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Yadav B, Singh D, Mantri S, Rishi V. Genome-wide Methylation Dynamics and Context-dependent Gene Expression Variability in Differentiating Preadipocytes. J Endocr Soc 2024; 8:bvae121. [PMID: 38966711 PMCID: PMC11222978 DOI: 10.1210/jendso/bvae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Indexed: 07/06/2024] Open
Abstract
Obesity, characterized by the accumulation of excess fat, is a complex condition resulting from the combination of genetic and epigenetic factors. Recent studies have found correspondence between DNA methylation and cell differentiation, suggesting a role of the former in cell fate determination. There is a lack of comprehensive understanding concerning the underpinnings of preadipocyte differentiation, specifically when cells are undergoing terminal differentiation (TD). To gain insight into dynamic genome-wide methylation, 3T3 L1 preadipocyte cells were differentiated by a hormone cocktail. The genomic DNA was isolated from undifferentiated cells and 4 hours, 2 days postdifferentiated cells, and 15 days TD cells. We employed whole-genome bisulfite sequencing (WGBS) to ascertain global genomic DNA methylation alterations at single base resolution as preadipocyte cells differentiate. The genome-wide distribution of DNA methylation showed similar overall patterns in pre-, post-, and terminally differentiated adipocytes, according to WGBS analysis. DNA methylation decreases at 4 hours after differentiation initiation, followed by methylation gain as cells approach TD. Studies revealed novel differentially methylated regions (DMRs) associated with adipogenesis. DMR analysis suggested that though DNA methylation is global, noticeable changes are observed at specific sites known as "hotspots." Hotspots are genomic regions rich in transcription factor (TF) binding sites and exhibit methylation-dependent TF binding. Subsequent analysis indicated hotspots as part of DMRs. The gene expression profile of key adipogenic genes in differentiating adipocytes is context-dependent, as we found a direct and inverse relationship between promoter DNA methylation and gene expression.
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Affiliation(s)
- Binduma Yadav
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
- Regional Center for Biotechnology, Faridabad, Haryana 160014, India
| | - Dalwinder Singh
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
- Department of Anatomy and Cell Biology, Western University, London, Ontario N6A 5C1, Canada
| | - Shrikant Mantri
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
| | - Vikas Rishi
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
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2
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Yaskolka Meir A, Yun H, Stampfer MJ, Liang L, Hu FB. Nutrition, DNA methylation and obesity across life stages and generations. Epigenomics 2023; 15:991-1015. [PMID: 37933548 DOI: 10.2217/epi-2023-0172] [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] [Indexed: 11/08/2023] Open
Abstract
Obesity is a complex multifactorial condition that often manifests in early life with a lifelong burden on metabolic health. Diet, including pre-pregnancy maternal diet, in utero nutrition and dietary patterns in early and late life, can shape obesity development. Growing evidence suggests that epigenetic modifications, specifically DNA methylation, might mediate or accompany these effects across life stages and generations. By reviewing human observational and intervention studies conducted over the past 10 years, this work provides a comprehensive overview of the evidence linking nutrition to DNA methylation and its association with obesity across different age periods, spanning from preconception to adulthood and identify future research directions in the field.
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Affiliation(s)
- Anat Yaskolka Meir
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Huan Yun
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Meir J Stampfer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Medicine, Channing Division of Network Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Medicine, Channing Division of Network Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
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3
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Calamita G, Delporte C. Insights into the Function of Aquaporins in Gastrointestinal Fluid Absorption and Secretion in Health and Disease. Cells 2023; 12:2170. [PMID: 37681902 PMCID: PMC10486417 DOI: 10.3390/cells12172170] [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: 07/01/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023] Open
Abstract
Aquaporins (AQPs), transmembrane proteins permeable to water, are involved in gastrointestinal secretion. The secretory products of the glands are delivered either to some organ cavities for exocrine glands or to the bloodstream for endocrine glands. The main secretory glands being part of the gastrointestinal system are salivary glands, gastric glands, duodenal Brunner's gland, liver, bile ducts, gallbladder, intestinal goblet cells, exocrine and endocrine pancreas. Due to their expression in gastrointestinal exocrine and endocrine glands, AQPs fulfill important roles in the secretion of various fluids involved in food handling. This review summarizes the contribution of AQPs in physiological and pathophysiological stages related to gastrointestinal secretion.
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Affiliation(s)
- Giuseppe Calamita
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy;
| | - Christine Delporte
- Laboratory of Pathophysiological and Nutritional Biochemistry, Faculty of Medicine, Université Libre de Bruxelles, 1070 Brussels, Belgium
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4
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Zheng M, Liu Y, Zhang G, Yang Z, Xu W, Chen Q. The Applications and Mechanisms of Superoxide Dismutase in Medicine, Food, and Cosmetics. Antioxidants (Basel) 2023; 12:1675. [PMID: 37759978 PMCID: PMC10525108 DOI: 10.3390/antiox12091675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Superoxide dismutase (SOD) is a class of enzymes that restrict the biological oxidant cluster enzyme system in the body, which can effectively respond to cellular oxidative stress, lipid metabolism, inflammation, and oxidation. Published studies have shown that SOD enzymes (SODs) could maintain a dynamic balance between the production and scavenging of biological oxidants in the body and prevent the toxic effects of free radicals, and have been shown to be effective in anti-tumor, anti-radiation, and anti-aging studies. This research summarizes the types, biological functions, and regulatory mechanisms of SODs, as well as their applications in medicine, food production, and cosmetic production. SODs have proven to be a useful tool in fighting disease, and mimetics and conjugates that report SODs have been developed successively to improve the effectiveness of SODs. There are still obstacles to solving the membrane permeability of SODs and the persistence of enzyme action, which is still a hot spot and difficulty in mining the effect of SODs and promoting their application in the future.
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Affiliation(s)
| | | | | | | | | | - Qinghua Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
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5
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Bellach L, Gard LI, Lindner SD, Baumgartner-Parzer S, Klimek P, Kautzky-Willer A, Leutner M. The Interplay of Adipokines, Body Composition and Glucose Homeostasis in Pregnant Women with a History of RYGB Operation. Nutrients 2023; 15:nu15112498. [PMID: 37299461 DOI: 10.3390/nu15112498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Roux-en-Y gastric bypass operations (RYGB-OP) and pregnancy alter glucose homeostasis and the adipokine profile. This study investigates the relationship between adipokines and glucose metabolism during pregnancy post-RYGB-OP. (1) Methods: This is a post hoc analysis of a prospective cohort study during pregnancy in 25 women with an RYGB-OP (RY), 19 women with obesity (OB), and 19 normal-weight (NW) controls. Bioimpedance analysis (BIA) was used for metabolic characterization. Plasma levels of adiponectin, leptin, fibroblast-growth-factor 21 (FGF21), adipocyte fatty acid binding protein (AFABP), afamin, and secretagogin were obtained. (2) Results: The phase angle (φ) was lower in RY compared to OB and NW. Compared to OB, RY, and NW had lower leptin and AFABP levels, and higher adiponectin levels. φ correlated positively with leptin in RY (R = 0.63, p < 0.05) and negatively with adiponectin in OB and NW (R = -0.69, R = -0.69, p < 0.05). In RY, the Matsuda index correlated positively with FGF21 (R = 0.55, p < 0.05) and negatively with leptin (R = -0.5, p < 0.05). In OB, FGF21 correlated negatively with the disposition index (R = -0.66, p < 0.05). (3) Conclusions: The leptin, adiponectin, and AFABP levels differ between RY, OB, and NW and correlate with glucose metabolism and body composition. Thus, adipokines might influence energy homeostasis and maintenance of cellular health during pregnancy.
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Affiliation(s)
- Luise Bellach
- Clinical Division of Endocrinology and Metabolism, Department of Internal Medicine III, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Liliana-Imi Gard
- Clinical Division of Endocrinology and Metabolism, Department of Internal Medicine III, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Simon David Lindner
- Section for Science of Complex Systems, CeMSIIS, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
- Complexity Science Hub Vienna, Josefstädter Strasse 39, A-1080 Vienna, Austria
| | - Sabina Baumgartner-Parzer
- Clinical Division of Endocrinology and Metabolism, Department of Internal Medicine III, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Peter Klimek
- Section for Science of Complex Systems, CeMSIIS, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
- Complexity Science Hub Vienna, Josefstädter Strasse 39, A-1080 Vienna, Austria
| | - Alexandra Kautzky-Willer
- Clinical Division of Endocrinology and Metabolism, Department of Internal Medicine III, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Michael Leutner
- Clinical Division of Endocrinology and Metabolism, Department of Internal Medicine III, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
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Humardani FM, Mulyanata LT, Dwi Putra SE. Adipose cell-free DNA in diabetes. Clin Chim Acta 2023; 539:191-197. [PMID: 36549639 DOI: 10.1016/j.cca.2022.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Cancer-associated necrosis is a well-known source of cell-free DNA (cfDNA). However, the origins of cfDNA are not strictly limited to cancer. Additionally, dietary exposure induces apoptosis-induced proliferation in adipocytes, leading to the release of cfDNA. The genetic information derived from cfDNA as a result of apoptosis-induced proliferation contains specific methylation patterns in adipose tissue that can be used as a marker to detect the risk of developing Type 2 diabetes Mellitus (T2DM) in the future. cfDNA is superior to peripheral blood leukocytes (PBL) and whole blood samples for reflecting tissue pathology due to the frequent use of PBL and whole blood samples that do not match tissue pathology. The difficulty of demonstrating that cfDNA is derived from adipose tissue. We propose several promising techniques by analyzing cfDNA derived from adipose tissue to detect T2DM risk. First, adipose-specific genes such as ADIPOQ and Leptin were utilized. Second, MCTA-Seq, EpiSCORE, deconvolution, multiplexing, and automated machine learning (AutoML) were used to determine the proportion of total methylation in related genes.
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Affiliation(s)
| | | | - Sulistyo Emantoko Dwi Putra
- Department of Biology, Faculty of Biotechnology, University of Surabaya, Surabaya, Indonesia; Raya Kalingrungkut Road, Kali Rungkut, State of Rungkut, Surabaya City, East Java 60293, Indonesia.
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7
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Costa IPD, Hautem N, Schiano G, Uchida S, Nishino T, Devuyst O. Fasting influences aquaporin expression, water transport and adipocyte metabolism in the peritoneal membrane. Nephrol Dial Transplant 2022; 38:1408-1420. [PMID: 36520078 DOI: 10.1093/ndt/gfac318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The water channels AQP1 and AQP7 are abundantly expressed in the peritoneal membrane. While AQP1 facilitates water transport during peritoneal dialysis (PD), the role of AQP7, which mediates glycerol transport during fasting, remains unknown. METHODS We investigated the distribution of AQP7 and AQP1 and used a mouse model of PD to investigate the role of AQP7 in the peritoneal membrane at baseline and after fasting. Results. Single nucleus RNA-sequencing revealed that AQP7 was mostly detected in mature adipocytes, whereas AQP1 was essentially expressed in endothelial cells. Fasting induced significant decreases in whole body fat, plasma glucose, insulin, and triglycerides, as well as higher plasma glycerol and corticosterone levels in mice, paralleled by major decreases in adipocyte size and levels of fatty acid synthase and leptin, and increased levels of hormone sensitive lipase mRNAs in the peritoneum. Mechanistically, fasting upregulated the expression of AQP1 and AQP7 in the peritoneum, with increased ultrafiltration but no change in small solute transport. Studies based on Aqp1 and Aqp7 knockout mice and RU-486 inhibition demonstrated that the glucocorticoid induction of AQP1 mediates the increase in ultrafiltration whereas AQP7 regulates the size of adipocytes in the peritoneum. CONCLUSIONS Fasting induces a coordinated regulation of lipolytic and lipogenic factors and aqua(glycero)porins in the peritoneum, driving structural and functional changes. These data yield novel information on the specific roles of aquaporins in the peritoneal membrane and indicate that fasting improves fluid removal in a mouse model of PD.
