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Duarte MR, de Moraes Heredia AS, Arantes VC, de Barros Reis MA, Rodrigues PRM, Gorgulho BM, Fregadolli CH, Latorraca MQ. The interaction of the FTO gene and age interferes with macronutrient and vitamin intake in women with morbid obesity. Exp Gerontol 2024; 193:112463. [PMID: 38789015 DOI: 10.1016/j.exger.2024.112463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024]
Abstract
Fat mass and obesity-related (FTO) gene single nucleotide polymorphisms (SNPs) interferes with food preferences that impact macronutrient intake. Few studies have investigated the relationship of this polymorphisms with the intake of micronutrients. Moreover, studies have shown multiple micronutrient deficiencies in patients with obesity. This work evaluated the effect of the FTO rs9939609 gene polymorphism on dietary nutritional quality and food intake of macronutrients and vitamins in of women with obesity candidates for metabolic surgery. The study included 106 women (24 to 60 years old) with BMIs of 36.1 to 64.8 kg/m2. A food frequency questionnaire validated for the local population was applied to obtain information about food intake. The Index of Nutritional Quality (INQ) was used to assess the adequacy of macronutrient and vitamin intake. Energy, protein and lipid intakes were higher in carriers of the A allele compared to TT in the younger age groups but were similar in the class of subjects aged ≥45 years. The INQ for protein was higher in carriers of the A allele than in carriers of the TT allele. The INQs for protein, carbohydrate, vitamins B2, B3 and B6 decreased, whereas the INQ for vitamin C increased with advancing age. The INQ for vitamin A was lower in AA than in TT, regardless of age, whereas vitamin E was higher in younger AA than in older AA. The INQ for vitamin B9 was higher in younger women than in older women. In conclusion, the FTO gene contributed to the intake of more energy, protein and lipids and interfered with the intake of vitamins B9, A and E. With the exception of vitamin A, the effect of the genotype was attenuated with ageing.
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Affiliation(s)
- Miriam Ribeiro Duarte
- Master in Nutrition, Food and Metabolism, Faculty of Nutrition, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | - Aline Souza de Moraes Heredia
- Master in Nutrition, Food and Metabolism, Faculty of Nutrition, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | - Vanessa Cristina Arantes
- Department of Food Nutrition, Faculty of Nutrition, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | | | | | - Bartira Mendes Gorgulho
- Department of Food Nutrition, Faculty of Nutrition, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | - Carlos Henrique Fregadolli
- Master in Nutrition, Food and Metabolism, Faculty of Nutrition, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | - Márcia Queiroz Latorraca
- Department of Food Nutrition, Faculty of Nutrition, Federal University of Mato Grosso, Cuiabá, MT, Brazil.
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Melnik BC, Weiskirchen R, Stremmel W, John SM, Schmitz G. Risk of Fat Mass- and Obesity-Associated Gene-Dependent Obesogenic Programming by Formula Feeding Compared to Breastfeeding. Nutrients 2024; 16:2451. [PMID: 39125332 PMCID: PMC11314333 DOI: 10.3390/nu16152451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/21/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
It is the purpose of this review to compare differences in postnatal epigenetic programming at the level of DNA and RNA methylation and later obesity risk between infants receiving artificial formula feeding (FF) in contrast to natural breastfeeding (BF). FF bears the risk of aberrant epigenetic programming at the level of DNA methylation and enhances the expression of the RNA demethylase fat mass- and obesity-associated gene (FTO), pointing to further deviations in the RNA methylome. Based on a literature search through Web of Science, Google Scholar, and PubMed databases concerning the dietary and epigenetic factors influencing FTO gene and FTO protein expression and FTO activity, FTO's impact on postnatal adipogenic programming was investigated. Accumulated translational evidence underscores that total protein intake as well as tryptophan, kynurenine, branched-chain amino acids, milk exosomal miRNAs, NADP, and NADPH are crucial regulators modifying FTO gene expression and FTO activity. Increased FTO-mTORC1-S6K1 signaling may epigenetically suppress the WNT/β-catenin pathway, enhancing adipocyte precursor cell proliferation and adipogenesis. Formula-induced FTO-dependent alterations of the N6-methyladenosine (m6A) RNA methylome may represent novel unfavorable molecular events in the postnatal development of adipogenesis and obesity, necessitating further investigations. BF provides physiological epigenetic DNA and RNA regulation, a compelling reason to rely on BF.
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Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany;
| | - Wolfgang Stremmel
- Praxis for Internal Medicine, Beethovenstrasse 2, D-76530 Baden-Baden, Germany;
| | - Swen Malte John
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany
- Institute for Interdisciplinary Dermatological Prevention and Rehabilitation (iDerm), University of Osnabrück, D-49076 Osnabrück, Germany;
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital of Regensburg, D-93053 Regensburg, Germany;
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3
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Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci 2024; 81:178. [PMID: 38602535 PMCID: PMC11008083 DOI: 10.1007/s00018-024-05206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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4
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Xu ZY, Jing X, Xiong XD. Emerging Role and Mechanism of the FTO Gene in Cardiovascular Diseases. Biomolecules 2023; 13:biom13050850. [PMID: 37238719 DOI: 10.3390/biom13050850] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The fat mass and obesity-associated (FTO) gene was the first obesity-susceptibility gene identified through a genome-wide association study (GWAS). A growing number of studies have suggested that genetic variants of FTO are strongly associated with the risk of cardiovascular diseases, including hypertension and acute coronary syndrome. In addition, FTO was also the first N6-methyladenosine (m6A) demethylase, suggesting the reversible nature of m6A modification. m6A is dynamically deposited, removed, and recognized by m6A methylases, demethylases, and m6A binding proteins, respectively. By catalyzing m6A demethylation on mRNA, FTO may participate in various biological processes by modulating RNA function. Recent studies demonstrated that FTO plays a pivotal role in the initiation and progression of cardiovascular diseases such as myocardial fibrosis, heart failure, and atherosclerosis and may hold promise as a potential therapeutic target for treating or preventing a variety of cardiovascular diseases. Here, we review the association between FTO genetic variants and cardiovascular disease risk, summarize the role of FTO as an m6A demethylase in cardiovascular disorders, and discuss future research directions and possible clinical implications.
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Affiliation(s)
- Zi-Yang Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
| | - Xia Jing
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
| | - Xing-Dong Xiong
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
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Hao J, Liu Y. Epigenetics of methylation modifications in diabetic cardiomyopathy. Front Endocrinol (Lausanne) 2023; 14:1119765. [PMID: 37008904 PMCID: PMC10050754 DOI: 10.3389/fendo.2023.1119765] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/01/2023] [Indexed: 03/17/2023] Open
Abstract
Type 2 diabetes is one of the most common metabolic diseases with complications including diabetic cardiomyopathy and atherosclerotic cardiovascular disease. Recently, a growing body of research has revealed that the complex interplay between epigenetic changes and the environmental factors may significantly contribute to the pathogenesis of cardiovascular complications secondary to diabetes. Methylation modifications, including DNA methylation and histone methylation among others, are important in developing diabetic cardiomyopathy. Here we summarized the literatures of studies focusing on the role of DNA methylation, and histone modifications in microvascular complications of diabetes and discussed the mechanism underlying these disorders, to provide the guidance for future research toward an integrated pathophysiology and novel therapeutic strategies to treat or prevent this frequent pathological condition.
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Affiliation(s)
- Jing Hao
- Department of Emergency, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Yao Liu
- Department of Pharmacy, Children’s Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Yao Liu,
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Dabeer S, Raisuddin S. Perinatal exposure to environmental endocrine disruptor bisphenol A aggravates the onset of non-alcoholic fatty liver disease (NAFLD) in weanling F1 offspring of obese rats. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:3146-3165. [PMID: 35945320 DOI: 10.1007/s11356-022-22246-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Bisphenol A (BPA) is a major environmental pollutant and food contaminant with endocrine-disrupting effects on human and animal health. Perinatal and developmental exposure to BPA has been known to cause hepatotoxicity in adulthood. However, its intergenerational effects in a metabolically challenged population have been scarcely investigated. Our study was designed to assess the intergenerational effect of an environmentally relevant dose of BPA and diet-induced parental obesity on the hepatic health outcome of F1 offspring. Wistar rats were given a high-fat diet to induce obesity, followed by chronic low dosages of BPA (10 ppm × 180 days) in drinking water. Post-treatment, rats were crossed within groups to obtain the F1 generation. Weanling pups were observed for weight gain, levels of hepatic antioxidants, liver function enzymes, cholesterol, C-reactive protein, and triglyceride in the serum. Histological changes in the liver tissue were also investigated. mRNA expression of energy homeostasis genes (FTO and MCR-4) in the liver was analyzed alongside blood biomarkers. We observed higher birth weight and rapid weight gain in the test group in comparison with controls, which was consistent with the changes in mRNA and protein expression of FTO and MCR-4. BPA caused a significant, treatment-related change in the inflammatory marker C-reactive protein, lipid peroxidation, antioxidants, and lipid profile. These findings were accompanied by histological changes in the liver tissue characteristic of hepatic steatosis indicating the onset of the non-alcoholic fatty liver disease (NAFLD). Our study offers a link between exposure to BPA in parents and onset of NAFLD in their offspring.
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Affiliation(s)
- Sadaf Dabeer
- Molecular Toxicology Laboratory, Department of Medical Elementology and Toxicology, Jamia Hamdard (Hamdard University), New Delhi, 110062, India
- Currently at The Department of Exercise Science and Sport Management, WellStar College of Health and Human Services, Kennesaw State University, Kennesaw, GA, 30144, USA
- Currently at The Division of Endocrinology, Metabolism, and Lipids, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Sheikh Raisuddin
- Molecular Toxicology Laboratory, Department of Medical Elementology and Toxicology, Jamia Hamdard (Hamdard University), New Delhi, 110062, India.
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7
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Cho AR, Hong KW, Kwon YJ, Choi JE, Lee HS, Kim HM, Bae SJ, Ahn SG, Jeong J, Lee JW. Effects of Single Nucleotide Polymorphisms and Mediterranean Diet in Overweight or Obese Postmenopausal Women With Breast Cancer Receiving Adjuvant Hormone Therapy: A Pilot Randomized Controlled Trial. Front Nutr 2022; 9:882717. [PMID: 35845810 PMCID: PMC9284001 DOI: 10.3389/fnut.2022.882717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/13/2022] [Indexed: 12/01/2022] Open
Abstract
Background and Aims Weight management is recommended in overweight or obese breast cancer patients, as they have an increased risk of cancer recurrence and poor prognosis. Furthermore, identifying the relationships between genetic factors and nutrition could help suggest possible individualized nutritional solutions in weight management. The objective of this pilot randomized controlled trial was to investigate the influence of two obesity-associated single nucleotide polymorphisms and the Mediterranean diet intervention on weight loss and modification of nutrient intake and metabolic parameters in overweight or obese, postmenopausal, breast cancer patients receiving adjuvant hormone therapy. Methods Seventy-eight breast cancer patients were randomly assigned to the Mediterranean diet (MeDiet) group or control group, and seventy-one were finally analyzed. Body composition, nutrient intake, and metabolic parameters were assessed at baseline and after the 8-week intervention. Fat mass and obesity-associated (FTO) rs7185735 and melanocortin-4 receptor (MC4R) rs476828 variants were genotyped. Results We found that both variants did not influence weight loss or improvement of metabolic parameters within the Mediterranean diet intervention. Intake of saturated fatty acid (SFA) and trans fat was significantly increased in C carriers compared with the TT genotype of MC4R rs476828 only in the control group (p = 0.002 for SFA; p = 0.016 for trans fat), whereas no significant difference was observed between genotypes in the MeDiet group. There were statistically significant interactions between MC4R rs476828 and dietary intervention for changes in SFA intake (p = 0.009) and trans fat intake (p = 0.049). Conclusion Our data suggest that considering the effects of genotype may be more necessary when the Mediterranean diet is not followed and that this diet may have a protective role against the effects of certain genotypes. Further studies are required to determine the potential mechanism of the observed gene-diet interaction. Clinical Trial Registration [www.ClinicalTrials.gov], identifier [NCT04045392].
