal lipolysis in women suggesting that epigenetic regulation of PLIN1 is important for increased adipocyte lipolysis in insulin resistance states.
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92
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de Toro-Martín J, Arsenault BJ, Després JP, Vohl MC. Precision Nutrition: A Review of Personalized Nutritional Approaches for the Prevention and Management of Metabolic Syndrome. Nutrients 2017; 9:E913. [PMID: 28829397 PMCID: PMC5579706 DOI: 10.3390/nu9080913] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/18/2017] [Accepted: 08/18/2017] [Indexed: 02/07/2023] Open
Abstract
The translation of the growing increase of findings emerging from basic nutritional science into meaningful and clinically relevant dietary advices represents nowadays one of the main challenges of clinical nutrition. From nutrigenomics to deep phenotyping, many factors need to be taken into account in designing personalized and unbiased nutritional solutions for individuals or population sub-groups. Likewise, a concerted effort among basic, clinical scientists and health professionals will be needed to establish a comprehensive framework allowing the implementation of these new findings at the population level. In a world characterized by an overwhelming increase in the prevalence of obesity and associated metabolic disturbances, such as type 2 diabetes and cardiovascular diseases, tailored nutrition prescription represents a promising approach for both the prevention and management of metabolic syndrome. This review aims to discuss recent works in the field of precision nutrition analyzing most relevant aspects affecting an individual response to lifestyle/nutritional interventions. Latest advances in the analysis and monitoring of dietary habits, food behaviors, physical activity/exercise and deep phenotyping will be discussed, as well as the relevance of novel applications of nutrigenomics, metabolomics and microbiota profiling. Recent findings in the development of precision nutrition are highlighted. Finally, results from published studies providing examples of new avenues to successfully implement innovative precision nutrition approaches will be reviewed.
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Affiliation(s)
- Juan de Toro-Martín
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, QC G1V 0A6, Canada.
- School of Nutrition, Laval University, Quebec City, QC G1V 0A6, Canada.
| | - Benoit J Arsenault
- Department of Medicine, Faculty of Medicine, Laval University, Quebec City, QC G1V 0A6, Canada.
- Quebec Heart and Lung Institute, Quebec City, QC G1V 4G5, Canada.
| | - Jean-Pierre Després
- Quebec Heart and Lung Institute, Quebec City, QC G1V 4G5, Canada.
- Department of Kinesiology, Faculty of Medicine, Laval University, Quebec City, QC G1V 0A6, Canada.
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec City, QC G1V 0A6, Canada.
- School of Nutrition, Laval University, Quebec City, QC G1V 0A6, Canada.
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93
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The importance of gene-environment interactions in human obesity. Clin Sci (Lond) 2017; 130:1571-97. [PMID: 27503943 DOI: 10.1042/cs20160221] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/23/2016] [Indexed: 12/16/2022]
Abstract
The worldwide obesity epidemic has been mainly attributed to lifestyle changes. However, who becomes obese in an obesity-prone environment is largely determined by genetic factors. In the last 20 years, important progress has been made in the elucidation of the genetic architecture of obesity. In parallel with successful gene identifications, the number of gene-environment interaction (GEI) studies has grown rapidly. This paper reviews the growing body of evidence supporting gene-environment interactions in the field of obesity. Heritability, monogenic and polygenic obesity studies provide converging evidence that obesity-predisposing genes interact with a variety of environmental, lifestyle and treatment exposures. However, some skepticism remains regarding the validity of these studies based on several issues, which include statistical modelling, confounding, low replication rate, underpowered analyses, biological assumptions and measurement precision. What follows in this review includes (1) an introduction to the study of GEI, (2) the evidence of GEI in the field of obesity, (3) an outline of the biological mechanisms that may explain these interaction effects, (4) methodological challenges associated with GEI studies and potential solutions, and (5) future directions of GEI research. Thus far, this growing body of evidence has provided a deeper understanding of GEI influencing obesity and may have tremendous applications in the emerging field of personalized medicine and individualized lifestyle recommendations.