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Affiliation(s)
| | | | - Gugliemo Schiano
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Shinichi Uchida
- Department of Nephrology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoya Nishino
- IREC, UCLouvain, Brussels, Belgium.,Department of Nephrology, Nagasaki University Hospital, Nagasaki, Japan
| | - Olivier Devuyst
- IREC, UCLouvain, Brussels, Belgium.,Institute of Physiology, University of Zurich, Zurich, Switzerland.,Cliniques Universitaires Saint-Luc, Brussels, Belgium
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8
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Bowers LW, Doerstling SS, Shamsunder MG, Lineberger CG, Rossi EL, Montgomery SA, Coleman MF, Gong W, Parker JS, Howell A, Harvie M, Hursting SD. Reversing the Genomic, Epigenetic, and Triple-Negative Breast Cancer-Enhancing Effects of Obesity. Cancer Prev Res (Phila) 2022; 15:581-594. [PMID: 35696725 PMCID: PMC9444913 DOI: 10.1158/1940-6207.capr-22-0113] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/02/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022]
Abstract
The reversibility of the procancer effects of obesity was interrogated in formerly obese C57BL/6 mice that lost weight via a nonrestricted low-fat diet (LFD) or 3 distinct calorie-restricted (CR) regimens (low-fat CR, Mediterranean-style CR, or intermittent CR). These mice, along with continuously obese mice and lean control mice, were orthotopically injected with E0771 cells, a mouse model of triple-negative breast cancer. Tumor weight, systemic cytokines, and incidence of lung metastases were elevated in the continuously obese and nonrestricted LFD mice relative to the 3 CR groups. Gene expression differed between the obese and all CR groups, but not the nonrestricted LFD group, for numerous tumoral genes associated with epithelial-to-mesenchymal transition as well as several genes in the normal mammary tissue associated with hypoxia, reactive oxygen species production, and p53 signaling. A high degree of concordance existed between differentially expressed mammary tissue genes from obese versus all CR mice and a microarray dataset from overweight/obese women randomized to either no intervention or a CR diet. Assessment of differentially methylated regions in mouse mammary tissues revealed that obesity, relative to the 4 weight loss groups, was associated with significant DNA hypermethylation. However, the anticancer effects of the CR interventions were independent of their ability to reverse obesity-associated mammary epigenetic reprogramming. Taken together, these preclinical data showing that the procancer effects of obesity are reversible by various forms of CR diets strongly support translational exploration of restricted dietary patterns for reducing the burden of obesity-associated cancers. PREVENTION RELEVANCE Obesity is an established risk and progression factor for triple-negative breast cancer (TNBC). Given rising global rates of obesity and TNBC, strategies to reduce the burden of obesity-driven TNBC are urgently needed. We report the genomic, epigenetic, and procancer effects of obesity are reversible by various calorie restriction regimens.
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Affiliation(s)
- Laura W. Bowers
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | - Emily L. Rossi
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Stephanie A. Montgomery
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Michael F. Coleman
- Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Anthony Howell
- Prevent Breast Cancer Research Unit, The Nightingale Centre, Manchester University NHS Foundation Trust, Manchester, England,Division of Cancer Sciences, The University of Manchester, Manchester, England
| | - Michelle Harvie
- Prevent Breast Cancer Research Unit, The Nightingale Centre, Manchester University NHS Foundation Trust, Manchester, England,Division of Cancer Sciences, The University of Manchester, Manchester, England
| | - Stephen D. Hursting
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA,Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA,Nutrition Research Institute, University of North Carolina, Kannapolis, NC, USA
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9
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Christiansen C, Tomlinson M, Eliot M, Nilsson E, Costeira R, Xia Y, Villicaña S, Mompeo O, Wells P, Castillo-Fernandez J, Potier L, Vohl MC, Tchernof A, Moustafa JES, Menni C, Steves CJ, Kelsey K, Ling C, Grundberg E, Small KS, Bell JT. Adipose methylome integrative-omic analyses reveal genetic and dietary metabolic health drivers and insulin resistance classifiers. Genome Med 2022; 14:75. [PMID: 35843982 PMCID: PMC9290282 DOI: 10.1186/s13073-022-01077-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/21/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND There is considerable evidence for the importance of the DNA methylome in metabolic health, for example, a robust methylation signature has been associated with body mass index (BMI). However, visceral fat (VF) mass accumulation is a greater risk factor for metabolic disease than BMI alone. In this study, we dissect the subcutaneous adipose tissue (SAT) methylome signature relevant to metabolic health by focusing on VF as the major risk factor of metabolic disease. We integrate results with genetic, blood methylation, SAT gene expression, blood metabolomic, dietary intake and metabolic phenotype data to assess and quantify genetic and environmental drivers of the identified signals, as well as their potential functional roles. METHODS Epigenome-wide association analyses were carried out to determine visceral fat mass-associated differentially methylated positions (VF-DMPs) in SAT samples from 538 TwinsUK participants. Validation and replication were performed in 333 individuals from 3 independent cohorts. To assess functional impacts of the VF-DMPs, the association between VF and gene expression was determined at the genes annotated to the VF-DMPs and an association analysis was carried out to determine whether methylation at the VF-DMPs is associated with gene expression. Further epigenetic analyses were carried out to compare methylation levels at the VF-DMPs as the response variables and a range of different metabolic health phenotypes including android:gynoid fat ratio (AGR), lipids, blood metabolomic profiles, insulin resistance, T2D and dietary intake variables. The results from all analyses were integrated to identify signals that exhibit altered SAT function and have strong relevance to metabolic health. RESULTS We identified 1181 CpG positions in 788 genes to be differentially methylated with VF (VF-DMPs) with significant enrichment in the insulin signalling pathway. Follow-up cross-omic analysis of VF-DMPs integrating genetics, gene expression, metabolomics, diet, and metabolic traits highlighted VF-DMPs located in 9 genes with strong relevance to metabolic disease mechanisms, with replication of signals in FASN, SREBF1, TAGLN2, PC and CFAP410. PC methylation showed evidence for mediating effects of diet on VF. FASN DNA methylation exhibited putative causal effects on VF that were also strongly associated with insulin resistance and methylation levels in FASN better classified insulin resistance (AUC=0.91) than BMI or VF alone. CONCLUSIONS Our findings help characterise the adiposity-associated methylation signature of SAT, with insights for metabolic disease risk.
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Affiliation(s)
- Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Max Tomlinson
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Melissa Eliot
- Department of Epidemiology, Brown University School of Public Health, Providence, R.I., USA
| | - Emma Nilsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Yujing Xia
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Olatz Mompeo
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Philippa Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Louis Potier
- Diabetology Department, Bichat Hospital, AP-HP, Université de Paris, Paris, France
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec, QC, Canada
| | - Andre Tchernof
- Québec Heart and Lung Institute, Université Laval, Québec, QC, Canada
| | | | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Karl Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, R.I., USA
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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10
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Ling C, Bacos K, Rönn T. Epigenetics of type 2 diabetes mellitus and weight change - a tool for precision medicine? Nat Rev Endocrinol 2022; 18:433-448. [PMID: 35513492 DOI: 10.1038/s41574-022-00671-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/29/2022] [Indexed: 12/12/2022]
Abstract
Pioneering studies performed over the past few decades demonstrate links between epigenetics and type 2 diabetes mellitus (T2DM), the metabolic disorder with the most rapidly increasing prevalence in the world. Importantly, these studies identified epigenetic modifications, including altered DNA methylation, in pancreatic islets, adipose tissue, skeletal muscle and the liver from individuals with T2DM. As non-genetic factors that affect the risk of T2DM, such as obesity, unhealthy diet, physical inactivity, ageing and the intrauterine environment, have been associated with epigenetic modifications in healthy individuals, epigenetics probably also contributes to T2DM development. In addition, genetic factors associated with T2DM and obesity affect the epigenome in human tissues. Notably, causal mediation analyses found DNA methylation to be a potential mediator of genetic associations with metabolic traits and disease. In the past few years, translational studies have identified blood-based epigenetic markers that might be further developed and used for precision medicine to help patients with T2DM receive optimal therapy and to identify patients at risk of complications. This Review focuses on epigenetic mechanisms in the development of T2DM and the regulation of body weight in humans, with a special focus on precision medicine.
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Affiliation(s)
- Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden.
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
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11
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Wang C, Duan M, Lin J, Wang G, Gao H, Yan M, Chen L, He J, Liu W, Yang F, Zhu S. LncRNA and mRNA expression profiles in brown adipose tissue of obesity-prone and obesity-resistant mice. iScience 2022; 25:104809. [PMID: 35992072 PMCID: PMC9382264 DOI: 10.1016/j.isci.2022.104809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/10/2022] [Accepted: 07/15/2022] [Indexed: 11/28/2022] Open
Abstract
Obesity-prone or obesity-resistant phenotypes can exist in individuals who consume the same diet type. Brown adipose tissue functions to dissipate energy in response to cold exposure or overfeeding. Long noncoding RNAs play important roles in a wide range of biological processes. However, systematic examination of lncRNAs in phenotypically divergent mice has not yet been reported. Here, the lncRNA expression profiles in BAT of HFD-induced C57BL/6J mice were investigated by high-throughput RNA sequencing. Genes that play roles in thermogenesis and related pathways were identified. We found lncRNA (Gm44502) may play a thermogenic role in obesity resistance by interacting with six mRNAs. Our results also indicated that seven differentially expressed lncRNAs (4930528G23Rik, Gm39490, Gm5627, Gm15551, Gm16083, Gm36860, Gm42002) may play roles in reducing heat production in obesity susceptibility by interacting with seven differentially expressed mRNAs. The screened lncRNAs may participate in the pathogenesis of weight regulation and provide insight into obesity therapy. First lncRNA profiles in BAT of OR and OP mice via bioinformatic analysis Gm44502 may play a thermogenic role by interacting with 6 mRNAs 7 DElncRNAs may reduce thermogenesis by interacting with 7 DEmRNAs Validation of expression changes of candidate genes in BAT by in vivo or in vitro
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Affiliation(s)
- Congcong Wang
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Meng Duan
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Jinhua Lin
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Guowei Wang
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - He Gao
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Mengsha Yan
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Lin Chen
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Jialing He
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Wei Liu
- Department of Biochemistry, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Fei Yang
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
- Corresponding author
| | - Shankuan Zhu
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
- Corresponding author
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12
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Yousefi PD, Suderman M, Langdon R, Whitehurst O, Davey Smith G, Relton CL. DNA methylation-based predictors of health: applications and statistical considerations. Nat Rev Genet 2022; 23:369-383. [PMID: 35304597 DOI: 10.1038/s41576-022-00465-w] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/12/2022]
Abstract
DNA methylation data have become a valuable source of information for biomarker development, because, unlike static genetic risk estimates, DNA methylation varies dynamically in relation to diverse exogenous and endogenous factors, including environmental risk factors and complex disease pathology. Reliable methods for genome-wide measurement at scale have led to the proliferation of epigenome-wide association studies and subsequently to the development of DNA methylation-based predictors across a wide range of health-related applications, from the identification of risk factors or exposures, such as age and smoking, to early detection of disease or progression in cancer, cardiovascular and neurological disease. This Review evaluates the progress of existing DNA methylation-based predictors, including the contribution of machine learning techniques, and assesses the uptake of key statistical best practices needed to ensure their reliable performance, such as data-driven feature selection, elimination of data leakage in performance estimates and use of generalizable, adequately powered training samples.
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Affiliation(s)
- Paul D Yousefi
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Ryan Langdon
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Oliver Whitehurst
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK.
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13
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Lyu M, Zhou J, Jiao L, Wang Y, Zhou Y, Lai H, Xu W, Ying B. Deciphering a TB-related DNA methylation biomarker and constructing a TB diagnostic classifier. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:37-49. [PMID: 34938605 PMCID: PMC8645423 DOI: 10.1016/j.omtn.2021.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/16/2021] [Indexed: 02/09/2023]
Abstract
We systemically identified tuberculosis (TB)-related DNA methylation biomarkers and further constructed classifiers for TB diagnosis. TB-related DNA methylation datasets were searched through October 3, 2020. Limma and DMRcate were employed to identify differentially methylated probes (DMPs) and regions (DMRs). Machine learning methods were used to construct classifiers. The performance of the classifiers was evaluated in discovery datasets and a prospective independent cohort. Eighty-nine DMPs and 24 DMRs were identified based on 67 TB patients and 45 healthy controls from 4 datasets. Nine and three DMRs were selected by elastic net regression and logistic regression, respectively. Among the selected DMRs, two regions (chr3: 195635643-195636243 and chr6: 29691631-29692475) were differentially methylated in the independent cohort (p = 4.19 × 10-5 and 0.024, respectively). Among the ten classifiers, the 3-DMR logistic regression classifier exhibited the strongest performance. The sensitivity, specificity, and area under the curve were, respectively, 79.1%, 84.4%, and 0.888 in the discovery datasets and 64.5%, 90.3%, and 0.838 in the independent cohort. The differential diagnostic ability of this classifier was also assessed. Collectively, these data showed that DNA methylation might be a promising TB diagnostic biomarker. The 3-DMR logistic regression classifier is a potential clinical tool for TB diagnosis, and further validation is needed.