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Affiliation(s)
- A-Ra Cho
- Chaum Life Center, CHA University, Seoul, South Korea
| | - Kyung-Won Hong
- Theragen Etex Bio Institute Co., Ltd., Suwon, South Korea
| | - Yu-Jin Kwon
- Department of Family Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, South Korea
| | - Ja-Eun Choi
- Theragen Etex Bio Institute Co., Ltd., Suwon, South Korea
| | - Hye-Sun Lee
- Biostatistics Collaboration Unit, Department of Research Affairs, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyung-Mi Kim
- Department of Food and Nutrition, Dongduk Women’s University, Seoul, South Korea
| | - Soong June Bae
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Gwe Ahn
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Joon Jeong
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- *Correspondence: Joon Jeong,
| | - Ji-Won Lee
- Department of Family Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Ji-Won Lee,
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Prandi FR, Lecis D, Illuminato F, Milite M, Celotto R, Lerakis S, Romeo F, Barillà F. Epigenetic Modifications and Non-Coding RNA in Diabetes-Mellitus-Induced Coronary Artery Disease: Pathophysiological Link and New Therapeutic Frontiers. Int J Mol Sci 2022; 23:4589. [PMID: 35562979 PMCID: PMC9105558 DOI: 10.3390/ijms23094589] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 12/21/2022] Open
Abstract
Diabetes mellitus (DM) is a glucose metabolism disorder characterized by chronic hyperglycemia resulting from a deficit of insulin production and/or action. DM affects more than 1 in 10 adults, and it is associated with an increased risk of cardiovascular morbidity and mortality. Cardiovascular disease (CVD) accounts for two thirds of the overall deaths in diabetic patients, with coronary artery disease (CAD) and ischemic cardiomyopathy as the main contributors. Hyperglycemic damage on vascular endothelial cells leading to endothelial dysfunction represents the main initiating factor in the pathogenesis of diabetic vascular complications; however, the underlying pathophysiological mechanisms are still not entirely understood. This review addresses the current knowledge on the pathophysiological links between DM and CAD with a focus on the role of epigenetic modifications, including DNA methylation, histone modifications and noncoding RNA control. Increased knowledge of epigenetic mechanisms has contributed to the development of new pharmacological treatments ("epidrugs") with epigenetic targets, although these approaches present several challenges. Specific epigenetic biomarkers may also be used to predict or detect the development and progression of diabetes complications. Further studies on diabetes and CAD epigenetics are needed in order to identify possible new therapeutic targets and advance personalized medicine with the prediction of individual drug responses and minimization of adverse effects.
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Affiliation(s)
- Francesca Romana Prandi
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (D.L.); (F.I.); (M.M.); (R.C.); (F.B.)
- Department of Cardiology, Mount Sinai Hospital, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Dalgisio Lecis
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (D.L.); (F.I.); (M.M.); (R.C.); (F.B.)
| | - Federica Illuminato
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (D.L.); (F.I.); (M.M.); (R.C.); (F.B.)
| | - Marialucia Milite
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (D.L.); (F.I.); (M.M.); (R.C.); (F.B.)
| | - Roberto Celotto
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (D.L.); (F.I.); (M.M.); (R.C.); (F.B.)
| | - Stamatios Lerakis
- Department of Cardiology, Mount Sinai Hospital, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Francesco Romeo
- Department of Departmental Faculty of Medicine, Unicamillus-Saint Camillus International University of Health and Medical Sciences, 00131 Rome, Italy;
| | - Francesco Barillà
- Division of Cardiology, Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy; (D.L.); (F.I.); (M.M.); (R.C.); (F.B.)
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Jighly A. When do autopolyploids need poly-sequencing data? Mol Ecol 2021; 31:1021-1027. [PMID: 34875138 DOI: 10.1111/mec.16313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022]
Abstract
The sequencing depth required to genotype autopolyploid populations is a very controversial topic. Different studies have adopted variable depth values without a clear guide on the optimal sequencing depth value. Many studies suggest high depth thresholds for different ploidies that may not be practical and substantially increase the overall genotyping cost for different projects. However, such conservative thresholds may not be required to achieve the most common research goals. In fact, some recent reports in the field of quantitative genetics found that much lower sequencing depth thresholds could achieve the same accuracy as high depth thresholds. In this manuscript, I discuss when researchers need to use stringent sequencing depth thresholds and when they can use more relaxed ones. I support my argument by calculating the probabilities of sampling different homologues at a given sequencing depth. I also discuss the uses and the uncertainty in calculating a continuous allelic dosage as the proportion of sequencing reads that hold the alternative allele, which is becoming a common method now in quantitative genetics to replace discrete dosage estimation.
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Affiliation(s)
- Abdulqader Jighly
- AgriBio, Centre for AgriBiosciences, Agriculture Victoria, Bundoora, Victoria, Australia
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10
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Khajebishak Y, Alivand M, Faghfouri AH, Moludi J, Payahoo L. The effects of vitamins and dietary pattern on epigenetic modification of non-communicable diseases. INT J VITAM NUTR RES 2021. [PMID: 34643416 DOI: 10.1024/0300-9831/a000735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Background: Non-communicable diseases (NCDs) have received more attention because of high prevalence and mortality rate. Besides genetic and environmental factors, the epigenetic abnormality is also involved in the pathogenesis of NCDs. Methylation of DNA, chromatin remodeling, modification of histone, and long non-coding RNAs are the main components of epigenetic phenomena. Methodology: In this review paper, the mechanistic role of vitamins and dietary patterns on epigenetic modification was discussed. All papers indexed in scientific databases, including PubMed, Scopus, Embase, Google Scholar, and Elsevier were searched during 2000 - 2021 using, vitamins, diet, epigenetic repression, histones, methylation, acetylation, and NCDs as keywords. Results: The components of healthy dietary patterns like Mediterranean and dietary approaches to stop hypertension diets have a beneficial effect on epigenetic hemostasis. Both quality and quantity of dietary components influence epigenetic phenomena. A diet with calorie deficiency in protein content and methyl-donor agents in a long time, with a high level of fat, disrupts epigenetic hemostasis and finally, causes genome instability. Also, soluble and insoluble vitamins have an obvious role in epigenetic modifications. Most vitamins interact directly with methylation, acetylation, and phosphorylation pathways of histone and DNA. However, numerous indirect functions related to the cell cycle stability and genome integrity have been recognized. Conclusion: Considering the crucial role of a healthy diet in epigenetic homeostasis, adherence to a healthy dietary pattern containing enough levels of vitamin and avoiding the western diet seems to be necessary. Having a healthy diet and consuming the recommended dietary level of vitamins can also contribute to epigenetic stability.
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Affiliation(s)
- Yaser Khajebishak
- Department of Nutrition and Food Sciences, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Mohammadreza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Jalal Moludi
- School of Nutrition Sciences and Food Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Laleh Payahoo
- Department of Nutrition and Food Sciences, Maragheh University of Medical Sciences, Maragheh, Iran
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Falbová D, Vorobeľová L, Siváková D, Beňuš R. Association between FTO (rs17817449) genetic variant, gamma-glutamyl transferase, and hypertension in Slovak midlife women. Am J Hum Biol 2021; 34:e23672. [PMID: 34436809 DOI: 10.1002/ajhb.23672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/11/2021] [Accepted: 08/13/2021] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES This cross-sectional study investigates associations between the FTO rs 17817449 genetic variant, liver enzymes, and hypertension in Slovak midlife women. METHODS We assessed 576 Slovak women aged 39 to 65 years. The women were interviewed and examined during their medical examination at local Health Centers and then divided into subgroups according to their blood pressure status; 255 women with hypertension and 321 normotensive. The FTO genetic variant was detected by polymerase chain reaction-restriction fragment length polymorphism. Resultant data was analyzed by linear regression analysis and general linear models to adjust for risk factors associated with gamma-glutamyl transferase levels (GGT), including waist to hip ratio (WHR) and uric acid (UA). RESULTS A significant association between the FTO variant and GGT levels was observed in the hypertensive group after control for confounding covariates, including WHR and UA (p = .004). The predicted GGT level for GT/TT hypertensive carriers is 0.158 μkat/L higher than for GG carriers. Moreover, the two-way analysis of covariance revealed significant interaction between FTO effects and hypertension on logGGT levels (p = .042). Finally, hypertensive women with the T-allele had the highest estimated marginal mean value of logGGT at -0.39 μkat/L while the GG-genotype in both hypertensive and normotensive women had the lowest value at -0.54 μkat/L. CONCLUSIONS This study suggests that the FTO (rs17817449) variant is associated with higher serum GGT levels in hypertensive midlife women.
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Affiliation(s)
- Darina Falbová
- Department of Anthropology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Lenka Vorobeľová
- Department of Anthropology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Daniela Siváková
- Department of Anthropology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Radoslav Beňuš
- Department of Anthropology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
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Capparelli R, Iannelli D. Role of Epigenetics in Type 2 Diabetes and Obesity. Biomedicines 2021; 9:977. [PMID: 34440181 PMCID: PMC8393970 DOI: 10.3390/biomedicines9080977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 12/23/2022] Open
Abstract
Epigenetic marks the genome by DNA methylation, histone modification or non-coding RNAs. Epigenetic marks instruct cells to respond reversibly to environmental cues and keep the specific gene expression stable throughout life. In this review, we concentrate on DNA methylation, the mechanism often associated with transgenerational persistence and for this reason frequently used in the clinic. A large study that included data from 10,000 blood samples detected 187 methylated sites associated with body mass index (BMI). The same study demonstrates that altered methylation results from obesity (OB). In another study the combined genetic and epigenetic analysis allowed us to understand the mechanism associating hepatic insulin resistance and non-alcoholic disease in Type 2 Diabetes (T2D) patients. The study underlines the therapeutic potential of epigenetic studies. We also account for seemingly contradictory results associated with epigenetics.
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Affiliation(s)
- Rosanna Capparelli
- Department of Agriculture Sciences, University of Naples “Federico II”, Via Università, 100-Portici, 80055 Naples, Italy
| | - Domenico Iannelli
- Department of Agriculture Sciences, University of Naples “Federico II”, Via Università, 100-Portici, 80055 Naples, Italy
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Rana S, Sultana A, Bhatti AA. Effect of interaction between obesity-promoting genetic variants and behavioral factors on the risk of obese phenotypes. Mol Genet Genomics 2021; 296:919-938. [PMID: 33966103 DOI: 10.1007/s00438-021-01793-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/22/2021] [Indexed: 01/28/2023]
Abstract
The studies investigating gene-gene and gene-environment (or gene-behavior) interactions provide valuable insight into the pathomechanisms underlying obese phenotypes. The Pakistani population due to its unique characteristics offers numerous advantages for conducting such studies. In this view, the current study was undertaken to examine the effects of gene-gene and gene-environment/behavior interactions on the risk of obesity in a sample of Pakistani population. A total of 578 adult participants including 290 overweight/obese cases and 288 normal-weight controls were involved. The five key obesity-associated genetic variants namely MC4R rs17782313, BDNF rs6265, FTO rs1421085, TMEM18 rs7561317, and NEGR1 rs2815752 were genotyped using the TaqMan allelic discrimination assays. The data related to behavioral factors, such as eating pattern, diet consciousness, the tendency toward fat-dense food (TFDF), sleep duration, sleep-wake cycle (SWC), shift work (SW), and physical activity levels were collected via a questionnaire. Gene-gene and gene-behavior interactions were analyzed by multifactor dimensionality reduction and linear regression, respectively. In our study, only TMEM18 rs7561317 was found to be significantly associated with anthropometric traits with no significant effect of gene-gene interactions were observed on obesity-related phenotypes. However, the genetic variants were found to interact with the behavioral factors to significantly influence various obesity-related anthropometric traits including BMI, waist circumference, hip circumference, waist-to-hip ratio, waist-to-height ratio, and percentage of body fat. In conclusion, the interaction between genetic architecture and behavior/environment determines the outcome of obesity-related anthropometric phenotypes. Thus, gene-environment/behavior interaction studies should be promoted to explore the risk of complex and multifactorial disorders, such as obesity.