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94
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Do C, Shearer A, Suzuki M, Terry MB, Gelernter J, Greally JM, Tycko B. Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era. Genome Biol 2017. [PMID: 28629478 PMCID: PMC5477265 DOI: 10.1186/s13059-017-1250-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Studies on genetic-epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in the post-genome-wide-association-study (GWAS) era. Such maps can nominate regulatory sequence variants that underlie GWAS signals for common diseases, ranging from neuropsychiatric disorders to cancers. Conversely, mQTLs need to be filtered out when searching for non-genetic effects in epigenome-wide association studies (EWAS). Sequence variants in CCCTC-binding factor (CTCF) and transcription factor binding sites have been mechanistically linked to mQTLs and hap-ASM. Identifying these sites can point to disease-associated transcriptional pathways, with implications for targeted treatment and prevention.
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Affiliation(s)
- Catherine Do
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Alyssa Shearer
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of Public Health, and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Joel Gelernter
- Departments of Psychiatry, Genetics, and Neurobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - John M Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Taub Institute for Research on Alzheimer's disease and the Aging Brain, New York, NY, 10032, USA. .,Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.
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95
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Jeon JP, Koh IU, Choi NH, Kim BJ, Han BG, Lee S. Differential DNA methylation of MSI2 and its correlation with diabetic traits. PLoS One 2017; 12:e0177406. [PMID: 28542303 PMCID: PMC5443489 DOI: 10.1371/journal.pone.0177406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 04/26/2017] [Indexed: 01/03/2023] Open
Abstract
Differential DNA methylation with hyperglycemia is significantly associated with Type 2 Diabetes (T2D). Longtime extended exposure to high blood glucose levels can affect the epigenetic signatures in all organs. However, the relevance of the differential DNA methylation changes with hyperglycemia in blood with pancreatic islets remains unclear. We investigated differential DNA methylation in relation to glucose homeostasis based on the Oral Glucose Tolerance Test (OGTT) in a population-based cohort. We found a total of 382 differential methylation sites from blood DNA in hyperglycemia and type 2 diabetes subgroups using a longitudinal and cross-sectional approach. Among them, three CpG sites were overlapped; they were mapped to the MSI2 and CXXC4 genes. In a DNA methylation replication study done by pyrosequencing (n = 440), the CpG site of MSI2 were shown to have strong associations with the T2D group (p value = 2.20E-16). The differential methylation of MSI2 at chr17:55484635 was associated with diabetes-related traits, in particular with insulin sensitivity (QUICKI, p value = 2.20E-16) and resistance (HOMA-IR, p value = 1.177E-07). In human pancreatic islets, at the single-base resolution (using whole-genome bisulfite sequencing), the 292 CpG sites in the ±5kb at chr17:55484635 were found to be significantly hypo-methylated in donors with T2D (average decrease = 13.91%, 95% confidence interval (CI) = 4.18~ 17.06) as compared to controls, and methylation patterns differed by sex (-9.57%, CI = -16.76~ -6.89) and age (0.12%, CI = -11.17~ 3.77). Differential methylation of the MSI2 gene (chr17:55484635) in blood and islet cells is strongly related to hyperglycemia. Our findings suggest that epigenetic perturbation on the target site of MSI2 gene in circulating blood and pancreatic islets should represent or affect hyperglycemia.