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Affiliation(s)
- Mengyuan Lyu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jian Zhou
- West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China.,Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Jiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yili Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongli Lai
- West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, 10-511, 610 University Avenue, Toronto, ON M5G 2M9 Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7 Canada
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
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14
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Do WL, Gohar J, McCullough LE, Galaviz KI, Conneely KN, Narayan KMV. Examining the association between adiposity and DNA methylation: A systematic review and meta-analysis. Obes Rev 2021; 22:e13319. [PMID: 34278703 DOI: 10.1111/obr.13319] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/26/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022]
Abstract
Obesity is associated with widespread differential DNA methylation (DNAm) patterns, though there have been limited overlap in the obesity-associated cytosine-guanine nucleotide pair (CpG) sites that have been identified in the literature. We systematically searched four databases for studies published until January 2020. Eligible studies included cross-sectional, longitudinal, or intervention studies examining adiposity and genome-wide DNAm in non-pregnant adults aged 18-75 in all tissue types. Study design and results were extracted in the descriptive review. Blood-based DNAm results in body mass index (BMI) and waist circumference (WC) were meta-analyzed using weighted sum of Z-score meta-analysis. Of the 10,548 studies identified, 46 studies were included in the systematic review with 18 and nine studies included in the meta-analysis of BMI and WC, respectively. In the blood, 77 and four CpG sites were significant in three or more studies of BMI and WC, respectively. Using a genome-wide threshold for significance, 52 blood-based CpG sites were significantly associated with BMI. These sites have previously been associated with many obesity-related diseases including type 2 diabetes, cardiovascular disease, Crohn's disease, and depression. Our study shows that DNAm at 52 CpG sites represent potential mediators of obesity-associated chronic diseases and may be novel intervention or therapeutic targets to protect against obesity-associated chronic diseases.
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Affiliation(s)
- Whitney L Do
- Nutrition and Health Sciences Program, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Jazib Gohar
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Lauren E McCullough
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Karla I Galaviz
- Department of Applied Health Science, School of Public Health, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - K M Venkat Narayan
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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15
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Integrative analysis of miRNAs and mRNAs revealed regulation of lipid metabolism in dairy cattle. Funct Integr Genomics 2021; 21:393-404. [PMID: 33963462 DOI: 10.1007/s10142-021-00786-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Lipid metabolism in bovine mammary epithelial cells has been the primary focus of the research of milk fat percentage of dairy cattle. Functional microRNAs can affect lipid metabolism by regulating the expression of candidate genes. The purpose of the study was to screen and identify differentially expressed miRNAs, candidate genes, and co-regulatory pathways related to the metabolism of milk fat. To achieve this aim, we used miRNA and transcriptome data from the mammary epithelial cells of dairy cattle with high (H, 4.85%) and low milk fat percentages (L, 3.41%) during mid-lactation. One hundred ninety differentially expressed genes and 33 differentially expressed miRNAs were significantly enriched in related regulatory networks, of which 27 candidate genes regulated by 18 differentially expressed miRNAs significantly enriched in pathways related to lipid metabolism (p < 0.05). Target relationships between PDE4D and bta-miR-148a, PEG10 and bta-miR-877, SOD3 and bta-miR-2382-5p, and ADAMTS1 and bta-miR-2425-5p were verified using luciferase reporter assays and quantitative RT-PCR. The detection of triglyceride production in BMECs showed that bta-miR-21-3p and bta-miR-148a promote triglyceride synthesis, whereas bta-miR-124a, bta-miR-877, bta-miR-2382-5p, and bta-miR-2425-5p inhibit triglyceride synthesis. The conjoint analysis could identify functional miRNAs and regulatory candidate genes involved in lipid metabolism within the co-expression networks of the dairy cattle mammary system, which contributes to the understanding of potential regulatory mechanisms of genetic element and gene signaling networks involved in milk fat metabolism.
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16
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Calamita G, Delporte C. Involvement of aquaglyceroporins in energy metabolism in health and disease. Biochimie 2021; 188:20-34. [PMID: 33689852 DOI: 10.1016/j.biochi.2021.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 11/27/2022]
Abstract
Aquaglyceroporins are a group of the aquaporin (AQP) family of transmembrane water channels. While AQPs facilitate the passage of water, small solutes, and gases across biological membranes, aquaglyceroporins allow passage of water, glycerol, urea and some other solutes. Thanks to their glycerol permeability, aquaglyceroporins are involved in energy homeostasis. This review provides an overview of what is currently known concerning the functional implication and control of aquaglyceroporins in tissues involved in energy metabolism, i.e. liver, adipose tissue and endocrine pancreas. The expression, role and (dys)regulation of aquaglyceroporins in disorders affecting energy metabolism, and the potential relevance of aquaglyceroporins as drug targets to treat the alterations of the energy balance is also addressed.
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Affiliation(s)
- Giuseppe Calamita
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Christine Delporte
- Laboratory of Pathophysiological and Nutritional Biochemistry, Université Libre de Bruxelles, Brussels, Belgium.
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17
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Raposo HF, Forsythe P, Chausse B, Castelli JZ, Moraes-Vieira PM, Nunes VS, Oliveira HCF. Novel role of cholesteryl ester transfer protein (CETP): attenuation of adiposity by enhancing lipolysis and brown adipose tissue activity. Metabolism 2021; 114:154429. [PMID: 33166579 DOI: 10.1016/j.metabol.2020.154429] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/13/2020] [Accepted: 11/04/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVE The systemic function of CETP has been well characterized. CETP plasma activity reduces HDL cholesterol and thus increases the risk of atherosclerosis. Here, we investigated whether CETP expression modulate adiposity. METHODS Body adiposity and energy metabolism related assays and gene/protein expression were compared in CETP transgenic and non-transgenic mice and in hamsters treated with CETP neutralizing antibody. RESULTS We found that transgenic mice expressing human CETP present less white adipose tissue mass and lower leptinemia than nontransgenic (NTg) littermates. No differences were found in physical activity, food intake, fat fecal excretion, lipogenesis or exogenous lipid accumulation in adipose depots. Nonetheless, adipose lipolysis rates and whole-body energy expenditure were elevated in CETP mice. In accordance, lipolysis-related gene expression and protein content were increased in visceral and brown adipose tissue (BAT). In addition, we verified increased BAT temperature and oxygen consumption. These results were confirmed in two other animal models: 1) hamsters treated with CETP neutralizing antibody and 2) an independent line of transgenic mice expressing simian CETP. CONCLUSIONS These findings reveal a novel anti-adipogenic role for CETP.
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Affiliation(s)
- Helena F Raposo
- Department of Structural and Functional Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil; Obesity and Comorbidities Research Center, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Patricia Forsythe
- Department of Structural and Functional Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Bruno Chausse
- Obesity and Comorbidities Research Center, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Júlia Z Castelli
- Department of Structural and Functional Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil; Obesity and Comorbidities Research Center, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Pedro M Moraes-Vieira
- Obesity and Comorbidities Research Center, Institute of Biology, State University of Campinas, Campinas, SP, Brazil; Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil; Experimental Medicine Research Cluster (EMRC), State University of Campinas, SP, Brazil
| | - Valéria S Nunes
- Laboratorio de Lipides (LIM10), Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Helena C F Oliveira
- Department of Structural and Functional Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil; Obesity and Comorbidities Research Center, Institute of Biology, State University of Campinas, Campinas, SP, Brazil.
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18
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Sharma NK, Comeau ME, Montoya D, Pellegrini M, Howard TD, Langefeld CD, Das SK. Integrative Analysis of Glucometabolic Traits, Adipose Tissue DNA Methylation, and Gene Expression Identifies Epigenetic Regulatory Mechanisms of Insulin Resistance and Obesity in African Americans. Diabetes 2020; 69:2779-2793. [PMID: 32928872 PMCID: PMC7679782 DOI: 10.2337/db20-0117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022]
Abstract
Decline in insulin sensitivity due to dysfunction of adipose tissue (AT) is one of the earliest pathogenic events in type 2 diabetes. We hypothesize that differential DNA methylation (DNAm) controls insulin sensitivity and obesity by modulating transcript expression in AT. Integrating AT DNAm profiles with transcript profile data measured in a cohort of 230 African Americans (AAs) from the African American Genetics of Metabolism and Expression cohort, we performed cis-expression quantitative trait methylation (cis-eQTM) analysis to identify epigenetic regulatory loci for glucometabolic trait-associated transcripts. We identified significantly associated cytosine-guanine dinucleotide regions for 82 transcripts (false discovery rate [FDR]-P < 0.05). The strongest eQTM locus was observed for the proopiomelanocortin (POMC; ρ = -0.632, P = 4.70 × 10-27) gene. Epigenome-wide association studies (EWAS) further identified 155, 46, and 168 cytosine-guanine dinucleotide regions associated (FDR-P < 0.05) with the Matsuda index, SI, and BMI, respectively. Intersection of EWAS, transcript level to trait association, and eQTM results, followed by causal inference test identified significant eQTM loci for 23 genes that were also associated with Matsuda index, SI, and/or BMI in EWAS. These associated genes include FERMT3, ITGAM, ITGAX, and POMC In summary, applying an integrative multiomics approach, our study provides evidence for DNAm-mediated regulation of gene expression at both previously identified and novel loci for many key AT transcripts influencing insulin resistance and obesity.
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Affiliation(s)
- Neeraj K Sharma
- Department of Internal Medicine, Section of Endocrinology and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC
| | - Mary E Comeau
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Dennis Montoya
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA
| | - Timothy D Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Swapan K Das
- Department of Internal Medicine, Section of Endocrinology and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC
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19
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Shrestha D, Ouidir M, Workalemahu T, Zeng X, Tekola-Ayele F. Placental DNA methylation changes associated with maternal prepregnancy BMI and gestational weight gain. Int J Obes (Lond) 2020; 44:1406-1416. [PMID: 32071425 PMCID: PMC7261634 DOI: 10.1038/s41366-020-0546-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/14/2020] [Accepted: 02/06/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Maternal obesity prior to or during pregnancy influences fetal growth, predisposing the offspring to increased risk for obesity across the life course. Placental epigenetic mechanisms may underlie these associations. We conducted an epigenome-wide association study to identify placental DNA methylation changes associated with maternal prepregnancy body mass index (BMI) and rate of gestational weight gain at first (GWG1), second (GWG2), and third trimester (GWG3). METHOD Participants of the NICHD Fetal Growth Studies with genome-wide placental DNA methylation (n = 301) and gene expression (n = 75) data were included. Multivariable-adjusted regression models were used to test the associations of 1 kg/m2 increase in prepregnancy BMI or 1 kg/week increase in GWG with DNA methylation levels. Genes harboring top differentially methylated CpGs (FDR P < 0.05) were evaluated for placental gene expression. We assessed whether DNA methylation sites known to be associated with BMI in child or adult tissues, were also associated with maternal prepregnancy BMI in placenta. RESULTS Prepregnancy BMI was associated with DNA methylation at cg14568196[EGFL7], cg15339142[VETZ], and cg02301019[AC092377.1] (FDR P < 0.05, P ranging from 1.4 × 10-10 to 1.7 × 10-9). GWG1 or GWG2 was associated with DNA methylation at cg17918270[MYT1L], cg20735365[DLX5], and cg17451688[SLC35F3] (FDR P < 0.05, P ranging from 6.4 × 10-10 to 1.2 × 10-8). Both prepregnancy BMI and DNA methylation at cg1456819 [EGFL7] were negatively correlated with EGFL7 expression in placenta (P < 0.05). Several CpGs previously implicated in obesity traits in children and adults were associated with prepregnancy BMI in placenta. Functional annotations revealed that EGFL7 is highly expressed in placenta and the differentially methylated CpG sites near EGFL7 and VEZT were cis-meQTL targets in blood. CONCLUSIONS We identified placental DNA methylation changes at novel loci associated with prepregnancy BMI and GWG. The overlap between CpGs associated with obesity traits in placenta and other tissues in children and adults suggests that epigenetic mechanisms in placenta may give insights to early origins of obesity.