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Affiliation(s)
- Sobia Rana
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan.
| | - Ayesha Sultana
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Adil Anwar Bhatti
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
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14
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Masi S, Ambrosini S, Mohammed SA, Sciarretta S, Lüscher TF, Paneni F, Costantino S. Epigenetic Remodeling in Obesity-Related Vascular Disease. Antioxid Redox Signal 2021; 34:1165-1199. [PMID: 32808539 DOI: 10.1089/ars.2020.8040] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Significance: The prevalence of obesity and cardiometabolic phenotypes is alarmingly increasing across the globe and is associated with atherosclerotic vascular complications and high mortality. In spite of multifactorial interventions, vascular residual risk remains high in this patient population, suggesting the need for breakthrough therapies. The mechanisms underpinning obesity-related vascular disease remain elusive and represent an intense area of investigation. Recent Advances: Epigenetic modifications-defined as environmentally induced chemical changes of DNA and histones that do not affect DNA sequence-are emerging as a potent modulator of gene transcription in the vasculature and might significantly contribute to the development of obesity-induced endothelial dysfunction. DNA methylation and histone post-translational modifications cooperate to build complex epigenetic signals, altering transcriptional networks that are implicated in redox homeostasis, mitochondrial function, vascular inflammation, and perivascular fat homeostasis in patients with cardiometabolic disturbances. Critical Issues: Deciphering the epigenetic landscape in the vasculature is extremely challenging due to the complexity of epigenetic signals and their function in regulating transcription. An overview of the most important epigenetic pathways is required to identify potential molecular targets to treat or prevent obesity-related endothelial dysfunction and atherosclerotic disease. This would enable the employment of precision medicine approaches in this setting. Future Directions: Current and future research efforts in this field entail a better definition of the vascular epigenome in obese patients as well as the unveiling of novel, cell-specific chromatin-modifying drugs that are able to erase specific epigenetic signals that are responsible for maladaptive transcriptional alterations and vascular dysfunction in obese patients. Antioxid. Redox Signal. 34, 1165-1199.
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Affiliation(s)
- Stefano Masi
- Dipartimento di Medicina Clinica e Sperimentale, Università di Pisa, Pisa, Italy
| | - Samuele Ambrosini
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
| | - Shafeeq A Mohammed
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
| | - Sebastiano Sciarretta
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy.,Department of AngioCardioNeurology, IRCCS Neuromed, Pozzilli, Italy
| | - Thomas F Lüscher
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland.,Heart Division, Royal Brompton and Harefield Hospital Trust, National Heart & Lung Institute, Imperial College, London, United Kingdom
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland.,Department of Cardiology, University Heart Center, University Hospital Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Zurich, Switzerland
| | - Sarah Costantino
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
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15
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Tseng CC, Wong MC, Liao WT, Chen CJ, Lee SC, Yen JH, Chang SJ. Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases. Int J Mol Sci 2021; 22:ijms22084187. [PMID: 33919522 PMCID: PMC8073710 DOI: 10.3390/ijms22084187] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Variants of transcription factor binding sites (TFBSs) constitute an important part of the human genome. Current evidence demonstrates close links between nucleotides within TFBSs and gene expression. There are multiple pathways through which genomic sequences located in TFBSs regulate gene expression, and recent genome-wide association studies have shown the biological significance of TFBS variation in human phenotypes. However, numerous challenges remain in the study of TFBS polymorphisms. This article aims to cover the current state of understanding as regards the genomic features of TFBSs and TFBS variants; the mechanisms through which TFBS variants regulate gene expression; the approaches to studying the effects of nucleotide changes that create or disrupt TFBSs; the challenges faced in studies of TFBS sequence variations; the effects of natural selection on collections of TFBSs; in addition to the insights gained from the study of TFBS alleles related to gout, its associated comorbidities (increased body mass index, chronic kidney disease, diabetes, dyslipidemia, coronary artery disease, ischemic heart disease, hypertension, hyperuricemia, osteoporosis, and prostate cancer), and the treatment responses of patients.
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Affiliation(s)
- Chia-Chun Tseng
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.T.); (J.-H.Y.)
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Man-Chun Wong
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Wei-Ting Liao
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Correspondence: (W.-T.L.); (S.-J.C.); Tel.: +886-7-3121101 (W.-T.L.); +886-7-5916679 (S.-J.C.); Fax:+886-7-3125339 (W.-T.L.); +886-7-5919264 (S.-J.C.)
| | - Chung-Jen Chen
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 80145, Taiwan;
| | - Su-Chen Lee
- Laboratory Diagnosis of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Jeng-Hsien Yen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.T.); (J.-H.Y.)
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu 30010, Taiwan
| | - Shun-Jen Chang
- Department of Kinesiology, Health and Leisure Studies, National University of Kaohsiung, Kaohsiung 81148, Taiwan
- Correspondence: (W.-T.L.); (S.-J.C.); Tel.: +886-7-3121101 (W.-T.L.); +886-7-5916679 (S.-J.C.); Fax:+886-7-3125339 (W.-T.L.); +886-7-5919264 (S.-J.C.)
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16
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Huang S, Qin P, Chen Q, Zhang D, Cheng C, Guo C, Li Q, Zhou Q, Tian G, Qie R, Han M, Wu X, Yang X, Feng Y, Li Y, Zhang Y, Wu Y, Liu D, Lu J, Zhang M, Zhao Y, Hu D. Association of FTO gene methylation with incident type 2 diabetes mellitus: A nested case-control study. Gene 2021; 786:145585. [PMID: 33753148 DOI: 10.1016/j.gene.2021.145585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVES This study aimed to investigate the association of FTO methylation level with type 2 diabetes mellitus (T2DM) in a nested case-control study. METHODS This nested case-control study included 287 pairs of T2DM cases and controls identified from a rural Chinese cohort study with a 6-year follow-up. Controls were matched to the cases on a 1:1 basis by age, sex, ethnicity, marital status, and residence. Conditional multivariate logistic regression models were used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) for the association of cytosine guanine (CpG) locus and tag-single nucleotide polymorphisms (Tag-SNPs) with T2DM. Spearman correlation analysis was used to evaluate the association between FTO methylation and possible risk factors for T2DM in the control group. RESULTS The methylation level on the CpG9 site significantly differs between cases and controls, with a significant association between the CpG9 site methylation and probability of T2DM: OR 2.19 (95%CI: 1.31-3.65) after adjusting for potential confounders. The Tag-SNPs (rs72803657, rs1558902, rs17817449, rs11076023) were not associated with T2DM. Further, FTO methylation was associated with some risk factors for T2DM. CONCLUSIONS A CpG locus of FTO was positively associated with T2DM, but SNPs were not. FTO methylation were also associated with some T2DM risk factors. Further study with a large sample size and data on metabolic product are needed to confirm the association.
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Affiliation(s)
- Shengbing Huang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Pei Qin
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Qing Chen
- Department of Mental Health, Bao'an Chronic Diseases Prevent and Cure Hospital, Shenzhen, Guangdong, People's Republic of China
| | - Dongdong Zhang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Cheng Cheng
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Chunmei Guo
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Quanman Li
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Qionggui Zhou
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Gang Tian
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Ranran Qie
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Minghui Han
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Xiaoyan Wu
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Xingjin Yang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yifei Feng
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yang Li
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yanyan Zhang
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yuying Wu
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Dechen Liu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Jie Lu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Ming Zhang
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, Guangdong, People's Republic of China
| | - Yang Zhao
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China.
| | - Dongsheng Hu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, People's Republic of China.
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17
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González LM, García-Herráiz A, Mota-Zamorano S, Flores I, Albuquerque D, Gervasini G. Variants in the Obesity-Linked FTO gene locus modulates psychopathological features of patients with Anorexia Nervosa. Gene 2021; 783:145572. [PMID: 33737121 DOI: 10.1016/j.gene.2021.145572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022]
Abstract
Our aim was to determine whether variability in the fat mass obesity (FTO) gene locus, consistently related to obesity, affects the risk of eating disorders (ED) and/or the psychopathology displayed by these patients. We analyzed 26 tag-single nucleotide polymorphisms (SNPs) that capture FTO variability in 352 ED patients [233 with Anorexia Nervosa (AN) and 119 with binge-eating] and 396 controls. Psychopathological symptoms and traits were evaluated by the Eating Disorders Inventory Test 2 (EDI-2) and Symptoms Checklist 90 Revised (SCL-90R) questionnaires. No associations were found for ED risk. The rs7205987 CC genotype correlated with higher scores in all but one of the EDI-2 scales in the AN group. Associations with Bulimia (p = 0.0019) and Interoceptive Awareness (p = 0.00007) retained significance after False Discovery Rate (FDR) correction for multiple testing. A 3-SNP sliding window analysis showed that FTO haplotypes were again highly associated with Interoceptive Awareness (rs9921255/rs6499662/rs7205987 haplotype; FDR-q = 0.04), Bulimia (rs1125338/rs2192872/rs708258; FDR-q = 0.00037), and Maturity Fears (rs708258/rs12599672/rs11076017; FDR-q = 0.041). In addition, a distal region of the gene between rs9924877 (position 53947509) and rs2192872 (54040715) was linked to Anxiety, Depression and Phobic Anxiety in AN patients, with FDR-q values ranging from 0.023 to 0.045. The results suggest that the FTO gene might be an important locus regarding traits and psychopathological symptoms often displayed by AN patients.
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Affiliation(s)
- Luz M González
- Dpt. Medical-Surgical Therapeutics, Medical School, University of Extremadura, Badajoz, Spain
| | - Angustias García-Herráiz
- Eating Disorders Unit, Institute of Mental Disorders, Health Service of Extremadura, Badajoz, Spain
| | - Sonia Mota-Zamorano
- Dpt. Medical-Surgical Therapeutics, Medical School, University of Extremadura, Badajoz, Spain
| | - Isalud Flores
- Eating Disorders Unit, Institute of Mental Disorders, Health Service of Extremadura, Badajoz, Spain
| | - David Albuquerque
- Genomics Group, Fundación Investigación Hospital General Universitario de Valencia, Valencia, Spain
| | - Guillermo Gervasini
- Dpt. Medical-Surgical Therapeutics, Medical School, University of Extremadura, Badajoz, Spain.
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18
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Yang HJ, Koh E, Sung MK, Kang H. Changes Induced by Mind-Body Intervention Including Epigenetic Marks and Its Effects on Diabetes. Int J Mol Sci 2021; 22:ijms22031317. [PMID: 33525677 PMCID: PMC7865217 DOI: 10.3390/ijms22031317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 12/20/2022] Open
Abstract
Studies have evidenced that epigenetic marks associated with type 2 diabetes (T2D) can be inherited from parents or acquired through fetal and early-life events, as well as through lifelong environments or lifestyles, which can increase the risk of diabetes in adulthood. However, epigenetic modifications are reversible, and can be altered through proper intervention, thus mitigating the risk factors of T2D. Mind-body intervention (MBI) refers to interventions like meditation, yoga, and qigong, which deal with both physical and mental well-being. MBI not only induces psychological changes, such as alleviation of depression, anxiety, and stress, but also physiological changes like parasympathetic activation, lower cortisol secretion, reduced inflammation, and aging rate delay, which are all risk factors for T2D. Notably, MBI has been reported to reduce blood glucose in patients with T2D. Herein, based on recent findings, we review the effects of MBI on diabetes and the mechanisms involved, including epigenetic modifications.
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Affiliation(s)
- Hyun-Jeong Yang
- Korea Institute of Brain Science, Seoul 06022, Korea; (M.-K.S.); (H.K.)