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Affiliation(s)
- Jae-Pil Jeon
- Center for Biomedical Science, National Research Institute of Health, Cheongju-si, Republic of Korea
| | - In-Uk Koh
- Center for Genome Science, National Research Institute of Health, Cheongju-si, Republic of Korea
| | - Nak-Hyun Choi
- Center for Genome Science, National Research Institute of Health, Cheongju-si, Republic of Korea
| | - Bong-Jo Kim
- Center for Genome Science, National Research Institute of Health, Cheongju-si, Republic of Korea
| | - Bok-Ghee Han
- Center for Genome Science, National Research Institute of Health, Cheongju-si, Republic of Korea
- * E-mail: (SL); (BGH)
| | - Suman Lee
- Center for Genome Science, National Research Institute of Health, Cheongju-si, Republic of Korea
- * E-mail: (SL); (BGH)
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96
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Koh IU, Lee HJ, Hwang JY, Choi NH, Lee S. Obesity-related CpG Methylation (cg07814318) of Kruppel-like Factor-13 (KLF13) Gene with Childhood Obesity and its cis-Methylation Quantitative Loci. Sci Rep 2017; 7:45368. [PMID: 28508896 PMCID: PMC5432839 DOI: 10.1038/srep45368] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/22/2017] [Indexed: 12/14/2022] Open
Abstract
The cg07814318 hypermethylation of Kruppel-like factor 13 (KLF13) gene has been reported for its relevancy with Body Mass Index (BMI) from European origin. We explored the cg07814318 methylation and its cis-meQTL (cis-methylation quantitative loci) of KLF13 from a childhood obesity cohort. The cg07814318 methylation in blood was significantly associated with obesity and correlated with several obesity-related physical and biochemical traits. We examined the same loci from purified three human cell types (n = 47), i.e., pre-adipocytes, adipocytes and islets. The cg07814318 methylation pattern in pre-adipocytes and islets were significant higher in cells from subjects with a higher BMI compared with control subjects. By exome sequencing of KLF13 gene in blood with the same cohort, we found nine SNPs (single nucleotide polymorphisms) within its gene body, and two SNPs (rs11537749 and rs12595641) were as cis-meQTL of cg07814318. There was the 2.01% methylation change of cg07814318 between homozygous dominant and recessive genotypes, especially, in rs12595641. The sequencing variations within KLF13 genes could drive dynamic modifications of obesity-related CpG methylation. Differential DNA methylation patterns in the KLF13 gene determined from separate blood samples showed that this criterion could be used as a surrogate for representing overall epigenetic changes in cells related to obesity.
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Affiliation(s)
- In-Uk Koh
- Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 363-951, Republic of Korea
| | - Hye-Ja Lee
- Division of Metabolic Diseases, Center for Biomedical Sciences, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea
| | - Joo-Yeon Hwang
- Division of Metabolic Diseases, Center for Biomedical Sciences, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea
| | - Nak-Hyun Choi
- Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 363-951, Republic of Korea
| | - Suman Lee
- Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 363-951, Republic of Korea
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97
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Epigenetic changes in blood leukocytes following an omega-3 fatty acid supplementation. Clin Epigenetics 2017; 9:43. [PMID: 28450971 PMCID: PMC5405524 DOI: 10.1186/s13148-017-0345-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/14/2017] [Indexed: 12/24/2022] Open
Abstract
Background Omega-3 polyunsaturated fatty acids (n-3 FAs) have several beneficial effects on cardiovascular (CV) disease risk factors. These effects on CV risk profile may be mediated by several factors, including epigenetic modifications. Our objective is to investigate, using genome-wide DNA methylation analyses, methylation changes following an n-3 FA supplementation in overweight and obese subjects and to identify specific biological pathways potentially altered by the supplementation. Results Blood leukocytes genome-wide DNA methylation profiles of 36 overweight and obese subjects before and after a 6-week supplementation with 3 g of n-3 FAs were compared using GenomeStudio software. After supplementation, 308 CpG sites, assigned to 231 genes, were differentially methylated (FDR-corrected Diffscore ≥│13│~ P ≤ 0.05). Using Ingenuity Pathway Analysis system, a total of 55 pathways were significantly overrepresented following supplementation. Among these pathways, 16 were related to inflammatory and immune response, lipid metabolism, type 2 diabetes, and cardiovascular signaling. Changes in methylation levels of CpG sites within AKT3, ATF1, HDAC4, and IGFBP5 were correlated with changes in plasma triglyceride and glucose levels as well as with changes in the ratio of total cholesterol/HDL-cholesterol following the supplementation. Conclusions These data provide key differences in blood leukocytes DNA methylation profiles of subjects following an n-3 FA supplementation, which brings new, potential insights on metabolic pathways underlying the effects of n-3 FAs on CV health. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0345-3) contains supplementary material, which is available to authorized users.