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Affiliation(s)
- Deepika Shrestha
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Marion Ouidir
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tsegaselassie Workalemahu
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Xuehuo Zeng
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Fasil Tekola-Ayele
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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20
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Bracht JR, Vieira‐Potter VJ, De Souza Santos R, Öz OK, Palmer BF, Clegg DJ. The role of estrogens in the adipose tissue milieu. Ann N Y Acad Sci 2019; 1461:127-143. [DOI: 10.1111/nyas.14281] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/24/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | - Orhan K. Öz
- Department of RadiologyUniversity of Texas Southwestern Medical Center Dallas Texas
| | - Biff F. Palmer
- Department of MedicineUniversity of Texas Southwestern Medical Center Dallas Texas
| | - Deborah J. Clegg
- College of Nursing and Health ProfessionsDrexel University Philadelphia Pennsylvania
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21
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Chu SH, Kelsey KT, Koestler DC, Loucks EB, Huang YT. Leveraging cell-specific differentially methylated regions to identify leukocyte infiltration in adipose tissue. Genet Epidemiol 2019; 43:1018-1029. [PMID: 31433079 PMCID: PMC6829028 DOI: 10.1002/gepi.22252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/02/2019] [Accepted: 07/16/2019] [Indexed: 12/16/2022]
Abstract
Obesity is understood to be an inflammatory condition characterized in part by changes in resident immune cell populations in adipose tissue. However, much of this knowledge has been obtained through experimental animal models. Epigenetic mechanisms, such as DNA methylation may be useful tools for characterizing the changes in immune cell populations in human subjects. In this study, we introduce a simple and intuitive method for assessing cellular infiltration by blood into other heterogeneous, admixed tissues such as adipose tissue, and apply this approach in a large human cohort study. Associations between higher leukocyte infiltration, measured by evaluating a distance measure between the methylation signatures of leukocytes and adipose tissue, and increasing body mass index (BMI) or android fat mass (AFM) were identified and validated in independent replication samples for CD4 (pBMI = 0.009, pAFM = 0.020), monocytes (pBMI = 0.001, pAFM = 4.3 × 10-4 ), and dendritic cells (pBMI = 0.571, pAFM = 0.012). Patterns of depletion with increasing adiposity were observed for plasma B (pBMI = 0.430, pAFM = 0.004) and immature B (pBMI = 0.022, pAFM = 0.042) cells. CD4, dendritic, monocytes, immature B, and plasma B cells may be important agents in the inflammatory process. Finally, the method used to assess leukocyte infiltration in this study is straightforwardly extended to other cell types and tissues in which infiltration might be of interest.
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Affiliation(s)
- Su H. Chu
- Department of Epidemiology, School of Public Health, Brown University, Providence, RI USA 02912
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA USA 02115
- Department of Medicine, Harvard Medical School, Boston, MA USA 02115
| | - Karl T. Kelsey
- Department of Epidemiology, School of Public Health, Brown University, Providence, RI USA 02912
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University
| | - Devin C. Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS USA
| | - Eric B. Loucks
- Department of Epidemiology, School of Public Health, Brown University, Providence, RI USA 02912
| | - Yen-Tsung Huang
- Department of Epidemiology, School of Public Health, Brown University, Providence, RI USA 02912
- Department of Biostatistics, School of Public Health, Brown University, Providence, RI USA 02912
- Institute of Statistical Science, Academia Sinica, Taipei City, Taiwan
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22
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Juvinao-Quintero DL, Hivert MF, Sharp GC, Relton CL, Elliott HR. DNA Methylation and Type 2 Diabetes: the Use of Mendelian Randomization to Assess Causality. CURRENT GENETIC MEDICINE REPORTS 2019; 7:191-207. [PMID: 32274260 PMCID: PMC7145450 DOI: 10.1007/s40142-019-00176-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Purpose of Review This review summarises recent advances in the field of epigenetics in order to understand the aetiology of type 2 diabetes (T2D). Recent Findings DNA methylation at a number of loci has been shown to be robustly associated with T2D, including TXNIP, ABCG1, CPT1A, and SREBF1. However, due to the cross-sectional nature of many epidemiological studies and predominant analysis in samples derived from blood rather than disease relevant tissues, inferring causality is difficult. We therefore outline the use of Mendelian randomisation (MR) as one method able to assess causality in epigenetic studies of T2D. Summary Epidemiological studies have been fruitful in identifying epigenetic markers of T2D. Triangulation of evidence including utilisation of MR is essential to delineate causal from non-causal biomarkers of disease. Understanding the causality of epigenetic markers in T2D more fully will aid prioritisation of CpG sites as early biomarkers to detect disease or in drug development to target epigenetic mechanisms in order to treat patients.
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Affiliation(s)
- Diana L Juvinao-Quintero
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, USA
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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23
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McCaffery JM. Precision behavioral medicine: Implications of genetic and genomic discoveries for behavioral weight loss treatment. ACTA ACUST UNITED AC 2019; 73:1045-1055. [PMID: 30394782 DOI: 10.1037/amp0000253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article reviews the concept of precision behavioral medicine and the progress toward applying genetics and genomics as tools to optimize weight management intervention. We discuss genetic, epigenetic, and genomic markers, as well as interactions between genetics and the environment as they relate to obesity and behavioral weight loss to date. Recommendations for the conditions under which genetics and genomics could be incorporated to support clinical decision-making in behavioral weight loss are outlined and illustrative scenarios of how this approach could improve clinical outcomes are provided. It is concluded that there is not yet sufficient evidence to leverage genetics or genomics to aid the treatment of obesity but the foundations are being laid. (PsycINFO Database Record (c) 2018 APA, all rights reserved).
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Affiliation(s)
- Jeanne M McCaffery
- Weight Control and Diabetes Research Center, Department of Psychiatry and Human Behavior, The Miriam Hospital
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24
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Mansell T, Ponsonby AL, Januar V, Novakovic B, Collier F, Burgner D, Vuillermin P, Ryan J, Saffery R. Early-life determinants of hypoxia-inducible factor 3A gene (HIF3A) methylation: a birth cohort study. Clin Epigenetics 2019; 11:96. [PMID: 31262346 PMCID: PMC6604333 DOI: 10.1186/s13148-019-0687-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/27/2019] [Indexed: 12/17/2022] Open
Abstract
Background Methylation of the hypoxia-inducible factor 3α gene (HIF3A) has been linked to pregnancy exposures, infant adiposity and later BMI. Genetic variation influences HIF3A methylation levels and may modify these relationships. However, data in very early life are limited, particularly in association with adverse pregnancy outcomes. We investigated the relationship between maternal and gestational factors, infant anthropometry, genetic variation and HIF3A DNA methylation in the Barwon Infant Study, a population-based birth cohort. Methylation of two previously studied regions of HIF3A were tested in the cord blood mononuclear cells of 938 infants. Results No compelling evidence was found of an association between birth weight, adiposity or maternal gestational diabetes with methylation at the most widely studied HIF3A region. Male sex (− 4.3%, p < 0.001) and pre-eclampsia (− 5.4%, p = 0.02) negatively associated with methylation at a second region of HIF3A; while positive associations were identified for gestational diabetes (4.8%, p = 0.01) and gestational age (1.2% increase per week, p < 0.001). HIF3A genetic variation also associated strongly with methylation at this region (p < 0.001). Conclusions Pre- and perinatal factors impact HIF3A methylation, including pre-eclampsia. This provides evidence that specific pregnancy complications, previously linked to adverse outcomes for both mother and child, impact the infant epigenome in a molecular pathway critical to several vascular and metabolic conditions. Further work is required to understand the mechanisms and clinical relevance, particularly the differing effects of in utero exposure to gestational diabetes or pre-eclampsia. Electronic supplementary material The online version of this article (10.1186/s13148-019-0687-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Toby Mansell
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Anne-Louise Ponsonby
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,The Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Vania Januar
- Murdoch Children's Research Institute, Parkville, Australia
| | - Boris Novakovic
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Fiona Collier
- Murdoch Children's Research Institute, Parkville, Australia.,School of Medicine, Deakin University, Geelong, Australia.,Child Health Research Unit, Barwon Health, Geelong, Australia
| | - David Burgner
- Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,Department of Paediatrics, Monash University, Clayton, Australia
| | - Peter Vuillermin
- Murdoch Children's Research Institute, Parkville, Australia.,School of Medicine, Deakin University, Geelong, Australia.,Child Health Research Unit, Barwon Health, Geelong, Australia
| | - Joanne Ryan
- Murdoch Children's Research Institute, Parkville, Australia.,School of Public Health & Preventive Medicine, Monash University, Melbourne, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Parkville, Australia. .,Department of Paediatrics, University of Melbourne, Parkville, Australia.
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25
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Sun W, von Meyenn F, Peleg‐Raibstein D, Wolfrum C. Environmental and Nutritional Effects Regulating Adipose Tissue Function and Metabolism Across Generations. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900275. [PMID: 31179229 PMCID: PMC6548959 DOI: 10.1002/advs.201900275] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/21/2019] [Indexed: 05/12/2023]
Abstract
The unabated rise in obesity prevalence during the last 40 years has spurred substantial interest in understanding the reasons for this epidemic. Studies in mice and humans have demonstrated that obesity is a highly heritable disease; however genetic variations within specific populations have so far not been able to explain this phenomenon to its full extent. Recent work has demonstrated that environmental cues can be sensed by an organism to elicit lasting changes, which in turn can affect systemic energy metabolism by different epigenetic mechanisms such as changes in small noncoding RNA expression, DNA methylation patterns, as well as histone modifications. These changes can directly modulate cellular function in response to environmental cues, however research during the last decade has demonstrated that some of these modifications might be transmitted to subsequent generations, thus modulating energy metabolism of the progeny in an inter- as well as transgenerational manner. In this context, adipose tissue has become a focus of research due to its plasticity, which allows the formation of energy storing (white) as well as energy wasting (brown/brite/beige) cells within the same depot. In this Review, the effects of environmental induced obesity with a particular focus on adipose tissue are discussed.
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Affiliation(s)
- Wenfei Sun
- Department of Health Science and TechnologiesETH ZürichSchorenstrasse 16SchwerzenbachCH‐8603Switzerland
| | - Ferdinand von Meyenn
- Department of Health Science and TechnologiesETH ZürichSchorenstrasse 16SchwerzenbachCH‐8603Switzerland
| | - Daria Peleg‐Raibstein
- Department of Health Science and TechnologiesETH ZürichSchorenstrasse 16SchwerzenbachCH‐8603Switzerland
| | - Christian Wolfrum
- Department of Health Science and TechnologiesETH ZürichSchorenstrasse 16SchwerzenbachCH‐8603Switzerland
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Abstract
The twin epidemics of obesity and type 2 diabetes (T2D) are a serious health, social, and economic issue. The dysregulation of adipose tissue biology is central to the development of these two metabolic disorders, as adipose tissue plays a pivotal role in regulating whole-body metabolism and energy homeostasis (1). Accumulating evidence indicates that multiple aspects of adipose biology are regulated, in part, by epigenetic mechanisms. The precise and comprehensive understanding of the epigenetic control of adipose tissue biology is crucial to identifying novel therapeutic interventions that target epigenetic issues. Here, we review the recent findings on DNA methylation events and machinery in regulating the developmental processes and metabolic function of adipocytes. We highlight the following points: 1) DNA methylation is a key epigenetic regulator of adipose development and gene regulation, 2) emerging evidence suggests that DNA methylation is involved in the transgenerational passage of obesity and other metabolic disorders, 3) DNA methylation is involved in regulating the altered transcriptional landscape of dysfunctional adipose tissue, 4) genome-wide studies reveal specific DNA methylation events that associate with obesity and T2D, and 5) the enzymatic effectors of DNA methylation have physiological functions in adipose development and metabolic function.
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Affiliation(s)
- Xiang Ma
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA
| | - Sona Kang
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA
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27
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Stols-Gonçalves D, Tristão LS, Henneman P, Nieuwdorp M. Epigenetic Markers and Microbiota/Metabolite-Induced Epigenetic Modifications in the Pathogenesis of Obesity, Metabolic Syndrome, Type 2 Diabetes, and Non-alcoholic Fatty Liver Disease. Curr Diab Rep 2019; 19:31. [PMID: 31044315 PMCID: PMC6494784 DOI: 10.1007/s11892-019-1151-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW The metabolic syndrome is a pathological state in which one of the key components is insulin resistance. A wide spectrum of body compartments is involved in its pathophysiology. Genetic and environmental factors such as diet and physical activity are both related to its etiology. Reversible modulation of gene expression without altering the DNA sequence, known as epigenetic modifications, has been shown to drive this complex metabolic cluster of conditions. Here, we aim to examine some of the recent research of specific epigenetically mediated mechanisms and microbiota-induced epigenetic modifications on the development of adipose tissue and obesity, β-cell dysfunction and diabetes, and hepatocytes and non-alcoholic fatty disease. RECENT FINDINGS DNA methylation patterns and histone modifications have been identified in this context; the integrated analysis of genome, epigenome, and transcriptome is likely to expand our knowledge of epigenetics in health and disease. Epigenetic modifications induced by diet-related microbiota or metabolites possibly contribute to the insulin-resistant state. The identification of epigenetic signatures on diabetes and obesity may give us the possibility of developing new interventions, prevention measures, and follow-up strategies.