- Department of Integrative Health Care, University of Brain Education, Cheonan 31228, Korea
- Correspondence:
| | - Eugene Koh
- Temasek Life Sciences Laboratories, Singapore 117604, Singapore;
| | - Min-Kyu Sung
- Korea Institute of Brain Science, Seoul 06022, Korea; (M.-K.S.); (H.K.)
| | - Hojung Kang
- Korea Institute of Brain Science, Seoul 06022, Korea; (M.-K.S.); (H.K.)
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19
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Keyhan S, Burke E, Schrott R, Huang Z, Grenier C, Price T, Raburn D, Corcoran DL, Soubry A, Hoyo C, Murphy SK. Male obesity impacts DNA methylation reprogramming in sperm. Clin Epigenetics 2021; 13:17. [PMID: 33494820 PMCID: PMC7831195 DOI: 10.1186/s13148-020-00997-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Male obesity has profound effects on morbidity and mortality, but relatively little is known about the impact of obesity on gametes and the potential for adverse effects of male obesity to be passed to the next generation. DNA methylation contributes to gene regulation and is erased and re-established during gametogenesis. Throughout post-pubertal spermatogenesis, there are continual needs to both maintain established methylation and complete DNA methylation programming, even during epididymal maturation. This dynamic epigenetic landscape may confer increased vulnerability to environmental influences, including the obesogenic environment, that could disrupt reprogramming fidelity. Here we conducted an exploratory analysis that showed that overweight/obesity (n = 20) is associated with differences in mature spermatozoa DNA methylation profiles relative to controls with normal BMI (n = 47). RESULTS We identified 3264 CpG sites in human sperm that are significantly associated with BMI (p < 0.05) using Infinium HumanMethylation450 BeadChips. These CpG sites were significantly overrepresented among genes involved in transcriptional regulation and misregulation in cancer, nervous system development, and stem cell pluripotency. Analysis of individual sperm using bisulfite sequencing of cloned alleles revealed that the methylation differences are present in a subset of sperm rather than being randomly distributed across all sperm. CONCLUSIONS Male obesity is associated with altered sperm DNA methylation profiles that appear to affect reprogramming fidelity in a subset of sperm, suggestive of an influence on the spermatogonia. Further work is required to determine the potential heritability of these DNA methylation alterations. If heritable, these changes have the potential to impede normal development.
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Affiliation(s)
- Sanaz Keyhan
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27713, USA
| | - Emily Burke
- Department of Biostatistics, Duke University, Durham, 27710, USA
| | - Rose Schrott
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, 501 W. Main Street, Suite 510, The Chestefield Building, PO Box 90534, Durham, NC, 27701, USA.,Duke University Integrated Toxicology and Environmental Health Program, The Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Zhiqing Huang
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, 501 W. Main Street, Suite 510, The Chestefield Building, PO Box 90534, Durham, NC, 27701, USA
| | - Carole Grenier
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, 501 W. Main Street, Suite 510, The Chestefield Building, PO Box 90534, Durham, NC, 27701, USA
| | - Thomas Price
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27713, USA
| | - Doug Raburn
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27713, USA
| | - David L Corcoran
- Center for Genomics and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Adelheid Soubry
- Epidemiology Research Group, Department of Public Health and Primary Care, Faculty of Medicine, KU Leuven University, 2000, Leuven, Belgium
| | - Catherine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27633, USA
| | - Susan K Murphy
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, 501 W. Main Street, Suite 510, The Chestefield Building, PO Box 90534, Durham, NC, 27701, USA. .,Duke University Integrated Toxicology and Environmental Health Program, The Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA.
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20
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Freitas ABD, Francisco RPV, Centofanti SF, Damasceno JG, Chehimi SN, Osmundo-Junior GDS, Kulikowski LD, Brizot MDL. Fetal gastroschisis: Maternal and fetal methylation profile. Prenat Diagn 2021; 41:449-456. [PMID: 33332636 DOI: 10.1002/pd.5881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 01/04/2023]
Abstract
OBJECTIVE The purpose of this study was to describe the genomic deoxyribonucleic acid (DNA) methylation profile in fetuses with gastroschisis, determine whether the profile was inherited, and investigate any possible correlations with maternal risk factors. METHOD Genome-wide DNA methylation analysis of 96 blood samples was performed using the Illumina Human Methylation 850K BeadChip. The blood samples were collected as follows: 32 from the umbilical cord of fetuses with gastroschisis, 32 from their respective mothers, 16 from the umbilical cord of fetuses without malformation, and 16 from their respective mothers. RESULTS The differential DNA methylation analysis showed a significant difference between the groups. The enrichment analysis resulted in 12 sites related to T-cell activation (p = 0.0128). The sites with different methylation status contained 10 genes, three of which were related to the beta-2-microglobulin gene. The methylation profile observed in the fetuses with gastroschisis was not inherited from the mothers. In addition, there was no association between maternal urinary tract infection, smoking, and alcohol use and different methylated sites. CONCLUSION We established the methylation profile of gastroschisis fetuses, which differs from that of normal fetuses. The profile was not inherited and did not correlate with maternal risk factors.
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Affiliation(s)
- Amanda Brasil de Freitas
- Department of Obstetrics and Gynecology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil.,Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | | | - Sandra Frankfurt Centofanti
- Department of Obstetrics and Gynecology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Jullian Gabriel Damasceno
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Samar Nasser Chehimi
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Gilmar de Souza Osmundo-Junior
- Department of Obstetrics and Gynecology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Leslie Domenici Kulikowski
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Maria de Lourdes Brizot
- Department of Obstetrics and Gynecology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
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21
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Kucher AN. The FTO Gene and Diseases: The Role of Genetic Polymorphism, Epigenetic Modifications, and Environmental Factors. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420090136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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22
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Todendi PF, Martínez JA, Reuter CP, Klinger EI, Fiegenbaum M, Rosane de Moura Valim A. Influence of FTO (Fat mass and obesity) gene and parental obesity on Brazilian children and adolescents adiposity. J Pediatr Endocrinol Metab 2020; 33:/j/jpem.ahead-of-print/jpem-2019-0594/jpem-2019-0594.xml. [PMID: 32697757 DOI: 10.1515/jpem-2019-0594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/14/2020] [Indexed: 12/13/2022]
Abstract
Objectives Evaluate the influence of the genetic variant rs9939609 of the FTO gene on anthropometric characteristics and whether parental obesity is related to children and adolescents being overweight. Methods A total of 2,364 children and adolescents between 6 and 17 years old were genotyped and the lipid profile, plasma glucose level, and anthropometric characteristics were measured to assess adiposity. Results The AA genotype (risk) was associated with higher body mass index (BMI Z-score; p = 0.006), waist circumference (WC; p = 0.001), and triglycerides (p = 0.033). The association of the participants' adiposity characteristics with the parents' BMI and FTO genotypes showed an association of the BMI Z-score when either the mother or father was overweight or obese (p = 0.028 and p = 0.029). In the overweight or obese father/eutrophic mother, we also observe an association of FTO rs9939609 with WC (p = 0.039). The effect of these variables on the risk of obesity was also tested: overweight or obese mother (OR = 1.82, p = 0.041), overweight and obese parents (OR = 3.09, p < 0.0001), and FTO rs9939609 AA genotype (OR = 2.08, p = 0.0004) were associated. With regard to altered WC and high body fat percentage (BF%), either overweight or obese parents (OR = 2.39, p < 0.0001; OR = 1.92, p < 0.002) showed an association. The FTO rs9939609 AA genotype (OR = 1.99, p = 0.0002) was associated with altered WC. Conclusions The results show that parental weight also contributes to obesity and may interact with the FTO genetic make-up.
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Affiliation(s)
- Pâmela Ferreira Todendi
- Post-Graduation Program in Pathology, Federal University of Health Sciences of Porto Alegre - UFCSPA, Porto Alegre, RS, Brazil
- Department of Nutrition and Food Sciences, Physiology and Toxicology, University of Navarra, Irunlarrea 1, Pamplona, Navarra, CIBERobn and IMDEA Food, Madrid, Spain
| | - J Alfredo Martínez
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Nutrition and Food Sciences, Physiology and Toxicology, University of Navarra, Irunlarrea 1, Pamplona, Navarra, CIBERobn and IMDEA Food, Madrid, Spain
- Cardiometabolic Nutrition Group, IMDEA Food, CEI UAM + CSIC, Madrid, Spain
| | - Cézane P Reuter
- Department of Physical Education and Health and the Post-Graduation Program in Health Promotion, University of Santa Cruz do Sul - UNISC, Santa Cruz do Sul, RS, Brazil
| | - Elisa I Klinger
- Post-Graduation Program in Health Promotion, University of Santa Cruz do Sul - UNISC, Santa Cruz do Sul, RS, Brazil
| | - Marilu Fiegenbaum
- Department of Basic Health Sciences, Federal University of Health Sciences of Porto Alegre - UFCSPA, Porto Alegre, RS, Brazil
| | - Andreia Rosane de Moura Valim
- Department of Biology and Pharmaceutical Sciences and the Post-Graduation Program in Health Promotion, Rua Gaspar Silveira Martins 888/05, DistritoSanto Inácio, Santa Cruz do Sul, RS, CEP 96820-002,Brazil
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Diels S, Vanden Berghe W, Van Hul W. Insights into the multifactorial causation of obesity by integrated genetic and epigenetic analysis. Obes Rev 2020; 21:e13019. [PMID: 32170999 DOI: 10.1111/obr.13019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/24/2020] [Accepted: 03/04/2020] [Indexed: 12/11/2022]
Abstract
Obesity is a highly heritable multifactorial disease that places an enormous burden on human health. Its increasing prevalence and the concomitant-reduced life expectancy has intensified the search for new analytical methods that can reduce the knowledge gap between genetic susceptibility and functional consequences of the disease pathology. Although the influence of genetics and epigenetics has been studied independently in the past, there is increasing evidence that genetic variants interact with environmental factors through epigenetic regulation. This suggests that a combined analysis of genetic and epigenetic variation may be more effective in characterizing the obesity phenotype. To date, limited genome-wide integrative analyses have been performed. In this review, we provide an overview of the latest findings, advantages, and challenges and discuss future perspectives.
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Affiliation(s)
- Sara Diels
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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24
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Association between impulsivity traits and body mass index at the observational and genetic epidemiology level. Sci Rep 2019; 9:17583. [PMID: 31772290 PMCID: PMC6879509 DOI: 10.1038/s41598-019-53922-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/07/2019] [Indexed: 01/09/2023] Open
Abstract
We investigated the association between impulsivity related traits and BMI at the observational and genetic epidemiology level in a cross-sectional population of healthy young American-European adults. We studied 998 students and university staff of European ancestry recruited from Chicago (Illinois) and Athens (Georgia). We measured 14 impulsivity variables using three broad categories: impulsive choice, action and personality. Weight and height of participants were measured by research assistants. The single-nucleotide polymorphism (SNP) rs3751812 in the fat mass and obesity-associated (FTO) gene was genotyped using the Illumina PsychArray BeadChip platform. Within the three broad domains of impulsivity, 4 parameters (delay discounting of rewards area under the curve and average of k indexes, Conner's continuous performance test, and negative urgency) were associated with BMI. The FTO rs3751812 minor allele T was associated with higher BMI. Of the 14 impulsivity variables, rs3751812 T was associated with more premeditation and perseverance, before and after adjusting for BMI. The association between FTO rs3751812 and BMI adjusted for premeditation remained significant, but disappeared after adjusting for perseverance and for both perseverance and premeditation traits. Our observational and genetic data indicate a complex pattern of association between impulsive behaviors and BMI in healthy young American-European adults.