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98
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Hjort L, Jørgensen SW, Gillberg L, Hall E, Brøns C, Frystyk J, Vaag AA, Ling C. 36 h fasting of young men influences adipose tissue DNA methylation of LEP and ADIPOQ in a birth weight-dependent manner. Clin Epigenetics 2017; 9:40. [PMID: 28439315 PMCID: PMC5399392 DOI: 10.1186/s13148-017-0340-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/12/2017] [Indexed: 12/18/2022] Open
Abstract
Background Subjects born with low birth weight (LBW) display a more energy-conserving response to fasting compared with normal birth weight (NBW) subjects. However, the molecular mechanisms explaining these metabolic differences remain unknown. Environmental influences may dynamically affect epigenetic marks, also in postnatal life. Here, we aimed to study the effects of short-term fasting on leptin (LEP) and adiponectin (ADIPOQ) DNA methylation and gene expression in subcutaneous adipose tissue (SAT) from subjects with LBW and NBW. Methods Twenty-one young LBW men and 18 matched NBW controls were studied during 36 h fasting. Eight subjects from each group completed a control study (overnight fast). We analyzed SAT LEP and ADIPOQ methylation (Epityper MassARRAY), gene expression (q-PCR), and adipokine plasma levels. Results After overnight fast (control study), LEP and ADIPOQ DNA methylation levels were higher in LBW compared to those in NBW subjects (p ≤ 0.03) and increased with 36 h fasting in NBW subjects only (p ≤ 0.06). Both LEP and ADIPOQ methylation levels were positively associated with total body fat percentage (p ≤ 0.05). Plasma leptin levels were higher in LBW versus NBW subjects after overnight fasting (p = 0.04) and decreased more than threefold in both groups after 36 h fasting (p ≤ 0.0001). Conclusions This is the first study to demonstrate that fasting induces changes in DNA methylation. This was shown in LEP and ADIPOQ promoters in SAT among NBW but not LBW subjects. The altered epigenetic flexibility in LBW subjects might contribute to their differential response to fasting, adipokine levels, and increased risk of metabolic disease. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0340-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Line Hjort
- Department of Endocrinology (Diabetes and Metabolism), Rigshospitalet, section 7652, Tagensvej 20, DK-2200 Copenhagen N, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,The Danish Diabetes Academy, Odense, Denmark
| | - Sine W Jørgensen
- Department of Endocrinology (Diabetes and Metabolism), Rigshospitalet, section 7652, Tagensvej 20, DK-2200 Copenhagen N, Denmark.,Steno Diabetes Center, Gentofte, Denmark
| | - Linn Gillberg
- Department of Endocrinology (Diabetes and Metabolism), Rigshospitalet, section 7652, Tagensvej 20, DK-2200 Copenhagen N, Denmark
| | - Elin Hall
- Epigenetics and Diabetes and Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Jan Waldentröms gata 35, SE-20502 Malmö, Sweden
| | - Charlotte Brøns
- Department of Endocrinology (Diabetes and Metabolism), Rigshospitalet, section 7652, Tagensvej 20, DK-2200 Copenhagen N, Denmark
| | - Jan Frystyk
- Institute of Clinical Medicine, University of Aarhus, Aarhus, Denmark
| | - Allan A Vaag
- Department of Endocrinology (Diabetes and Metabolism), Rigshospitalet, section 7652, Tagensvej 20, DK-2200 Copenhagen N, Denmark.,AstraZeneca, Mölndal, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes and Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Jan Waldentröms gata 35, SE-20502 Malmö, Sweden
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99
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Johnson ND, Wiener HW, Smith AK, Nishitani S, Absher DM, Arnett DK, Aslibekyan S, Conneely KN. Non-linear patterns in age-related DNA methylation may reflect CD4 + T cell differentiation. Epigenetics 2017; 12:492-503. [PMID: 28387568 DOI: 10.1080/15592294.2017.1314419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA methylation (DNAm) is an important epigenetic process involved in the regulation of gene expression. While many studies have identified thousands of loci associated with age, few have differentiated between linear and non-linear DNAm trends with age. Non-linear trends could indicate early- or late-life gene regulatory processes. Using data from the Illumina 450K array on 336 human peripheral blood samples, we identified 21 CpG sites that associated with age (P<1.03E-7) and exhibited changing rates of DNAm change with age (P<1.94E-6). For 2 of these CpG sites (cg07955995 and cg22285878), DNAm increased with age at an increasing rate, indicating that differential DNAm was greatest among elderly individuals. We observed significant replication for both CpG sites (P<5.0E-8) in a second set of peripheral blood samples. In 8 of 9 additional data sets comprising samples of monocytes, T cell subtypes, and brain tissue, we observed a pattern directionally consistent with DNAm increasing with age at an increasing rate, which was nominally significant in the 3 largest data sets (4.3E-15<P<0.039). cg07955995 and cg22285878 reside in the promoter region of KLF14, which encodes a protein involved in immune cell differentiation via the repression of FOXP3. These findings may suggest a possible role for cg07955995 and cg22285878 in immunosenescence.