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Affiliation(s)
- Daniela Stols-Gonçalves
- Department of Vascular Medicine, Amsterdam UMC, Location AMC, Meibergdreef 9 (Room A01-112), 1105 AZ Amsterdam, The Netherlands
| | - Luca Schiliró Tristão
- Faculdade de Ciências Médicas de Santos (UNILUS), R. Oswaldo Cruz, 179, Boqueirão, Santos, SP 11025-020 Brazil
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, Meibergdreef 9 (Room A01-112), 1105 AZ Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Vascular Medicine, Amsterdam UMC, Location AMC, Meibergdreef 9 (Room A01-112), 1105 AZ Amsterdam, The Netherlands
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28
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Huang YT. Genome-wide analyses of sparse mediation effects under composite null hypotheses. Ann Appl Stat 2019. [DOI: 10.1214/18-aoas1181] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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Arpón A, Milagro FI, Ramos-Lopez O, Mansego ML, Santos JL, Riezu-Boj JI, Martínez JA. Epigenome-wide association study in peripheral white blood cells involving insulin resistance. Sci Rep 2019; 9:2445. [PMID: 30792424 PMCID: PMC6385280 DOI: 10.1038/s41598-019-38980-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/11/2019] [Indexed: 02/06/2023] Open
Abstract
Insulin resistance (IR) is a hallmark of type 2 diabetes, metabolic syndrome and cardiometabolic risk. An epigenetic phenomena such as DNA methylation might be involved in the onset and development of systemic IR. The aim of this study was to explore the genetic DNA methylation levels in peripheral white blood cells with the objective of identifying epigenetic signatures associated with IR measured by the Homeostatic Model Assessment of IR (HOMA-IR) following an epigenome-wide association study approach. DNA methylation levels were assessed using Infinium Methylation Assay (Illumina), and were associated with HOMA-IR values of participants from the Methyl Epigenome Network Association (MENA) project, finding statistical associations for at least 798 CpGs. A stringent statistical analysis revealed that 478 of them showed a differential methylation pattern between individuals with HOMA-IR ≤ 3 and > 3. ROC curves of top four CpGs out of 478 allowed differentiating individuals between both groups (AUC≈0.88). This study demonstrated the association between DNA methylation in some specific CpGs and HOMA-IR values that will help to the understanding and in the development of new strategies for personalized approaches to predict and prevent IR-associated diseases.
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Affiliation(s)
- Ana Arpón
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - Fermín I Milagro
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain.,Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, Madrid, Spain
| | - Omar Ramos-Lopez
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - M Luisa Mansego
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain
| | - José Luis Santos
- Department of Nutrition, Diabetes and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José-Ignacio Riezu-Boj
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain. .,Navarra Institute for Health Research (IdiSNa), Pamplona, Spain.
| | - J Alfredo Martínez
- University of Navarra, Department of Nutrition, Food Sciences and Physiology & Centre for Nutrition Research, Pamplona, Spain.,Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, Madrid, Spain.,Navarra Institute for Health Research (IdiSNa), Pamplona, Spain.,Madrid Institute for Advanced Studies (IMDEA), IMDEA Food, Madrid, Spain
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30
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Divoux A, Sandor K, Bojcsuk D, Talukder A, Li X, Balint BL, Osborne TF, Smith SR. Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes. Clin Epigenetics 2018; 10:148. [PMID: 30477572 PMCID: PMC6258289 DOI: 10.1186/s13148-018-0582-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022] Open
Abstract
Background Increased lower body fat is associated with reduced cardiometabolic risk. The molecular basis for depot-specific differences in gluteofemoral (GF) compared with abdominal (A) subcutaneous adipocyte function is poorly understood. In the current report, we used a combination of Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-seq), RNA-seq, and chromatin immunoprecipitation (ChIP)-qPCR analyses that provide evidence that depot-specific gene expression patterns are associated with differential epigenetic chromatin signatures. Methods Preadipocytes cultured from A and GF adipose tissue obtained from premenopausal apple-shaped women were used to perform transcriptome analysis by RNA-seq and assess accessible chromatin regions by ATAC-seq. We measured mRNA expression and performed ChIP-qPCR experiments for histone modifications of active (H3K4me3) and repressed chromatin (H3K27me3) regions respectively on the promoter regions of differentially expressed genes. Results RNA-seq experiments revealed an A-fat and GF-fat selective gene expression signature, with 126 genes upregulated in abdominal preadipocytes and 90 genes upregulated in GF cells. ATAC-seq identified almost 10-times more A-specific chromatin-accessible regions. Using a combined analysis of ATAC-seq and global gene expression data, we identified 74 of the 126 abdominal-specific genes (59%) with A-specific accessible chromatin sites within 200 kb of the transcription start site (TSS), including HOXA3, HOXA5, IL8, IL1b, and IL6. Interestingly, only 14 of the 90 GF-specific genes (15%) had GF-specific accessible chromatin sites within 200 kb of the corresponding TSS, including HOXC13 and HOTAIR, whereas 25 of them (28%) had abdominal-specific accessible chromatin sites. ChIP-qPCR experiments confirmed that the active H3K4me3 chromatin mark was significantly enriched at the promoter regions of HOXA5 and HOXA3 genes in abdominal preadipocytes, while H3K27me3 was less abundant relative to chromatin from GF. This is consistent with their A-fat specific gene expression pattern. Conversely, analysis of the promoter regions of the GF specific HOTAIR and HOXC13 genes exhibited high H3K4me3 and low H3K27me3 levels in GF chromatin compared to A chromatin. Conclusions Global transcriptome and open chromatin analyses of depot-specific preadipocytes identified their gene expression signature and differential open chromatin profile. Interestingly, A-fat-specific open chromatin regions can be observed in the proximity of GF-fat genes, but not vice versa. Trial registration Clinicaltrials.gov, NCT01745471. Registered 5 December 2012. Electronic supplementary material The online version of this article (10.1186/s13148-018-0582-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adeline Divoux
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, 301 E. Princeton Street, Orlando, FL, 32804, USA. .,Diabetes and Obesity Research Center, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA.
| | - Katalin Sandor
- Diabetes and Obesity Research Center, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA.,Present address: Department of Medicine, Johns Hopkins All Children's Hospital, Johns Hopkins University School of Medicine, St. Petersburg, FL, 33701, USA
| | - Dora Bojcsuk
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Nagyerdei krt 98, Debrecen, 4032, Hungary
| | - Amlan Talukder
- Department of Computer Science, University of Central Florida, 4000 Central Florida Blvd, Orlando, 32816, USA
| | - Xiaoman Li
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Boulevard, Orlando, FL, USA
| | - Balint L Balint
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Nagyerdei krt 98, Debrecen, 4032, Hungary
| | - Timothy F Osborne
- Diabetes and Obesity Research Center, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA.,Present address: Department of Medicine, Johns Hopkins All Children's Hospital, Johns Hopkins University School of Medicine, St. Petersburg, FL, 33701, USA
| | - Steven R Smith
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, 301 E. Princeton Street, Orlando, FL, 32804, USA.,Diabetes and Obesity Research Center, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA
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Gómez-Zorita S, Trepiana J, Fernández-Quintela A, González M, Portillo MP. Resveratrol and Pterostilbene, Two Analogue Phenolic Compounds, Affect Aquaglyceroporin Expression in a Different Manner in Adipose Tissue. Int J Mol Sci 2018; 19:ijms19092654. [PMID: 30205436 PMCID: PMC6165208 DOI: 10.3390/ijms19092654] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/25/2018] [Accepted: 09/03/2018] [Indexed: 12/19/2022] Open
Abstract
Aquaglyceroporins (AQPs) are transmembrane channels that mediate glycerol release and glycerol uptake. They are involved in fat metabolism, with implications in obesity. The aim was to determine whether the administration of resveratrol and pterostilbene during the six weeks of the experimental period would modify AQPs expression in white and brown adipose tissues from Wistar rats fed an obesogenic diet, and to establish a potential relationship with the delipidating properties of these compounds. Consequently, thirty-six rats were divided into four groups: (a) group fed a standard diet; and three more groups fed a high-fat high-sucrose diet: (b) high-fat high-sucrose group: (c) pterostilbene-treated group (30 mg/kg/d): (d) resveratrol-treated group (30 mg/kg/d). Epididymal, subcutaneous white adipose tissues and interscapular brown adipose tissue were dissected. AQPs gene expression (RT-PCR) and protein expression (western-blot) were measured. In white adipose tissue, pterostilbene reduced subcutaneous adipose tissue weight and prevented the decrease in AQP9 induced by obesogenic feeding, and thus glycerol uptake for triglyceride accumulation. Resveratrol reduced epididymal adipose tissue weight and avoided the decrease in AQPs related to glycerol release induced by high-fat high-sucrose feeding, suggesting the involvement of lipolysis in its body-fat lowering effect. Regarding brown adipose tissue, AQP7 seemed not to be involved in the previously reported thermogenic activity of both phenolic compounds.
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Affiliation(s)
- Saioa Gómez-Zorita
- Nutrition and Obesity Group, Department of Nutrition and Food Science, University of the Basque Country (UPV/EHU) and Lucio Lascaray Research Institute, 48940 Vitoria, Spain.
- Biomedical Research Networking Centres, Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, 28029 Madrid, Spain.
| | - Jenifer Trepiana
- Nutrition and Obesity Group, Department of Nutrition and Food Science, University of the Basque Country (UPV/EHU) and Lucio Lascaray Research Institute, 48940 Vitoria, Spain.
| | - Alfredo Fernández-Quintela
- Nutrition and Obesity Group, Department of Nutrition and Food Science, University of the Basque Country (UPV/EHU) and Lucio Lascaray Research Institute, 48940 Vitoria, Spain.
- Biomedical Research Networking Centres, Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, 28029 Madrid, Spain.
| | - Marcela González
- Nutrition and Food Science Department, Faculty of Biochemistry and Biological Sciences, National University of Litoral and National Scientific and Technical Research Council (CONICET), 3000 Santa Fe, Argentina.
| | - María P Portillo
- Nutrition and Obesity Group, Department of Nutrition and Food Science, University of the Basque Country (UPV/EHU) and Lucio Lascaray Research Institute, 48940 Vitoria, Spain.
- Biomedical Research Networking Centres, Physiopathology of Obesity and Nutrition (CIBERobn), Institute of Health Carlos III, 28029 Madrid, Spain.
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32
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Huang YT. Joint significance tests for mediation effects of socioeconomic adversity on adiposity via epigenetics. Ann Appl Stat 2018. [DOI: 10.1214/17-aoas1120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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33
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Population DNA methylation studies in the Developmental Origins of Health and Disease (DOHaD) framework. J Dev Orig Health Dis 2018; 10:306-313. [PMID: 30101736 DOI: 10.1017/s2040174418000442] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic changes represent a potential mechanism underlying associations of early-life exposures and later life health outcomes. Population-based cohort studies starting in early life are an attractive framework to study the role of such changes. DNA methylation is the most studied epigenetic mechanism in population research. We discuss the application of DNA methylation in early-life population studies, some recent findings, key challenges and recommendations for future research. Studies into DNA methylation within the Developmental Origins of Health and Disease framework generally either explore associations between prenatal exposures and offspring DNA methylation or associations between offspring DNA methylation in early life and later health outcomes. Only a few studies to date have integrated prospective exposure, epigenetic and phenotypic data in order to explicitly test the role of DNA methylation as a potential biological mediator of environmental effects on health outcomes. Population epigenetics is an emerging field which has challenges in terms of methodology and interpretation of the data. Key challenges include tissue specificity, cell type adjustment, issues of power and comparability of findings, genetic influences, and exploring causality and functional consequences. Ongoing studies are working on addressing these issues. Large collaborative efforts of prospective cohorts are emerging, with clear benefits in terms of optimizing power and use of resources, and in advancing methodology. In the future, multidisciplinary approaches, within and beyond longitudinal birth and preconception cohorts will advance this complex, but highly promising, the field of research.
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Frank AP, de Souza Santos R, Palmer BF, Clegg DJ. Determinants of body fat distribution in humans may provide insight about obesity-related health risks. J Lipid Res 2018; 60:1710-1719. [PMID: 30097511 DOI: 10.1194/jlr.r086975] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/07/2018] [Indexed: 12/24/2022] Open
Abstract
Obesity increases the risks of developing cardiovascular and metabolic diseases and degrades quality of life, ultimately increasing the risk of death. However, not all forms of obesity are equally dangerous: some individuals, despite higher percentages of body fat, are at less risk for certain chronic obesity-related complications. Many open questions remain about why this occurs. Data suggest that the physical location of fat and the overall health of fat dramatically influence disease risk; for example, higher concentrations of visceral relative to subcutaneous adipose tissue are associated with greater metabolic risks. As such, understanding the determinants of the location and health of adipose tissue can provide insight about the pathological consequences of obesity and can begin to outline targets for novel therapeutic approaches to combat the obesity epidemic. Although age and sex hormones clearly play roles in fat distribution and location, much remains unknown about gene regulation at the level of adipose tissue or how genetic variants regulate fat distribution. In this review, we discuss what is known about the determinants of body fat distribution, and we highlight the important roles of sex hormones, aging, and genetic variation in the determination of body fat distribution and its contribution to obesity-related comorbidities.