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25
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Al Bkhetan Z, Zobel J, Kowalczyk A, Verspoor K, Goudey B. Exploring effective approaches for haplotype block phasing. BMC Bioinformatics 2019; 20:540. [PMID: 31666002 PMCID: PMC6822470 DOI: 10.1186/s12859-019-3095-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/10/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Knowledge of phase, the specific allele sequence on each copy of homologous chromosomes, is increasingly recognized as critical for detecting certain classes of disease-associated mutations. One approach for detecting such mutations is through phased haplotype association analysis. While the accuracy of methods for phasing genotype data has been widely explored, there has been little attention given to phasing accuracy at haplotype block scale. Understanding the combined impact of the accuracy of phasing tool and the method used to determine haplotype blocks on the error rate within the determined blocks is essential to conduct accurate haplotype analyses. RESULTS We present a systematic study exploring the relationship between seven widely used phasing methods and two common methods for determining haplotype blocks. The evaluation focuses on the number of haplotype blocks that are incorrectly phased. Insights from these results are used to develop a haplotype estimator based on a consensus of three tools. The consensus estimator achieved the most accurate phasing in all applied tests. Individually, EAGLE2, BEAGLE and SHAPEIT2 alternate in being the best performing tool in different scenarios. Determining haplotype blocks based on linkage disequilibrium leads to more correctly phased blocks compared to a sliding window approach. We find that there is little difference between phasing sections of a genome (e.g. a gene) compared to phasing entire chromosomes. Finally, we show that the location of phasing error varies when the tools are applied to the same data several times, a finding that could be important for downstream analyses. CONCLUSIONS The choice of phasing and block determination algorithms and their interaction impacts the accuracy of phased haplotype blocks. This work provides guidance and evidence for the different design choices needed for analyses using haplotype blocks. The study highlights a number of issues that may have limited the replicability of previous haplotype analysis.
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Affiliation(s)
- Ziad Al Bkhetan
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia
| | - Justin Zobel
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia
| | - Adam Kowalczyk
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia.,Centre for Neural Engineering, University of Melbourne, Carlton, 3053, Australia.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, 00-662, Poland.,Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, 3010, Australia
| | - Karin Verspoor
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia.
| | - Benjamin Goudey
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, 3010, Australia.,IBM Australia - Research, Southgate, 3006, Australia
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26
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Yamada Y, Sasaki S. A method for identifying allele-specific hydroxymethylation. Epigenetics 2019; 15:231-250. [PMID: 31533538 DOI: 10.1080/15592294.2019.1664228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
We previously identified sequence-dependent allele-specific methylation (sd-ASM) in adult human peripheral blood leukocytes, in which ASM occurs in cis depending on adjacent polymorphic sequences. A number of groups have identified sd-ASM sites in the human and mouse genomes, illustrating the prevalence of sd-ASM in mammalian genomes. In addition, sd-ASM can lead to sequence-dependent allele-specific expression of neighbouring genes. Imprinted genes also often exhibit parent-of-origin-dependent allele-specific methylation (pd-ASM), which causes parent-of-origin-dependent allele-specific expression. However, whether most of the already known sd-ASM and pd-ASM sites are methylated or hydroxymethylated remains unclear due to technical restrictions. Accordingly, a novel method that enables examination of allelic methylation and hydroxymethylation status and also overcomes the drawbacks of conventional methods is needed. Such a method could also be used to elucidate the mechanisms underlying polymorphism-associated inter-individual differences in disease susceptibility and the mechanism of genomic imprinting. Here, we developed a simple method to determine allelic hydroxymethylation status and identified novel sequence- and parent-of-origin-dependent allele-specific hydroxymethylation sites. Correlation analyses of TF binding sequences and methylation or hydroxymethylation between three mouse strains revealed the involvement of Pax5 in strain-specific methylation and hydroxymethylation in exon 7 of Pdgfrb.
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Affiliation(s)
- Yoichi Yamada
- Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Sho Sasaki
- Division of Electrical and Computer Engineering, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
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Guilherme JPLF, Egorova ES, Semenova EA, Kostryukova ES, Kulemin NA, Borisov OV, Khabibova SA, Larin AK, Ospanova EA, Pavlenko AV, Lyubaeva EV, Popov DV, Lysenko EA, Vepkhvadze TF, Lednev EM, Govorun VM, Generozov EV, Ahmetov II, Lancha Junior AH. The A-allele of the FTO Gene rs9939609 Polymorphism Is Associated With Decreased Proportion of Slow Oxidative Muscle Fibers and Over-represented in Heavier Athletes. J Strength Cond Res 2019; 33:691-700. [PMID: 30694969 DOI: 10.1519/jsc.0000000000003032] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Guilherme, JPLF, Egorova, ES, Semenova, EA, Kostryukova, ES, Kulemin, NA, Borisov, OV, Khabibova, SA, Larin, AK, Ospanova, EA, Pavlenko, AV, Lyubaeva, EV, Popov, DV, Lysenko, EA, Vepkhvadze, TF, Lednev, EM, Govorun, VM, Generozov, EV, Ahmetov, II, and Lancha Junior, AH. The A-allele of the FTO gene rs9939609 polymorphism is associated with decreased proportion of slow oxidative muscle fibers and over-represented in heavier athletes. J Strength Cond Res 33(3): 691-700, 2019-The purpose of this study was to explore the frequency of the FTO T > A (rs9939609) polymorphism in elite athletes from 2 cohorts (Brazil and Russia), as well as to find a relationship between FTO genotypes and muscle fiber composition. A total of 677 athletes and 652 nonathletes were evaluated in the Brazilian cohort, whereas a total of 920 athletes and 754 nonathletes were evaluated in the Russian cohort. It was found a trend for a lower frequency of A/A genotype in long-distance athletes compared with nonathletes (odds ratio [OR]: 0.65; p = 0.054). By contrast, it was found an increased frequency of the A-allele in Russian power athletes. The presence of the T/A + A/A genotypes rather than T/T increased the OR of being a Russian power athlete compared with matched nonathletes (OR: 1.45; p = 0.002). Different from that observed in combat sports athletes of lighter weight categories, the A-allele was also over-represented in combat sports athletes of heavier weight categories. The presence of the T/A + A/A genotypes rather than T/T increased the OR of being a combat sports athlete of heavier weight categories compared with nonathletes (OR: 1.79; p = 0.018). Regarding the muscle fibers, we found that carriers of the A/A genotype had less slow-twitch muscle fibers than T-allele carriers (p = 0.029). In conclusion, the A/A genotype of the FTO T > A polymorphism is under-represented in athletes more reliant on a lean phenotype and associated with decreased proportion of slow-twitch muscle fibers, while is over-represented in strength and heavier athletes.
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Affiliation(s)
- João Paulo L F Guilherme
- Laboratory of Applied Nutrition and Metabolism, Department of Biodynamics of the Human Body Movement, School of Physical Education and Sport, University of Sao Paulo, São Paulo, Brazil
| | - Emiliya S Egorova
- Laboratory of Molecular Genetics, Kazan State Medical University, Kazan, Russia
| | - Ekaterina A Semenova
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.,Department of Biochemistry, Kazan Federal University, Kazan, Russia
| | - Elena S Kostryukova
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Nickolay A Kulemin
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Oleg V Borisov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.,Moscow Institute of Physics and Technology (State University), Moscow, Russia
| | - Sofya A Khabibova
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrey K Larin
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Elena A Ospanova
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Alexander V Pavlenko
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ekaterina V Lyubaeva
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Daniil V Popov
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Evgeny A Lysenko
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Tatiana F Vepkhvadze
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Egor M Lednev
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Vadim M Govorun
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Edward V Generozov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ildus I Ahmetov
- Laboratory of Molecular Genetics, Kazan State Medical University, Kazan, Russia.,Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.,Sports Genetics Laboratory, St Petersburg Research Institute of Physical Culture, St Petersburg, Russia.,Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Antonio H Lancha Junior
- Laboratory of Applied Nutrition and Metabolism, Department of Biodynamics of the Human Body Movement, School of Physical Education and Sport, University of Sao Paulo, São Paulo, Brazil
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Ingelsson E, McCarthy MI. Human Genetics of Obesity and Type 2 Diabetes Mellitus: Past, Present, and Future. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e002090. [PMID: 29899044 DOI: 10.1161/circgen.118.002090] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Type 2 diabetes mellitus (T2D) and obesity already represent 2 of the most prominent risk factors for cardiovascular disease, and are destined to increase in importance given the global changes in lifestyle. Ten years have passed since the first round of genome-wide association studies for T2D and obesity. During this decade, we have witnessed remarkable developments in human genetics. We have graduated from the despair of candidate gene-based studies that generated few consistently replicated genotype-phenotype associations, to the excitement of an exponential harvest of loci robustly associated with medical outcomes through ever larger genome-wide association study meta-analyses. As well as discovering hundreds of loci, genome-wide association studies have provided transformative insights into the genetic architecture of T2D and other complex traits, highlighting the extent of polygenicity and the tiny effect sizes of many common risk alleles. Genome-wide association studies have also provided a critical starting point for discovering new biology relevant to these traits. Expectations are high that these discoveries will foster development of more effective strategies for intervention, through optimization of precision medicine approaches. In this article, we review current knowledge and provide suggestions for the next steps in genetic research for T2D and obesity. We focus on four areas relevant to precision medicine: genetic architecture, pharmacogenetics and other gene-environment interactions, mechanistic inference, and drug development. As we describe, the genetic architecture of complex traits has major implications for the prospects of precision medicine, rendering some anticipated approaches decidedly unrealistic. We highlight obstacles to the translation of human genetic findings into mechanism inference but are optimistic that, as these are overcome, there is untapped potential for novel drugs and more effective strategies for treating and preventing T2D and obesity.
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Affiliation(s)
- Erik Ingelsson
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, CA (E.I.) .,Stanford Cardiovascular Institute, Stanford University, CA (E.I.)
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics (M.I.M.).,Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, University of Oxford, United Kingdom (M.I.M.).,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, United Kingdom (M.I.M.)
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29
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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: 487] [Impact Index Per Article: 97.4] [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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30
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Babenko V, Babenko R, Gamieldien J, Markel A. FTO haplotyping underlines high obesity risk for European populations. BMC Med Genomics 2019; 12:46. [PMID: 30871540 PMCID: PMC6417164 DOI: 10.1186/s12920-019-0491-x] [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] [Indexed: 12/22/2022] Open
Abstract
Background Fat mass and obesity-associated (FTO) gene has been under close investigation since the discovery of its high impact on the obesity status in 2007 by a range of publications. Recent report on its implication in adipocytes underscored its molecular and functional mechanics in pathology. Still, the population specific features of the locus structure have not been approached in detail. Methods We analyzed the population specific haplotype profiles of FTO genomic locus identified by Genome Wide Association Studies (GWAS) for the high obesity risk by examining eighteen 1000G populations from 4 continental groups. The GWAS SNPs cluster is located in the FTO gene intron 1 spanning around 70 kb. Results We reconstructed the ancestral state of the locus, which comprised low-risk major allele found in all populations, and two minor risk-associated alleles, each one specific for African and European populations, correspondingly. The locus structure and its allele frequency distribution underscore the high risk allele frequency specifically for the European population. South Asian populations have the second highest frequency of risk alleles, while East Asian populations have the lowest. African population-specific minor allele was only partially risk-associated. All of the GWAS SNPs considered are manifested by low risk alleles as reference (major) ones (p > 0.5) in each of the continental groups. Strikingly, rs1421085, recently reported as a causal SNP, was found to be monomorphic in ancestral (African) populations, implying possible selection sweep in the course of its rapid fixation, as reported previously. Conclusion The observations underscore varying FTO -linked risk in the manifestation of population specific epidemiology of genetically bound obesity. The results imply that the FTO locus is one of the major genetic determinants for obesity risk from GWAS SNPs set. Electronic supplementary material The online version of this article (10.1186/s12920-019-0491-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vladimir Babenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, 10 Lavrentieva Ave, Novosibirsk, Russian Federation, 630090. .,Novosibirsk State University, 2 Pirogova Str, Novosibirsk, Russian Federation, 630090.