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Affiliation(s)
| | - Howard W Wiener
- b Department of Epidemiology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - Alicia K Smith
- c Department of Gynecology and Obstetrics , Emory University , Atlanta , GA , USA.,d Department of Psychiatry and Behavioral Sciences , Emory University , Atlanta , GA , USA
| | - Shota Nishitani
- c Department of Gynecology and Obstetrics , Emory University , Atlanta , GA , USA.,d Department of Psychiatry and Behavioral Sciences , Emory University , Atlanta , GA , USA
| | - Devin M Absher
- e HudsonAlpha Institute for Biotechnology , Huntsville , AL , USA
| | - Donna K Arnett
- f College of Public Health , University of Kentucky , Lexington , KY , USA
| | - Stella Aslibekyan
- b Department of Epidemiology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - Karen N Conneely
- a Department of Human Genetics , Emory University , Atlanta , GA , USA
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100
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Durso DF, Bacalini MG, Sala C, Pirazzini C, Marasco E, Bonafé M, do Valle ÍF, Gentilini D, Castellani G, Faria AMC, Franceschi C, Garagnani P, Nardini C. Acceleration of leukocytes' epigenetic age as an early tumor and sex-specific marker of breast and colorectal cancer. Oncotarget 2017; 8:23237-23245. [PMID: 28423572 PMCID: PMC5410300 DOI: 10.18632/oncotarget.15573] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/12/2017] [Indexed: 01/12/2023] Open
Abstract
Changes in blood epigenetic age have been associated with several pathological conditions and have recently been described to anticipate cancer development. In this work, we analyze a publicly available leukocytes methylation dataset to evaluate the relation between DNA methylation age and the prospective development of specific types of cancer. We calculated DNA methylation age acceleration using five state-of-the-art estimators (three multi-site: Horvath, Hannum, Weidner; and two CpG specific: ELOV2 and FHL2) in a cohort including 845 subjects from the EPIC-Italy project and we compared 424 samples that remained cancer-free over the approximately ten years of follow-up with 235 and 166 subjects who developed breast and colorectal cancer, respectively. We show that the epigenetic age estimated from blood DNA methylation data is statistically significantly associated to future breast and male colorectal cancer development. These results are corroborated by survival analysis that shows significant association between age acceleration and cancer incidence suggesting that the chance of developing age-related diseases may be predicted by circulating epigenetic markers, with a dependence upon tumor type, sex and age estimator. These are encouraging results towards the non-invasive and perspective usage of epigenetic biomarkers.
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Affiliation(s)
- Danielle Fernandes Durso
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- National Counsel of Technological and Scientific Development (CNPq), Ministry of Science Technology and Innovation (MCTI), Brasilia, Brazil
| | | | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Massimiliano Bonafé
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | | | - Davide Gentilini
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Ana Maria Caetano Faria
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna, Italy
- Interdepartmental Center “L. Galvani”, University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Christine Nardini
- Personal Genomics S.r.l., Verona, Italy
- CNR IAC “Mauro Picone”, Rome, Italy
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