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Affiliation(s)
- Aaron P Frank
- Diabetes, Obesity, and Wellness Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Roberta de Souza Santos
- Diabetes, Obesity, and Wellness Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Biff F Palmer
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Deborah J Clegg
- Diabetes, Obesity, and Wellness Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
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35
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Chu SH, Loucks EB, Kelsey KT, Gilman SE, Agha G, Eaton CB, Buka SL, Huang YT. Sex-specific epigenetic mediators between early life social disadvantage and adulthood BMI. Epigenomics 2018; 10:707-722. [PMID: 29888956 DOI: 10.2217/epi-2017-0146] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM The objective of this study was to identify potential epigenetic mediating pathways linking early life social disadvantage (ELSD) to adulthood BMI. METHODS Sex-specific epigenome-wide two-stage mediation analyses were conducted in blood and adipose tissue, and mediation estimates were obtained using cross-product mediation analysis. Pathway analyses were conducted using GREAT software (Bejerano Lab, CA, USA). RESULTS Candidate mediation CpG sites were identified in adipose tissue, but not blood, and were sex-specific. Significant mediation sites in females included CpG loci in genes: PKHG1, BCAR3, ADAM5P, PIEZO1, FGFRL1, FASN and DPP9, among others. Pathway analyses revealed evidence of enrichment for processes associated with TFG-β signaling and immunologic signatures. In males, significant mediation loci included sites in MAP3K5 and RPTOR, which have previously been associated with adipogenesis, inflammation and insulin resistance. CONCLUSION Our findings provide supportive evidence for the mediating role of epigenetic mechanisms in the effect of early life social disadvantage on adulthood BMI.
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Affiliation(s)
- Su H Chu
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA.,Channing Division of Network Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, 02115, USA
| | - Eric B Loucks
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA.,Department of Pathology & Laboratory Medicine, Brown University Warren Alpert Medical School, Providence, RI, 02912, USA
| | - Stephen E Gilman
- Health Behavior Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health & Human Development, Bethesda, MD, 20892, USA.,Department of Social & Behavioral Sciences, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA.,Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Golareh Agha
- Columbia Aging Center, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Charles B Eaton
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA.,Department of Family Medicine, Brown University Warren Alpert Medical School, Providence, RI, 02912, USA
| | - Stephen L Buka
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA
| | - Yen-Tsung Huang
- Department of Epidemiology, Brown School of Public Health, Providence, RI, 02912, USA.,Department of Biostatistics, Brown School of Public Health, Providence, RI, 02912, USA.,Institute of Statistical Science, Academia Sinica, Taipei, 11529, Taiwan
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Zhang SJ, Wang Y, Yang YL, Zheng H. Aberrant DNA Methylation Involved in Obese Women with Systemic Insulin Resistance. Open Life Sci 2018; 13:201-207. [PMID: 33817084 PMCID: PMC7874722 DOI: 10.1515/biol-2018-0024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/08/2018] [Indexed: 01/03/2023] Open
Abstract
Background Epigenetics has been recognized as a significant regulator in many diseases. White adipose tissue (WAT) epigenetic dysregulation is associated with systemic insulin resistance (IR). The aim of this study was to survey the differential methylation of genes in obese women with systemic insulin resistance by DNA methylation microarray. Methods The genome-wide methylation profile of systemic insulin resistant obese women was obtained from Gene Expression Omnibus database. After data preprocessing, differing methylation patterns between insulin resistant and sensitive obese women were identified by Student's t-test and methylation value differences. Network analysis was then performed to reveal co-regulated genes of differentially methylated genes. Functional analysis was also implemented to reveal the underlying biological processes related to systemic insulin resistance in obese women. Results Relative to insulin sensitive obese women, we initially screened 10,874 differentially methylated CpGs, including 7402 hyper-methylated sites and 6073 hypo-methylated CpGs. Our analysis identified 4 significantly differentially methylated genes, including SMYD3, UST, BCL11A, and BAI3. Network and functional analyses found that these differentially methylated genes were mainly involved in chondroitin and dermatan sulfate biosynthetic processes. Conclusion Based on our study, we propose several epigenetic biomarkers that may be related to obesity-associated insulin resistance. Our results provide new insights into the epigenetic regulation of disease etiology and also identify novel targets for insulin resistance treatment in obese women.
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Affiliation(s)
- Shao-Jun Zhang
- Department of Endocrinology, The People's Hospital of Shanxi Province, Taiyuan, Shanxi 030012, China.,Department of Endocrinology, The Sixth Division Hospital of Xinjiang Production and Construction Corps, Wujiaqu, Xinjiang 830025, China
| | - Yan Wang
- Medical Laboratory Diagnosis Center, Jinan Central Hospital, Jinan, Shandong 250013, China
| | - Yan-Lan Yang
- Department of Endocrinology, The People's Hospital of Shanxi Province, Taiyuan, Shanxi 030012, China
| | - Hong Zheng
- Department of Endocrinology, The Second Affiliated Hospital of Dalian Medical University, No. 467 Zhongshan Road, Shahekou District, Dalian, Liaoning 116023, China
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Jiao C, Zhang C, Dai R, Xia Y, Wang K, Giase G, Chen C, Liu C. Positional effects revealed in Illumina methylation array and the impact on analysis. Epigenomics 2018; 10:643-659. [PMID: 29469594 PMCID: PMC6021926 DOI: 10.2217/epi-2017-0105] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/17/2018] [Indexed: 12/18/2022] Open
Abstract
AIM We aimed to prove the existence of positional effects in the Illumina methylation beadchip data and to find an optimal correction method. MATERIALS & METHODS Three HumanMethylation450, three HumanMethylation27 datasets and two EPIC datasets were analyzed. ComBat, linear regression, functional normalization and single-sample Noob were used for minimizing positional effects. The corrected results were evaluated by four methods. RESULTS We detected 52,988 CpG loci significantly associated with sample positions, 112 remained after ComBat correction in the primary dataset. The pre- and postcorrection comparisons indicate the positional effects could alter the measured methylation values and downstream analysis results. CONCLUSION Positional effects exist in the Illumina methylation array and may bias the analyses. Using ComBat to correct positional effects is recommended.
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Affiliation(s)
- Chuan Jiao
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
| | - Chunling Zhang
- Department of Neurology and Physiology, SUNY Upstate Medical University, Syracuse, NY 13201, USA
| | - Rujia Dai
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
| | - Yan Xia
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
| | - Kangli Wang
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
| | - Gina Giase
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Chao Chen
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan 410012, PR China
| | - Chunyu Liu
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13201, USA
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Cheng Y, Monteiro C, Matos A, You J, Fraga A, Pereira C, Catalán V, Rodríguez A, Gómez-Ambrosi J, Frühbeck G, Ribeiro R, Hu P. Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity-a pilot study. Clin Epigenetics 2018; 10:54. [PMID: 29692867 PMCID: PMC5904983 DOI: 10.1186/s13148-018-0490-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022] Open
Abstract
Background Periprostatic adipose tissue (PPAT) has been recognized to associate with prostate cancer (PCa) aggressiveness and progression. Here, we sought to investigate whether excess adiposity modulates the methylome of PPAT in PCa patients. DNA methylation profiling was performed in PPAT from obese/overweight (OB/OW, BMI > 25 kg m−2) and normal weight (NW, BMI < 25 kg m−2) PCa patients. Significant differences in methylated CpGs between OB/OW and NW groups were inferred by statistical modeling. Results Five thousand five hundred twenty-six differentially methylated CpGs were identified between OB/OW and NW PCa patients with 90.2% hypermethylated. Four hundred eighty-three of these CpGs were found to be located at both promoters and CpG islands, whereas the representing 412 genes were found to be involved in pluripotency of stem cells, fatty acid metabolism, and many other biological processes; 14 of these genes, particularly FADS1, MOGAT1, and PCYT2, with promoter hypermethylation presented with significantly decreased gene expression in matched samples. Additionally, 38 genes were correlated with antigen processing and presentation of endogenous antigen via MHC class I, which might result in fatty acid accumulation in PPAT and tumor immune evasion. Conclusions Results showed that the whole epigenome methylation profiles of PPAT were significantly different in OB/OW compared to normal weight PCa patients. The epigenetic variation associated with excess adiposity likely resulted in altered lipid metabolism and immune dysregulation, contributing towards unfavorable PCa microenvironment, thus warranting further validation studies in larger samples. Electronic supplementary material The online version of this article (10.1186/s13148-018-0490-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Cheng
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada.,2Experimental Center, Northwest University for Nationalities, Lanzhou, People's Republic of China
| | - Cátia Monteiro
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,Research Department, Portuguese League Against Cancer-North, Porto, Portugal
| | - Andreia Matos
- 5Laboratory of Genetics and Environmental Health Institute, Faculty of Medicine, University of Lisboa, Lisbon, Portugal.,6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal
| | - Jiaying You
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
| | - Avelino Fraga
- 6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal.,7Department of Urology, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Carina Pereira
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,8CINTESIS, Center for Health Technology and Services Research, Faculty of Medicine, e, University of Porto, Porto, Portugal
| | - Victoria Catalán
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Amaia Rodríguez
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Gómez-Ambrosi
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Frühbeck
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain.,11Department of Endocrinology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ricardo Ribeiro
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,5Laboratory of Genetics and Environmental Health Institute, Faculty of Medicine, University of Lisboa, Lisbon, Portugal.,6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal.,12Department of Clinical Pathology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,13i3S/INEB, Instituto de Investigação e Inovação em Saúde/Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Tumor & Microenvironment Interactions, Rua Alfredo Allen, 208 4200-135 Porto, Portugal
| | - Pingzhao Hu
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
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Chen Y, Hong T, Wang S, Mo J, Tian T, Zhou X. Epigenetic modification of nucleic acids: from basic studies to medical applications. Chem Soc Rev 2018; 46:2844-2872. [PMID: 28352906 DOI: 10.1039/c6cs00599c] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The epigenetic modification of nucleic acids represents one of the most significant areas of study in the field of nucleic acids because it makes gene regulation more complex and heredity more complicated, thus indicating its profound impact on aspects of heredity, growth, and diseases. The recent characterization of epigenetic modifications of DNA and RNA using chemical labelling strategies has promoted the discovery of these modifications, and the newly developed single-base or single-cell resolution mapping strategies have enabled large-scale epigenetic studies in eukaryotes. Due to these technological breakthroughs, several new epigenetic marks have been discovered that have greatly extended the scope and impact of epigenetic modifications in nucleic acids over the past few years. Because epigenetics is reversible and susceptible to environmental factors, it could potentially be a promising direction for clinical medicine research. In this review, we have comprehensively discussed how these epigenetic marks are involved in disease, including the pathogenesis, prevention, diagnosis and treatment of disease. These findings have revealed that the epigenetic modification of nucleic acids has considerable significance in various areas from methodology to clinical medicine and even in biomedical applications.
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Affiliation(s)
- Yuqi Chen
- College of Chemistry and Molecular Sciences, Institute of Advanced Studies, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Hubei, Wuhan 430072, P. R. China.
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Davegårdh C, García-Calzón S, Bacos K, Ling C. DNA methylation in the pathogenesis of type 2 diabetes in humans. Mol Metab 2018; 14:12-25. [PMID: 29496428 PMCID: PMC6034041 DOI: 10.1016/j.molmet.2018.01.022] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 02/08/2023] Open
Abstract
Background Type 2 diabetes (T2D) is a multifactorial, polygenic disease caused by impaired insulin secretion and insulin resistance. Genome-wide association studies (GWAS) were expected to resolve a large part of the genetic component of diabetes; yet, the single nucleotide polymorphisms identified by GWAS explain less than 20% of the estimated heritability for T2D. There was subsequently a need to look elsewhere to find disease-causing factors. Mechanisms mediating the interaction between environmental factors and the genome, such as epigenetics, may be of particular importance in the pathogenesis of T2D. Scope of Review This review summarizes knowledge of the impact of epigenetics on the pathogenesis of T2D in humans. In particular, the review will focus on alterations in DNA methylation in four human tissues of importance for the disease; pancreatic islets, skeletal muscle, adipose tissue, and the liver. Case–control studies and studies examining the impact of non-genetic and genetic risk factors on DNA methylation in humans will be considered. These studies identified epigenetic changes in tissues from subjects with T2D versus non-diabetic controls. They also demonstrate that non-genetic factors associated with T2D such as age, obesity, energy rich diets, physical activity and the intrauterine environment impact the epigenome in humans. Additionally, interactions between genetics and epigenetics seem to influence the pathogenesis of T2D. Conclusions Overall, previous studies by our group and others support a key role for epigenetics in the growing incidence of T2D.