| | - Roman Babenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, 10 Lavrentieva Ave, Novosibirsk, Russian Federation, 630090.,Novosibirsk State University, 2 Pirogova Str, Novosibirsk, Russian Federation, 630090
| | - Junaid Gamieldien
- South African National Bioinformatics Institute/SAMRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Cape Town, 7535, South Africa
| | - Arcady Markel
- Federal Research Center Institute of Cytology and Genetics SB RAS, 10 Lavrentieva Ave, Novosibirsk, Russian Federation, 630090.,Novosibirsk State University, 2 Pirogova Str, Novosibirsk, Russian Federation, 630090
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31
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Rohde K, Keller M, la Cour Poulsen L, Blüher M, Kovacs P, Böttcher Y. Genetics and epigenetics in obesity. Metabolism 2019; 92:37-50. [PMID: 30399374 DOI: 10.1016/j.metabol.2018.10.007] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/15/2018] [Accepted: 10/21/2018] [Indexed: 12/20/2022]
Abstract
Obesity is among the most threatening health burdens worldwide and its prevalence has markedly increased over the last decades. Obesity maybe considered a heritable trait. Identifications of rare cases of monogenic obesity unveiled that hypothalamic circuits and the brain-adipose axis play an important role in the regulation of energy homeostasis, appetite, hunger and satiety. For example, mutations in the leptin gene cause obesity through almost unsuppressed overeating. Common (multifactorial) obesity, most likely resulting from a concerted interplay of genetic, epigenetic and environmental factors, is clearly linked to genetic predisposition by multiple risk variants, which, however only account for a minor part of the general BMI variability. Although GWAS opened new avenues in elucidating the complex genetics behind common obesity, understanding the biological mechanisms relative to the specific risk contributing to obesity remains poorly understood. Non-genetic factors such as eating behavior or physical activity strongly modulate the individual risk for developing obesity. These factors may interact with genetic predisposition for obesity through epigenetic mechanisms. Thus, here, we review the current knowledge about monogenic and common (multifactorial) obesity highlighting the important recent advances in our knowledge on how epigenetic regulation is involved in the etiology of obesity.
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Affiliation(s)
- Kerstin Rohde
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany; University of Oslo, Institute of Clinical Medicine, Oslo 0316, Norway.
| | - Maria Keller
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany.
| | - Lars la Cour Poulsen
- Akershus University Hospital, Department of Clinical Molecular Biology, Medical Division, Lørenskog 1478, Norway.
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany.
| | - Peter Kovacs
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany.
| | - Yvonne Böttcher
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany; University of Oslo, Institute of Clinical Medicine, Oslo 0316, Norway; Akershus University Hospital, Department of Clinical Molecular Biology, Medical Division, Lørenskog 1478, Norway.
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32
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Shah UJ, Xie W, Flyvbjerg A, Nolan JJ, Højlund K, Walker M, Relton CL, Elliott HR. Differential methylation of the type 2 diabetes susceptibility locus KCNQ1 is associated with insulin sensitivity and is predicted by CpG site specific genetic variation. Diabetes Res Clin Pract 2019; 148:189-199. [PMID: 30641161 PMCID: PMC6395844 DOI: 10.1016/j.diabres.2019.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/28/2018] [Accepted: 01/04/2019] [Indexed: 01/02/2023]
Abstract
AIMS Epigenetic mechanisms regulate gene expression and may influence the pathogenesis of type 2 diabetes through the loss of insulin sensitivity. The aims of this study were to measure variation in DNA methylation at the type 2 diabetes locus KCNQ1 and assess its relationship with metabolic measures and with genotype. METHODS DNA methylation from whole blood DNA was quantified using pyrosequencing at 5 CpG sites at the KCNQ1 locus in 510 individuals without diabetes from the 'Relationship between Insulin Sensitivity and Cardiovascular disease' (RISC) cohort. Genotype data was analysed at the same locus in 1119 individuals in the same cohort. Insulin sensitivity was assessed by euglycaemic-hyperinsulinaemic clamp. RESULTS DNA methylation at the KCNQ1 locus was inversely associated with insulin sensitivity and serum adiponectin. This association was driven by a methylation-altering Single Nucleotide Polymorphism (SNP) (rs231840) which ablated a methylation site and reduced methylation levels. A second SNP (rs231357), in weak Linkage Disequilibrium (LD) with rs231840, was also associated with insulin sensitivity and DNA methylation. These SNPs have not been previously reported to be associated with type 2 diabetes risk or insulin sensitivity. CONCLUSION Evidence indicates that genetic and epigenetic determinants at the KCNQ1 locus influence insulin sensitivity.
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Affiliation(s)
- Ushma J Shah
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; MedGenome Labs Ltd., Bangalore 560 099, India
| | - Weijia Xie
- Peninsula School of Medicine and Dentistry, Exeter EX2 5DW, UK
| | - Allan Flyvbjerg
- Steno Diabetes Center Copenhagen, The Capital Region of Denmark and University of Copenhagen, Copenhagen, Denmark
| | - John J Nolan
- European Association for the Study of Diabetes (EASD), 40591 Düsseldorf, Germany
| | - Kurt Højlund
- Steno Diabetes Center Odense, Odense University Hospital, DK-5000, Denmark
| | - Mark Walker
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Caroline L Relton
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Hannah R Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK.
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Husquin LT, Rotival M, Fagny M, Quach H, Zidane N, McEwen LM, MacIsaac JL, Kobor MS, Aschard H, Patin E, Quintana-Murci L. Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation. Genome Biol 2018; 19:222. [PMID: 30563547 PMCID: PMC6299574 DOI: 10.1186/s13059-018-1601-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/04/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND DNA methylation is influenced by both environmental and genetic factors and is increasingly thought to affect variation in complex traits and diseases. Yet, the extent of ancestry-related differences in DNA methylation, their genetic determinants, and their respective causal impact on immune gene regulation remain elusive. RESULTS We report extensive population differences in DNA methylation between 156 individuals of African and European descent, detected in primary monocytes that are used as a model of a major innate immunity cell type. Most of these differences (~ 70%) are driven by DNA sequence variants nearby CpG sites, which account for ~ 60% of the variance in DNA methylation. We also identify several master regulators of DNA methylation variation in trans, including a regulatory hub nearby the transcription factor-encoding CTCF gene, which contributes markedly to ancestry-related differences in DNA methylation. Furthermore, we establish that variation in DNA methylation is associated with varying gene expression levels following mostly, but not exclusively, a canonical model of negative associations, particularly in enhancer regions. Specifically, we find that DNA methylation highly correlates with transcriptional activity of 811 and 230 genes, at the basal state and upon immune stimulation, respectively. Finally, using a Bayesian approach, we estimate causal mediation effects of DNA methylation on gene expression in ~ 20% of the studied cases, indicating that DNA methylation can play an active role in immune gene regulation. CONCLUSION Using a system-level approach, our study reveals substantial ancestry-related differences in DNA methylation and provides evidence for their causal impact on immune gene regulation.
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Affiliation(s)
- Lucas T. Husquin
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Maud Fagny
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine (CNRGH), CEA-Institut de Biologie François Jacob, 91000 Evry, France
| | - Hélène Quach
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Nora Zidane
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Lisa M. McEwen
- Department of Medical Genetics, University of British Columbia, Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, BC Canada
| | - Julia L. MacIsaac
- Department of Medical Genetics, University of British Columbia, Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, BC Canada
| | - Michael S. Kobor
- Department of Medical Genetics, University of British Columbia, Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, BC Canada
| | - Hugues Aschard
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Etienne Patin
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Lluis Quintana-Murci
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
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González-Herrera L, Zavala-Castro J, Ayala-Cáceres C, Pérez-Mendoza G, López-González MJ, Pinto-Escalante D, Canto-Cetina T, García-Escalante MG, Rubi-Castellanos R, Contreras-Capetillo S, Herrera-Sanchez F, Méndez-Domínguez N, Alcocer-Gamboa A. Genetic variation of FTO: rs1421085 T>C, rs8057044 G>A, rs9939609 T>A, and copy number (CNV) in Mexican Mayan school-aged children with obesity/overweight and with normal weight. Am J Hum Biol 2018; 31:e23192. [PMID: 30537186 DOI: 10.1002/ajhb.23192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/22/2018] [Accepted: 10/03/2018] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVES Genetic variation of the fat mass and obesity associated gene (FTO) has been identified as a risk factor for obesity and obesity traits. Distribution of FTO single nutleotide polymorphisms (SNPs) rs1421085T>C, rs9939609T>A, rs8057044G>A and copy number variation (CNV) was evaluated in association with childhood obesity or overweight status in children with Mayan ethnicity. METHODS We included 318 school-aged children with obesity or overweight status (body mass index [BMI]: >85th percentile) and 303 children with normal weight (BMI: 15th-85th percentile). Genotyping was performed using real-time polymerase chain reaction (RT-PCR) with TaqMan probes. The cross-sectional study was carried out using univariate and multivariate logistic regression models adjusted for gender. RESULTS FTO-SNP rs1421085 showed significant differences between children with obesity and children with normal weight for the heterozygous genotype (P = 0.003) and for allele frequencies (P = 0.023). Adjusting by gender, significant differences were found in frequencies of the hetezygous genotype of SNPs rs9939609 (P = 0.023) and rs1421085 (P = 0.003) as well as in allele frequencies (P = 0.042 and P = 0.013, respectively) between girls with obesity and girls without obesity. In contrast, SNP rs8057044 was significantly different only between heterozygous overweight versus normal weight boys (P = 0.035) and for the allele frequency of rs8057044 (P = 0.021). The mean relative CNV was significantly higher in male overweight children than in boys with normal weight (P = 0.000). CONCLUSIONS The FTO SNP rs1421085 is a genetic factor associated with obesity in Mayan school-aged children. FTO SNPs rs1421085 and rs9939609 affect genetic susceptibility for obesity only in girls, whereas, SNP rs8057044 and CNV are associated with overweight status only in boys.
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Affiliation(s)
| | - Jorge Zavala-Castro
- Centro de Investigaciones Regionales, Universidad Autónoma de Yucatán, Yucatán, Mexico
| | - Claudia Ayala-Cáceres
- Escuela de Nutrición, Universidad Vizcaya de las Américas Plantel Mérida, Yucatán, México
| | - Gerardo Pérez-Mendoza
- Centro de Investigaciones Regionales, Universidad Autónoma de Yucatán, Yucatán, Mexico
| | | | - Doris Pinto-Escalante
- Centro de Investigaciones Regionales, Universidad Autónoma de Yucatán, Yucatán, Mexico
| | - Thelma Canto-Cetina
- Centro de Investigaciones Regionales, Universidad Autónoma de Yucatán, Yucatán, Mexico
| | | | | | | | | | | | - Alberto Alcocer-Gamboa
- Programa Integral de Atención a la Obesidad, Secretaria de Educación del Gobierno del Estado de Yucatán, Mérida, Yucatán, Mexico
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35
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Hwang JY, Lee HJ, Go MJ, Jang HB, Choi NH, Bae JB, Castillo-Fernandez JE, Bell JT, Spector TD, Lee HJ, Kim BJ. Genome-wide methylation analysis identifies ELOVL5 as an epigenetic biomarker for the risk of type 2 diabetes mellitus. Sci Rep 2018; 8:14862. [PMID: 30291282 PMCID: PMC6173741 DOI: 10.1038/s41598-018-33238-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/25/2018] [Indexed: 12/16/2022] Open
Abstract
Genome-wide DNA methylation has been implicated in complex human diseases. Here, we identified epigenetic biomarkers for type 2 diabetes (T2D) underlying obesogenic environments. In a blood-based DNA methylation analysis of 11 monozygotic twins (MZTW) discordant for T2D, we discovered genetically independent candidate methylation sites. In a follow-up replication study (17 MZTW pairs) for external validation, we replicated the T2D-association at a novel CpG signal in the ELOVL fatty acid elongase 5 (ELOVL5) gene specific to T2D-discordant MZTW. For concordant DNA methylation signatures in tissues, we further confirmed that a CpG site (cg18681426) was associated with adipogenic differentiation between human preadipocytes and adipocytes isolated from the same biopsy sample. In addition, the ELOVL5 gene was significantly differentially expressed in adipose tissues from unrelated T2D patients and in human pancreatic islets. Our results demonstrate that blood-derived DNA methylation is associated with T2D risk as a proxy for cumulative epigenetic status in human adipose and pancreatic tissues. Moreover, ELOVL5 expression was increased in cellular and mouse models of induced obesity-related diabetes. These findings may provide new insights into epigenetic architecture by uncovering methylation-based biomarkers.
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Affiliation(s)
- Joo-Yeon Hwang
- Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, Republic of Korea.,Center for Biomedical Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheonbuk-do, Republic of Korea
| | - Hyo Jung Lee
- Center for Biomedical Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheonbuk-do, Republic of Korea
| | - Min Jin Go
- Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, Republic of Korea
| | - Han Byul Jang
- Center for Biomedical Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheonbuk-do, Republic of Korea
| | - Nak-Hyun Choi
- Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, Republic of Korea
| | - Jae Bum Bae
- Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, Republic of Korea
| | | | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Hye-Ja Lee
- Center for Biomedical Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheonbuk-do, Republic of Korea.
| | - Bong-Jo Kim
- Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, Republic of Korea.
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36
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Corbin KD, Driscoll KA, Pratley RE, Smith SR, Maahs DM, Mayer-Davis EJ. Obesity in Type 1 Diabetes: Pathophysiology, Clinical Impact, and Mechanisms. Endocr Rev 2018; 39:629-663. [PMID: 30060120 DOI: 10.1210/er.2017-00191] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 06/21/2018] [Indexed: 02/07/2023]
Abstract
There has been an alarming increase in the prevalence of obesity in people with type 1 diabetes in recent years. Although obesity has long been recognized as a major risk factor for the development of type 2 diabetes and a catalyst for complications, much less is known about the role of obesity in the initiation and pathogenesis of type 1 diabetes. Emerging evidence suggests that obesity contributes to insulin resistance, dyslipidemia, and cardiometabolic complications in type 1 diabetes. Unique therapeutic strategies may be required to address these comorbidities within the context of intensive insulin therapy, which promotes weight gain. There is an urgent need for clinical guidelines for the prevention and management of obesity in type 1 diabetes. The development of these recommendations will require a transdisciplinary research strategy addressing metabolism, molecular mechanisms, lifestyle, neuropsychology, and novel therapeutics. In this review, the prevalence, clinical impact, energy balance physiology, and potential mechanisms of obesity in type 1 diabetes are described, with a special focus on the substantial gaps in knowledge in this field. Our goal is to provide a framework for the evidence base needed to develop type 1 diabetes-specific weight management recommendations that account for the competing outcomes of glycemic control and weight management.
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Affiliation(s)
- Karen D Corbin
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, Florida
| | - Kimberly A Driscoll
- Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, Colorado.,Barbara Davis Center for Diabetes, Aurora, Colorado
| | - Richard E Pratley
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, Florida
| | - Steven R Smith
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, Florida
| | - David M Maahs
- Division of Pediatric Endocrinology, Department of Pediatrics, Stanford University, Stanford, California
| | - Elizabeth J Mayer-Davis
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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37
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Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science 2018; 361:eaar3146. [PMID: 30139913 PMCID: PMC6198826 DOI: 10.1126/science.aar3146] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 05/07/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
To assess the impact of genetic variation in regulatory loci on human health, we constructed a high-resolution map of allelic imbalances in DNA methylation, histone marks, and gene transcription in 71 epigenomes from 36 distinct cell and tissue types from 13 donors. Deep whole-genome bisulfite sequencing of 49 methylomes revealed sequence-dependent CpG methylation imbalances at thousands of heterozygous regulatory loci. Such loci are enriched for stochastic switching, which is defined as random transitions between fully methylated and unmethylated states of DNA. The methylation imbalances at thousands of loci are explainable by different relative frequencies of the methylated and unmethylated states for the two alleles. Further analyses provided a unifying model that links sequence-dependent allelic imbalances of the epigenome, stochastic switching at gene regulatory loci, and disease-associated genetic variation.
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Affiliation(s)
- Vitor Onuchic
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Eugene Lurie
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Ivenise Carrero
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Piotr Pawliczek
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Ronak Y Patel
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Zhuoyi Huang
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Robert C Altshuler
- NIH Roadmap Epigenomics Project
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhizhuo Zhang
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - R Alan Harris
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Cristian Coarfa
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Lillian Ashmore
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Jessica W Bertol
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Walid D Fakhouri
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Fuli Yu
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Manolis Kellis
- NIH Roadmap Epigenomics Project
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Aleksandar Milosavljevic
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA.
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
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Veenstra J, Kalsbeek A, Koster K, Ryder N, Bos A, Huisman J, VanderBerg L, VanderWoude J, Tintle NL. Epigenome wide association study of SNP-CpG interactions on changes in triglyceride levels after pharmaceutical intervention: a GAW20 analysis. BMC Proc 2018; 12:58. [PMID: 30275900 PMCID: PMC6157099 DOI: 10.1186/s12919-018-0144-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In the search for an understanding of how genetic variation contributes to the heritability of common human disease, the potential role of epigenetic factors, such as methylation, is being explored with increasing frequency. Although standard analyses test for associations between methylation levels at individual cytosine-phosphate-guanine (CpG) sites and phenotypes of interest, some investigators have begun testing for methylation and how methylation may modulate the effects of genetic polymorphisms on phenotypes. In our analysis, we used both a genome-wide and candidate gene approach to investigate potential single-nucleotide polymorphism (SNP)–CpG interactions on changes in triglyceride levels. Although we were able to identify numerous loci of interest when using an exploratory significance threshold, we did not identify any significant interactions using a strict genome-wide significance threshold. We were also able to identify numerous loci using the candidate gene approach, in which we focused on 18 genes with prior evidence of association of triglyceride levels. In particular, we identified GALNT2 loci as containing potential CpG sites that moderate the impact of genetic polymorphisms on triglyceride levels. Further work is needed to provide clear guidance on analytic strategies for testing SNP–CpG interactions, although leveraging prior biological understanding may be needed to improve statistical power in data sets with smaller sample sizes.
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Affiliation(s)
- Jenna Veenstra
- 1Department of Biology, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA.,2Department of Mathematics and Statistics, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA
| | - Anya Kalsbeek
- 1Department of Biology, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA.,2Department of Mathematics and Statistics, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA
| | - Karissa Koster
- 2Department of Mathematics and Statistics, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA
| | - Nathan Ryder
- 2Department of Mathematics and Statistics, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA
| | - Abbey Bos
- 1Department of Biology, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA
| | - Jordan Huisman
- 2Department of Mathematics and Statistics, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA
| | - Lucas VanderBerg
- 2Department of Mathematics and Statistics, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA
| | - Jason VanderWoude
- 2Department of Mathematics and Statistics, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA.,3Department of Computer Science, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA
| | - Nathan L Tintle
- 2Department of Mathematics and Statistics, Dordt College, 498 4th Ave. NE, Sioux Center, IA 51250 USA
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39
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Dong SS, Zhang YJ, Chen YX, Yao S, Hao RH, Rong Y, Niu HM, Chen JB, Guo Y, Yang TL. Comprehensive review and annotation of susceptibility SNPs associated with obesity-related traits. Obes Rev 2018. [PMID: 29527783 DOI: 10.1111/obr.12677] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We aimed to summarize the results of genetic association studies for obesity and provide a comprehensive annotation of all susceptibility single nucleotide polymorphisms (SNPs). A total of 72 studies were summarized, resulting in 90,361 susceptibility SNPs (738 index SNPs and 89,623 linkage disequilibrium SNPs). Over 90% of the susceptibility SNPs are located in non-coding regions, and it is challenging to understand their functional significance. Therefore, we annotated these SNPs by using various functional databases. We identified 24,623 functional SNPs, including 4 nonsense SNPs, 479 missense SNPs, 399 untranslated region SNPs which might affect microRNA binding, 262 promoter and 5,492 enhancer SNPs which might affect transcription factor binding, 7 splicing sites, 76 SNPs which might affect gene methylation levels, 1,839 SNPs under natural selection and 17,351 SNPs which might modify histone binding. Expression quantitative trait loci analyses for functional SNPs identified 98 target genes, including 69 protein coding genes, 27 long non-coding RNAs and 3 processed transcripts. The percentage of protein coding genes that could be correlated with obesity-related pathways directly or through gene-gene interaction is 75.36 (52/69). Our results may serve as an encyclopaedia of obesity susceptibility SNPs and offer guide for functional experiments.
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Affiliation(s)
- S-S Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Y-J Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Y-X Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - S Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - R-H Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Y Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - H-M Niu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - J-B Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Y Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - T-L Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
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40
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Abstract
PURPOSE OF REVIEW Following a life-threatening traumatic exposure, about 10% of those exposed are at considerable risk for developing posttraumatic stress disorder (PTSD), a severe and disabling syndrome characterized by uncontrollable intrusive memories, nightmares, avoidance behaviors, and hyperarousal in addition to impaired cognition and negative emotion symptoms. This review will explore recent genetic and epigenetic approaches to PTSD that explain some of the differential risk following trauma exposure. RECENT FINDINGS A substantial portion of the variance explaining differential risk responses to trauma exposure may be explained by differential inherited and acquired genetic and epigenetic risk. This biological risk is complemented by alterations in the functional regulation of genes via environmentally induced epigenetic changes, including prior childhood and adult trauma exposure. This review will cover recent findings from large-scale genome-wide association studies as well as newer epigenome-wide studies. We will also discuss future "phenome-wide" studies utilizing electronic medical records as well as targeted genetic studies focusing on mechanistic ways in which specific genetic or epigenetic alterations regulate the biological risk for PTSD.
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41
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Qasim A, Turcotte M, de Souza RJ, Samaan MC, Champredon D, Dushoff J, Speakman JR, Meyre D. On the origin of obesity: identifying the biological, environmental and cultural drivers of genetic risk among human populations. Obes Rev 2018; 19:121-149. [PMID: 29144594 DOI: 10.1111/obr.12625] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/28/2017] [Accepted: 09/08/2017] [Indexed: 12/12/2022]
Abstract
Genetic predisposition to obesity presents a paradox: how do genetic variants with a detrimental impact on human health persist through evolutionary time? Numerous hypotheses, such as the thrifty genotype hypothesis, attempt to explain this phenomenon yet fail to provide a justification for the modern obesity epidemic. In this critical review, we appraise existing theories explaining the evolutionary origins of obesity and explore novel biological and sociocultural agents of evolutionary change to help explain the modern-day distribution of obesity-predisposing variants. Genetic drift, acting as a form of 'blind justice,' may randomly affect allele frequencies across generations while gene pleiotropy and adaptations to diverse environments may explain the rise and subsequent selection of obesity risk alleles. As an adaptive response, epigenetic regulation of gene expression may impact the manifestation of genetic predisposition to obesity. Finally, exposure to malnutrition and disease epidemics in the wake of oppressive social systems, culturally mediated notions of attractiveness and desirability, and diverse mating systems may play a role in shaping the human genome. As an important first step towards the identification of important drivers of obesity gene evolution, this review may inform empirical research focused on testing evolutionary theories by way of population genetics and mathematical modelling.