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Affiliation(s)
- Cajsa Davegårdh
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden.
| | - Sonia García-Calzón
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden
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Petrus P, Bialesova L, Checa A, Kerr A, Naz S, Bäckdahl J, Gracia A, Toft S, Dahlman-Wright K, Hedén P, Dahlman I, Wheelock CE, Arner P, Mejhert N, Gao H, Rydén M. Adipocyte Expression of SLC19A1 Links DNA Hypermethylation to Adipose Tissue Inflammation and Insulin Resistance. J Clin Endocrinol Metab 2018; 103:710-721. [PMID: 29121255 DOI: 10.1210/jc.2017-01382] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 11/02/2017] [Indexed: 02/07/2023]
Abstract
CONTEXT Insulin resistance (IR) is promoted by a chronic low-grade inflammation in white adipose tissue (WAT). The latter might be regulated through epigenetic mechanisms such as DNA methylation. The one carbon cycle (1CC) is a central metabolic process governing DNA methylation. OBJECTIVE To identify adipocyte-expressed 1CC genes linked to WAT inflammation, IR, and their causal role. DESIGN Cohort study. SETTING Outpatient academic clinic. PARTICIPANTS Obese and nonobese subjects. METHODS Gene expression and DNA methylation arrays were performed in subcutaneous WAT and isolated adipocytes. In in vitro differentiated human adipocytes, gene knockdown was achieved by small interfering RNA, and analyses included microarray, quantitative polymerase chain reaction, DNA methylation by enzyme-linked immunosorbent assay and pyrosequencing, protein secretion by enzyme-linked immunosorbent assay, targeted metabolomics, and luciferase reporter and thermal shift assays. MAIN OUTCOME MEASURES Effects on adipocyte inflammation. RESULTS In adipocytes from obese individuals, global DNA hypermethylation was associated positively with gene expression of proinflammatory pathways. Among the 1CC genes, IR in vivo and proinflammatory gene expression in WAT were most strongly and inversely associated with SLC19A1, a gene encoding a membrane folate carrier. SLC19A1 knockdown in human adipocytes perturbed intracellular 1CC metabolism, induced global DNA hypermethylation, and increased expression of proinflammatory genes. Several CpG loci linked SLC19A1 to inflammation; validation studies were focused on the chemokine C-C motif chemokine ligand 2 (CCL2) in which methylation in the promoter (cg12698626) regulated CCL2 expression and CCL2 secretion through altered transcriptional activity. CONCLUSIONS Reduced SLC19A1 expression in human adipocytes induces DNA hypermethylation, resulting in increased expression of specific proinflammatory genes, including CCL2. This constitutes an epigenetic mechanism that might link dysfunctional adipocytes to WAT inflammation and IR.
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Affiliation(s)
- Paul Petrus
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lucia Bialesova
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Antonio Checa
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alastair Kerr
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shama Naz
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Bäckdahl
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ana Gracia
- Department of Nutrition and Food Science, University of Basque Country (UPV/EHU), Vitoria, Spain
- CIBER Physiopathology of Obesity and Nutrition, Institute of Health Carlos III, Madrid, Spain
| | - Sofia Toft
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Karin Dahlman-Wright
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Per Hedén
- Department of Plastic Surgery, Akademikliniken, Stockholm, Sweden
| | - Ingrid Dahlman
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Wheelock
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Arner
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Niklas Mejhert
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Hui Gao
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Rydén
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
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Iena FM, Lebeck J. Implications of Aquaglyceroporin 7 in Energy Metabolism. Int J Mol Sci 2018; 19:ijms19010154. [PMID: 29300344 PMCID: PMC5796103 DOI: 10.3390/ijms19010154] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 12/29/2017] [Accepted: 12/31/2017] [Indexed: 12/14/2022] Open
Abstract
The aquaglyceroporin AQP7 is a pore-forming transmembrane protein that facilitates the transport of glycerol across cell membranes. Glycerol is utilized both in carbohydrate and lipid metabolism. It is primarily stored in white adipose tissue as part of the triglyceride molecules. During states with increased lipolysis, such as fasting and diabetes, glycerol is released from adipose tissue and metabolized in other tissues. AQP7 is expressed in adipose tissue where it facilitates the efflux of glycerol, and AQP7 deficiency has been linked to increased glycerol kinase activity and triglyceride accumulation in adipose tissue, leading to obesity and secondary development of insulin resistance. However, AQP7 is also expressed in a wide range of other tissues, including kidney, muscle, pancreatic β-cells and liver, where AQP7 also holds the potential to influence whole body energy metabolism. The aim of the review is to summarize the current knowledge on AQP7 in adipose tissue, as well as AQP7 expressed in other tissues where AQP7 might play a significant role in modulating whole body energy metabolism.
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Affiliation(s)
- Francesco Maria Iena
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, 8000 Aarhus, Denmark.
| | - Janne Lebeck
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, 8000 Aarhus, Denmark.
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DNA-Methylation and Body Composition in Preschool Children: Epigenome-Wide-Analysis in the European Childhood Obesity Project (CHOP)-Study. Sci Rep 2017; 7:14349. [PMID: 29084944 PMCID: PMC5662763 DOI: 10.1038/s41598-017-13099-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 09/19/2017] [Indexed: 01/16/2023] Open
Abstract
Adiposity and obesity result from the interaction of genetic variation and environmental factors from very early in life, possibly mediated by epigenetic processes. Few Epigenome-Wide-Association-Studies have identified DNA-methylation (DNAm) signatures associated with BMI and body composition in children. Body composition by Bio-Impedance-Analysis and genome-wide DNAm in whole blood were assessed in 374 pre-school children from four European countries. Associations were tested by linear regression adjusted for sex, age, centre, education, 6 WBC-proportions according to Houseman and 30 principal components derived from control probes. Specific DNAm variants were identified to be associated with BMI (212), fat-mass (230), fat-free-mass (120), fat-mass-index (24) and fat-free-mass-index (15). Probes in genes SNED1(IRE-BP1), KLHL6, WDR51A(POC1A), CYTH4-ELFN2, CFLAR, PRDM14, SOS1, ZNF643(ZFP69B), ST6GAL1, C3orf70, CILP2, MLLT4 and ncRNA LOC101929268 remained significantly associated after Bonferroni-correction of P-values. We provide novel evidence linking DNAm with (i) altered lipid and glucose metabolism, (ii) diabetes and (iii) body size and composition in children. Both common and specific epigenetic signatures among measures were also revealed. The causal direction with phenotypic measures and stability of DNAm variants throughout the life course remains unclear and longitudinal analysis in other populations is required. These findings give support for potential epigenetic programming of body composition and obesity.
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Cheng Z, Zheng L, Almeida FA. Epigenetic reprogramming in metabolic disorders: nutritional factors and beyond. J Nutr Biochem 2017; 54:1-10. [PMID: 29154162 DOI: 10.1016/j.jnutbio.2017.10.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/26/2017] [Accepted: 10/10/2017] [Indexed: 12/13/2022]
Abstract
Environmental factors (e.g., malnutrition and physical inactivity) contribute largely to metabolic disorders including obesity, type 2 diabetes, cardiometabolic disease and nonalcoholic fatty liver diseases. The abnormalities in metabolic activity and pathways have been increasingly associated with altered DNA methylation, histone modification and noncoding RNAs, whereas lifestyle interventions targeting diet and physical activity can reverse the epigenetic and metabolic changes. Here we review recent evidence primarily from human studies that links DNA methylation reprogramming to metabolic derangements or improvements, with a focus on cross-tissue (e.g., the liver, skeletal muscle, pancreas, adipose tissue and blood samples) epigenetic markers, mechanistic mediators of the epigenetic reprogramming, and the potential of using epigenetic traits to predict disease risk and intervention response. The challenges in epigenetic studies addressing the mechanisms of metabolic diseases and future directions are also discussed and prospected.
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Affiliation(s)
- Zhiyong Cheng
- Department of Human Nutrition, Foods, and Exercise, Fralin Translational Obesity Research Center, College of Agriculture and Life Science, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Louise Zheng
- Department of Human Nutrition, Foods, and Exercise, Fralin Translational Obesity Research Center, College of Agriculture and Life Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Fabio A Almeida
- Department of Health Promotion, Social & Behavioral Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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Sharp GC, Salas LA, Monnereau C, Allard C, Yousefi P, Everson TM, Bohlin J, Xu Z, Huang RC, Reese SE, Xu CJ, Baïz N, Hoyo C, Agha G, Roy R, Holloway JW, Ghantous A, Merid SK, Bakulski KM, Küpers LK, Zhang H, Richmond RC, Page CM, Duijts L, Lie RT, Melton PE, Vonk JM, Nohr EA, Williams-DeVane C, Huen K, Rifas-Shiman SL, Ruiz-Arenas C, Gonseth S, Rezwan FI, Herceg Z, Ekström S, Croen L, Falahi F, Perron P, Karagas MR, Quraishi BM, Suderman M, Magnus MC, Jaddoe VWV, Taylor JA, Anderson D, Zhao S, Smit HA, Josey MJ, Bradman A, Baccarelli AA, Bustamante M, Håberg SE, Pershagen G, Hertz-Picciotto I, Newschaffer C, Corpeleijn E, Bouchard L, Lawlor DA, Maguire RL, Barcellos LF, Davey Smith G, Eskenazi B, Karmaus W, Marsit CJ, Hivert MF, Snieder H, Fallin MD, Melén E, Munthe-Kaas MC, Arshad H, Wiemels JL, Annesi-Maesano I, Vrijheid M, Oken E, Holland N, Murphy SK, Sørensen TIA, Koppelman GH, Newnham JP, Wilcox AJ, Nystad W, London SJ, Felix JF, Relton CL. Maternal BMI at the start of pregnancy and offspring epigenome-wide DNA methylation: findings from the pregnancy and childhood epigenetics (PACE) consortium. Hum Mol Genet 2017; 26:4067-4085. [PMID: 29016858 PMCID: PMC5656174 DOI: 10.1093/hmg/ddx290] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/23/2017] [Accepted: 07/17/2017] [Indexed: 12/16/2022] Open
Abstract
Pre-pregnancy maternal obesity is associated with adverse offspring outcomes at birth and later in life. Individual studies have shown that epigenetic modifications such as DNA methylation could contribute. Within the Pregnancy and Childhood Epigenetics (PACE) Consortium, we meta-analysed the association between pre-pregnancy maternal BMI and methylation at over 450,000 sites in newborn blood DNA, across 19 cohorts (9,340 mother-newborn pairs). We attempted to infer causality by comparing the effects of maternal versus paternal BMI and incorporating genetic variation. In four additional cohorts (1,817 mother-child pairs), we meta-analysed the association between maternal BMI at the start of pregnancy and blood methylation in adolescents. In newborns, maternal BMI was associated with small (<0.2% per BMI unit (1 kg/m2), P < 1.06 × 10-7) methylation variation at 9,044 sites throughout the genome. Adjustment for estimated cell proportions greatly attenuated the number of significant CpGs to 104, including 86 sites common to the unadjusted model. At 72/86 sites, the direction of the association was the same in newborns and adolescents, suggesting persistence of signals. However, we found evidence for acausal intrauterine effect of maternal BMI on newborn methylation at just 8/86 sites. In conclusion, this well-powered analysis identified robust associations between maternal adiposity and variations in newborn blood DNA methylation, but these small effects may be better explained by genetic or lifestyle factors than a causal intrauterine mechanism. This highlights the need for large-scale collaborative approaches and the application of causal inference techniques in epigenetic epidemiology.
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Affiliation(s)
- Gemma C Sharp
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - Lucas A Salas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Claire Monnereau
- The Generation R Study Group
- Department of Epidemiology
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier, Université de Sherbrooke, QC, Canada
| | - Paul Yousefi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - Todd M Everson
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jon Bohlin
- Department of Infection Epidemiology and Modeling, Norwegian Institute of Public Health, Oslo, Norway
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Crawley, WA 6009, Australia
| | - Sarah E Reese
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Cheng-Jian Xu
- Department of Pulmonology, GRIAC Research Institute
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Nour Baïz
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Sorbonne Université, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Saint-Antoine Medical School, Paris, France
| | - Cathrine Hoyo
- Department of Biological Sciences
- Center for Human Health and the Environment, North Carolina State University, NC, USA
| | - Golareh Agha
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Ritu Roy
- University of California San Francisco, CA, USA
- HDF Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Computational Biology Core
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, UK
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Simon K Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, MI, USA
| | - Leanne K Küpers
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
| | - Christian M Page
- Department of Non-Communicable Disease, Norwegian Institute of Public Health, Oslo, Norway
| | - Liesbeth Duijts
- The Generation R Study Group
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Norway
- Medical Birth Registry of Norway, Norwegian Institute of Public Health, Bergen, Norway
| | - Phillip E Melton
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health Sciences, Curtin University Health Sciences, Curtin University and Faculty of Medicine Dentistry & Health Sciences, The University of Western Australia, Perth, Australia
- Faculty of Medicine Dentistry & Health Sciences, The University of Western Australia, Perth, Australia
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, GRIAC Research Institute Groningen, The Netherlands
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | | | - Karen Huen
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - Sheryl L Rifas-Shiman
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
| | - Carlos Ruiz-Arenas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Semira Gonseth
- Department of Epidemiology and Biostatistics, University of California San Francisco, CA, USA
- School of Public Health, University of California Berkeley, CA, USA
| | - Faisal I Rezwan
- Human Development & Health, Faculty of Medicine, University of Southampton, UK
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Sandra Ekström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lisa Croen
- Division of Research, Kaiser Permanente Northern California, CA, UDA
| | - Fahimeh Falahi
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier, Université de Sherbrooke, QC, Canada
- Department of Medicine, Université de Sherbrooke, QC, Canada
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
| | - Bilal M Quraishi
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
| | - Maria C Magnus
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
- Department of Non-Communicable Disease, Norwegian Institute of Public Health, Oslo, Norway
| | - Vincent W V Jaddoe
- The Generation R Study Group
- Department of Epidemiology
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Crawley, WA 6009, Australia
| | - Shanshan Zhao
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Henriette A Smit
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Michele J Josey
- Department of Biological & Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Epidemiology and Biostatistics Department, University of South Carolina (Columbia), SC, USA
| | - Asa Bradman
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Mariona Bustamante
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Siri E Håberg
- Domain of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Center for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Irva Hertz-Picciotto
- Department of Public Health, School of Medicine, University of California, Davis, CA, USA
| | - Craig Newschaffer
- AJ Drexel Autism Institute, Drexel University, Philadelphia, PA, USA
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Luigi Bouchard
- Department of Biochemistry, Université de Sherbrooke, QC, Canada
- ECOGENE-21 and Lipid Clinic, Chicoutimi Hospital, Saguenay, QC, Canada
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
| | - Rachel L Maguire
- Department of Biological Sciences
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA
| | - Lisa F Barcellos
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - George Davey Smith
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - Wilfried Karmaus
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Marie-France Hivert
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
- Department of Medicine, Université de Sherbrooke, QC, Canada
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Center for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
- Sachs’ Children’s Hospital, South General Hospital, Stockholm, Sweden
| | - Monica C Munthe-Kaas
- Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Norway
- Norwegian Institute of Public Health, Oslo Norway
| | - Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, University of California San Francisco, CA, USA
| | - Isabella Annesi-Maesano
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Sorbonne Université, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Saint-Antoine Medical School, Paris, France
| | - Martine Vrijheid
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Emily Oken
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
| | - Nina Holland
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Epidemiology, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Gerard H Koppelman
- Department of Paediatric Pulmonology and Paediatric Allergy, University of Groningen, University Medical Center Groningen, Beatrix Children’s Hospital, GRIAC Research Institute, Groningen, the Netherlands
| | - John P Newnham
- School of Women's and Infants' Health, The University of Western Australia, Crawley, WA 6009, Australia
| | - Allen J Wilcox
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Wenche Nystad
- Department of Non-Communicable Disease, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Janine F Felix
- The Generation R Study Group
- Department of Epidemiology
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
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46
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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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47
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Normal breast tissue DNA methylation differences at regulatory elements are associated with the cancer risk factor age. Breast Cancer Res 2017; 19:81. [PMID: 28693600 PMCID: PMC5504720 DOI: 10.1186/s13058-017-0873-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/21/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The underlying biological mechanisms through which epidemiologically defined breast cancer risk factors contribute to disease risk remain poorly understood. Identification of the molecular changes associated with cancer risk factors in normal tissues may aid in determining the earliest events of carcinogenesis and informing cancer prevention strategies. METHODS Here we investigated the impact cancer risk factors have on the normal breast epigenome by analyzing DNA methylation genome-wide (Infinium 450 K array) in cancer-free women from the Susan G. Komen Tissue Bank (n = 100). We tested the relation of established breast cancer risk factors, age, body mass index, parity, and family history of disease, with DNA methylation adjusting for potential variation in cell-type proportions. RESULTS We identified 787 cytosine-guanine dinucleotide (CpG) sites that demonstrated significant associations (Q value <0.01) with subject age. Notably, DNA methylation was not strongly associated with the other evaluated breast cancer risk factors. Age-related DNA methylation changes are primarily increases in methylation enriched at breast epithelial cell enhancer regions (P = 7.1E-20), and binding sites of chromatin remodelers (MYC and CTCF). We validated the age-related associations in two independent populations, using normal breast tissue samples (n = 18) and samples of normal tissue adjacent to tumor tissue (n = 97). The genomic regions classified as age-related were more likely to be regions altered in both pre-invasive (n = 40, P = 3.0E-03) and invasive breast tumors (n = 731, P = 1.1E-13). CONCLUSIONS DNA methylation changes with age occur at regulatory regions, and are further exacerbated in cancer, suggesting that age influences breast cancer risk in part through its contribution to epigenetic dysregulation in normal breast tissue.
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48
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San-Cristobal R, Navas-Carretero S, Milagro FI, Riezu-Boj JI, Guruceaga E, Celis-Morales C, Livingstone KM, Brennan L, Lovegrove JA, Daniel H, Saris WH, Traczyk I, Manios Y, Gibney ER, Gibney MJ, Mathers JC, Martinez JA. Gene methylation parallelisms between peripheral blood cells and oral mucosa samples in relation to overweight. J Physiol Biochem 2017; 73:465-474. [DOI: 10.1007/s13105-017-0560-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/16/2017] [Indexed: 01/08/2023]
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49
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Lin X, Lim IY, Wu Y, Teh AL, Chen L, Aris IM, Soh SE, Tint MT, MacIsaac JL, Morin AM, Yap F, Tan KH, Saw SM, Kobor MS, Meaney MJ, Godfrey KM, Chong YS, Holbrook JD, Lee YS, Gluckman PD, Karnani N. Developmental pathways to adiposity begin before birth and are influenced by genotype, prenatal environment and epigenome. BMC Med 2017; 15:50. [PMID: 28264723 PMCID: PMC5340003 DOI: 10.1186/s12916-017-0800-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/21/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Obesity is an escalating health problem worldwide, and hence the causes underlying its development are of primary importance to public health. There is growing evidence that suboptimal intrauterine environment can perturb the metabolic programing of the growing fetus, thereby increasing the risk of developing obesity in later life. However, the link between early exposures in the womb, genetic susceptibility, and perturbed epigenome on metabolic health is not well understood. In this study, we shed more light on this aspect by performing a comprehensive analysis on the effects of variation in prenatal environment, neonatal methylome, and genotype on birth weight and adiposity in early childhood. METHODS In a prospective mother-offspring cohort (N = 987), we interrogated the effects of 30 variables that influence the prenatal environment, umbilical cord DNA methylation, and genotype on offspring weight and adiposity, over the period from birth to 48 months. This is an interim analysis on an ongoing cohort study. RESULTS Eleven of 30 prenatal environments, including maternal adiposity, smoking, blood glucose and plasma unsaturated fatty acid levels, were associated with birth weight. Polygenic risk scores derived from genetic association studies on adult adiposity were also associated with birth weight and child adiposity, indicating an overlap between the genetic pathways influencing metabolic health in early and later life. Neonatal methylation markers from seven gene loci (ANK3, CDKN2B, CACNA1G, IGDCC4, P4HA3, ZNF423 and MIRLET7BHG) were significantly associated with birth weight, with a subset of these in genes previously implicated in metabolic pathways in humans and in animal models. Methylation levels at three of seven birth weight-linked loci showed significant association with prenatal environment, but none were affected by polygenic risk score. Six of these birth weight-linked loci continued to show a longitudinal association with offspring size and/or adiposity in early childhood. CONCLUSIONS This study provides further evidence that developmental pathways to adiposity begin before birth and are influenced by environmental, genetic and epigenetic factors. These pathways can have a lasting effect on offspring size, adiposity and future metabolic outcomes, and offer new opportunities for risk stratification and prevention of obesity. CLINICAL TRIAL REGISTRATION This birth cohort is a prospective observational study, designed to study the developmental origins of health and disease, and was retrospectively registered on 1 July 2010 under the identifier NCT01174875 .
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Affiliation(s)
- Xinyi Lin
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Ives Yubin Lim
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Yonghui Wu
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Ai Ling Teh
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Li Chen
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Izzuddin M Aris
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Shu E Soh
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Mya Thway Tint
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Alexander M Morin
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Fabian Yap
- KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Kok Hian Tan
- KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Seang Mei Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117597, Singapore.,Singapore Eye Research Institute, Singapore, 169856, Singapore.,Duke NUS Medical School, Singapore, 169857, Singapore
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Michael J Meaney
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Ludmer Centre for Neuroinformatics and Mental Health, Douglas University Mental Health Institute, McGill University, Montreal, Quebec, H4H 1R3, Canada
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Joanna D Holbrook
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Yung Seng Lee
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Division of Paediatric Endocrinology and Diabetes, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, 119228, Singapore
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Centre for Human Evolution, Adaptation and Disease, Liggins Institute, University of Auckland, Auckland, 1142, New Zealand
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.
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50
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Arner P, Sahlqvist AS, Sinha I, Xu H, Yao X, Waterworth D, Rajpal D, Loomis AK, Freudenberg JM, Johnson T, Thorell A, Näslund E, Ryden M, Dahlman I. The epigenetic signature of systemic insulin resistance in obese women. Diabetologia 2016; 59:2393-2405. [PMID: 27535281 PMCID: PMC5506095 DOI: 10.1007/s00125-016-4074-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/13/2016] [Indexed: 02/07/2023]
Abstract
AIMS/HYPOTHESIS Insulin resistance (IR) links obesity to type 2 diabetes. The aim of this study was to explore whether white adipose tissue (WAT) epigenetic dysregulation is associated with systemic IR by genome-wide CG dinucleotide (CpG) methylation and gene expression profiling in WAT from insulin-resistant and insulin-sensitive women. A secondary aim was to determine whether the DNA methylation signature in peripheral blood mononuclear cells (PBMCs) reflects WAT methylation and, if so, can be used as a marker for systemic IR. METHODS From 220 obese women, we selected a total of 80 individuals from either of the extreme ends of the distribution curve of HOMA-IR, an indirect measure of systemic insulin sensitivity. Genome-wide transcriptome and DNA CpG methylation profiling by array was performed on subcutaneous (SAT) and visceral (omental) adipose tissue (VAT). CpG methylation in PBMCs was assayed in the same cohort. RESULTS There were 647 differentially expressed genes (false discovery rate [FDR] 10%) in SAT, all of which displayed directionally consistent associations in VAT. This suggests that IR is associated with dysregulated expression of a common set of genes in SAT and VAT. The average degree of DNA methylation did not differ between the insulin-resistant and insulin-sensitive group in any of the analysed tissues/cells. There were 223 IR-associated genes in SAT containing a total of 336 nominally significant differentially methylated sites (DMS). The 223 IR-associated genes were over-represented in pathways related to integrin cell surface interactions and insulin signalling and included COL5A1, GAB1, IRS2, PFKFB3 and PTPRJ. In VAT there were a total of 51 differentially expressed genes (FDR 10%); 18 IR-associated genes contained a total of 29 DMS. CONCLUSIONS/INTERPRETATION In individuals discordant for insulin sensitivity, the average DNA CpG methylation in SAT and VAT is similar, although specific genes, particularly in SAT, display significantly altered expression and DMS in IR, possibly indicating that epigenetic regulation of these genes influences metabolism.
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Affiliation(s)
- Peter Arner
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital, C2:94, Huddinge, S-141 86, Stockholm, Sweden
| | | | - Indranil Sinha
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Huan Xu
- GlaxoSmithKline R&D, Research Triangle Park, NC, USA
| | - Xiang Yao
- Computational and Systems Biology, Discovery Sciences, Janssen Pharmaceutical, Research & Development, LLC, San Diego, CA, USA
| | | | | | | | | | | | - Anders Thorell
- Department of Surgery, Ersta Hospital, Stockholm, Sweden
- Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Danderyd, Sweden
| | - Erik Näslund
- Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Danderyd, Sweden
| | - Mikael Ryden
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital, C2:94, Huddinge, S-141 86, Stockholm, Sweden
| | - Ingrid Dahlman
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital, C2:94, Huddinge, S-141 86, Stockholm, Sweden.
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