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Affiliation(s)
- A Qasim
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - M Turcotte
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - R J de Souza
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - M C Samaan
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,Department of Pediatrics, McMaster University, Hamilton, ON, Canada.,Division of Pediatric Endocrinology, McMaster Children's Hospital, Hamilton, ON, Canada
| | - D Champredon
- Department of Biology, McMaster University, Hamilton, ON, Canada.,Agent-Based Modelling Laboratory, York University, Toronto, ON, Canada
| | - J Dushoff
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - J R Speakman
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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42
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Bell CG, Gao F, Yuan W, Roos L, Acton RJ, Xia Y, Bell J, Ward K, Mangino M, Hysi PG, Wang J, Spector TD. Obligatory and facilitative allelic variation in the DNA methylome within common disease-associated loci. Nat Commun 2018; 9:8. [PMID: 29295990 PMCID: PMC5750212 DOI: 10.1038/s41467-017-01586-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 09/29/2017] [Indexed: 12/16/2022] Open
Abstract
Integrating epigenetic data with genome-wide association study (GWAS) results can reveal disease mechanisms. The genome sequence itself also shapes the epigenome, with CpG density and transcription factor binding sites (TFBSs) strongly encoding the DNA methylome. Therefore, genetic polymorphism impacts on the observed epigenome. Furthermore, large genetic variants alter epigenetic signal dosage. Here, we identify DNA methylation variability between GWAS-SNP risk and non-risk haplotypes. In three subsets comprising 3128 MeDIP-seq peripheral-blood DNA methylomes, we find 7173 consistent and functionally enriched Differentially Methylated Regions. 36.8% can be attributed to common non-SNP genetic variants. CpG-SNPs, as well as facilitative TFBS-motifs, are also enriched. Highlighting their functional potential, CpG-SNPs strongly associate with allele-specific DNase-I hypersensitivity sites. Our results demonstrate strong DNA methylation allelic differences driven by obligatory or facilitative genetic effects, with potential direct or regional disease-related repercussions. These allelic variations require disentangling from pure tissue-specific modifications, may influence array studies, and imply underestimated population variability in current reference epigenomes. Genomic polymorphisms affect the epigenome, which in turn influences how epigenome- and genome-wide analysis are interpreted. Here, the authors characterise allelic differences in DNA methylation driven by obligatory or facilitative genetic effects, which may affect disease-related loci.
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Affiliation(s)
- Christopher G Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK. .,MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK. .,Epigenomic Medicine, Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, SO17 1BJ, UK. .,Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, SO16 6YD, UK.
| | - Fei Gao
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Wei Yuan
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Leonie Roos
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,MRC London Institute of Medical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Richard J Acton
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK.,Epigenomic Medicine, Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, SO17 1BJ, UK.,Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | | | - Jordana Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Kirsten Ward
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Pirro G Hysi
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jun Wang
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK
| | - Timothy D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
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43
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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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44
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Stryjecki C, Alyass A, Meyre D. Ethnic and population differences in the genetic predisposition to human obesity. Obes Rev 2018; 19:62-80. [PMID: 29024387 DOI: 10.1111/obr.12604] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/17/2017] [Accepted: 08/02/2017] [Indexed: 12/22/2022]
Abstract
Obesity rates have escalated to the point of a global pandemic with varying prevalence across ethnic groups. These differences are partially explained by lifestyle factors in addition to genetic predisposition to obesity. This review provides a comprehensive examination of the ethnic differences in the genetic architecture of obesity. Using examples from evolution, heritability, admixture, monogenic and polygenic studies of obesity, we provide explanations for ethnic differences in the prevalence of obesity. The debate over definitions of race and ethnicity, the advantages and limitations of multi-ethnic studies and future directions of research are also discussed. Multi-ethnic studies have great potential to provide a better understanding of ethnic differences in the prevalence of obesity that may result in more targeted and personalized obesity treatments.
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Affiliation(s)
- C Stryjecki
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - A Alyass
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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45
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Yadav DK, Shrestha S, Lillycrop KA, Joglekar CV, Pan H, Holbrook JD, Fall CH, Yajnik CS, Chandak GR. Vitamin B 12 supplementation influences methylation of genes associated with Type 2 diabetes and its intermediate traits. Epigenomics 2017; 10:71-90. [PMID: 29135286 DOI: 10.2217/epi-2017-0102] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To investigate the effect of B12 and/or folic acid supplementation on genome-wide DNA methylation. METHODS We performed Infinium HumanMethylation450 BeadChip (Zymo Research, CA, USA) assay in children supplemented with B12 and/or folic acid (n = 12 in each group) and investigated the functional mechanism of selected differentially methylated loci. RESULTS We noted significant methylation changes postsupplementation in B12 (589 differentially methylated CpGs and 2892 regions) and B12 + folic acid (169 differentially methylated CpGs and 3241 regions) groups. Type 2 diabetes-associated genes TCF7L2 and FTO; and a miRNA, miR21 were further investigated in another B12-supplementation cohort. We also demonstrate that methylation influences miR21 expression and FTO, TCF7L2, CREBBP/CBP and SIRT1 are direct targets of miR21-3p. CONCLUSION B12 supplementation influences regulation of several metabolically important Type 2 diabetes-associated genes through methylation of miR21. Hence, our study provides novel epigenetic explanation for the association between disordered one carbon metabolism and risk of adiposity, insulin resistance and diabetes and has translational potential.
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Affiliation(s)
- Dilip K Yadav
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology, Hyderabad, Telangana, 500 007, India
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology, Hyderabad, Telangana, 500 007, India.,Building No 7, School of Basic & Applied Sciences, Dayananda Sagar University, Shavige Malleshwara Hills, Kumaraswamy Layout, Bangalore 560 078, Karnataka, India
| | - Karen A Lillycrop
- Research Centre for Biological Sciences, Institute of Developmental Sciences, Southampton General Hospital, Southampton, SO16 6 YD, UK
| | - Charu V Joglekar
- Diabetes Unit, King Edward Memorial Hospital & Research Centre, Rasta Peth, Pune, Maharashtra, 411 011, India
| | - Hong Pan
- Singapore Institute for Clinical Sciences, A*STAR, Brenner Centre for Molecular Medicine, 30 Medical Drive, 119521, Singapore
| | - Joanna D Holbrook
- Singapore Institute for Clinical Sciences, A*STAR, Brenner Centre for Molecular Medicine, 30 Medical Drive, 119521, Singapore.,Human Development & Health Academic Unit, University of Southampton & National Institute for Health Research Southampton Biomedical Research Centre, University of Southampton & University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, SO16 6 YD, UK
| | - Caroline Hd Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, SO16 6 YD, UK
| | - Chittaranjan S Yajnik
- Diabetes Unit, King Edward Memorial Hospital & Research Centre, Rasta Peth, Pune, Maharashtra, 411 011, India
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology, Hyderabad, Telangana, 500 007, India.,Adjunct Faculty, Human Genetics Unit, Genome Institute of Singapore, Biopolis, 138672, Singapore
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46
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Molnos S, Baumbach C, Wahl S, Müller-Nurasyid M, Strauch K, Wang-Sattler R, Waldenberger M, Meitinger T, Adamski J, Kastenmüller G, Suhre K, Peters A, Grallert H, Theis FJ, Gieger C. pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms. BMC Bioinformatics 2017; 18:429. [PMID: 28962546 PMCID: PMC5622569 DOI: 10.1186/s12859-017-1838-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/20/2017] [Indexed: 01/23/2023] Open
Abstract
Background Genome-wide association studies allow us to understand the genetics of complex diseases. Human metabolism provides information about the disease-causing mechanisms, so it is usual to investigate the associations between genetic variants and metabolite levels. However, only considering genetic variants and their effects on one trait ignores the possible interplay between different “omics” layers. Existing tools only consider single-nucleotide polymorphism (SNP)–SNP interactions, and no practical tool is available for large-scale investigations of the interactions between pairs of arbitrary quantitative variables. Results We developed an R package called pulver to compute p-values for the interaction term in a very large number of linear regression models. Comparisons based on simulated data showed that pulver is much faster than the existing tools. This is achieved by using the correlation coefficient to test the null-hypothesis, which avoids the costly computation of inversions. Additional tricks are a rearrangement of the order, when iterating through the different “omics” layers, and implementing this algorithm in the fast programming language C++. Furthermore, we applied our algorithm to data from the German KORA study to investigate a real-world problem involving the interplay among DNA methylation, genetic variants, and metabolite levels. Conclusions The pulver package is a convenient and rapid tool for screening huge numbers of linear regression models for significant interaction terms in arbitrary pairs of quantitative variables. pulver is written in R and C++, and can be downloaded freely from CRAN at https://cran.r-project.org/web/packages/pulver/. Electronic supplementary material The online version of this article (10.1186/s12859-017-1838-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sophie Molnos
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany. .,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany. .,German Center for Diabetes Research (DZD), Neuherberg, Germany.
| | - Clemens Baumbach
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany.,Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Rui Wang-Sattler
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Jerzy Adamski
- German Center for Diabetes Research (DZD), Neuherberg, Germany.,Genome Analysis Center, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Experimental Genetics, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Twins Research and Genetic Epidemiology, Kings College, London, UK
| | - Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Biophysics and Physiology, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Mathematics, Technische Universitat München, Garching, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
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Zhou Y, Hambly BD, McLachlan CS. FTO associations with obesity and telomere length. J Biomed Sci 2017; 24:65. [PMID: 28859657 PMCID: PMC5580219 DOI: 10.1186/s12929-017-0372-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 08/23/2017] [Indexed: 12/16/2022] Open
Abstract
This review examines the biology of the Fat mass- and obesity-associated gene (FTO), and the implications of genetic association of FTO SNPs with obesity and genetic aging. Notably, we focus on the role of FTO in the regulation of methylation status as possible regulators of weight gain and genetic aging. We present a theoretical review of the FTO gene with a particular emphasis on associations with UCP2, AMPK, RBL2, IRX3, CUX1, mTORC1 and hormones involved in hunger regulation. These associations are important for dietary behavior regulation and cellular nutrient sensing via amino acids. We suggest that these pathways may also influence telomere regulation. Telomere length (TL) attrition may be influenced by obesity-related inflammation and oxidative stress, and FTO gene-involved pathways. There is additional emerging evidence to suggest that telomere length and obesity are bi-directionally associated. However, the role of obesity risk-related genotypes and associations with TL are not well understood. The FTO gene may influence pathways implicated in regulation of TL, which could help to explain some of the non-consistent relationship between weight phenotype and telomere length that is observed in population studies investigating obesity.
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Affiliation(s)
- Yuling Zhou
- Rural Clinical School, University of New South Wales, Sydney, 2052, Australia
| | - Brett D Hambly
- Discipline of Pathology and Bosch Institute, University of Sydney, Sydney, Australia
| | - Craig S McLachlan
- Rural Clinical School, University of New South Wales, Sydney, 2052, Australia.
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48
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Bell CG. The Epigenomic Analysis of Human Obesity. Obesity (Silver Spring) 2017; 25:1471-1481. [PMID: 28845613 DOI: 10.1002/oby.21909] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/09/2017] [Accepted: 05/11/2017] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Analysis of the epigenome-the chemical modifications and packaging of the genome that can influence or indicate its activity-enables molecular insight into cell type-specific machinery. It can, therefore, reveal the pathophysiological mechanisms at work in disease. Detected changes can also represent physiological responses to adverse environmental exposures, thus enabling the epigenetic mark of DNA methylation to act as an epidemiological biomarker, even in surrogate tissue. This makes epigenomic analysis an attractive prospect to further understand the pathobiology and epidemiological aspects of obesity. Furthermore, integrating epigenomic data with known obesity-associated common genetic variation can aid in deciphering their molecular mechanisms. METHODS AND CONCLUSIONS This review primarily examines epidemiological or population-based studies of epigenetic modifications in relation to adiposity traits, as opposed to animal or cell models. It discusses recent work exploring the epigenome with respect to human obesity, which to date has predominately consisted of array-based studies of DNA methylation in peripheral blood. It is of note that highly replicated BMI DNA methylation associations are not causal, but strongly driven by coassociations for more precisely measured intertwined outcomes and factors, such as hyperlipidemia, hyperglycemia, and inflammation. Finally, the potential for the future exploration of the epigenome in obesity and related disorders is considered.
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Affiliation(s)
- Christopher G Bell
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- Epigenomic Medicine, Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, UK
- Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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Konstantinidou MK, Karaglani M, Panagopoulou M, Fiska A, Chatzaki E. Are the Origins of Precision Medicine Found in the Corpus Hippocraticum? Mol Diagn Ther 2017; 21:601-606. [DOI: 10.1007/s40291-017-0291-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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50
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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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