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Rönn T, Ofori JK, Perfilyev A, Hamilton A, Pircs K, Eichelmann F, Garcia-Calzon S, Karagiannopoulos A, Stenlund H, Wendt A, Volkov P, Schulze MB, Mulder H, Eliasson L, Ruhrmann S, Bacos K, Ling C. Genes with epigenetic alterations in human pancreatic islets impact mitochondrial function, insulin secretion, and type 2 diabetes. Nat Commun 2023; 14:8040. [PMID: 38086799 PMCID: PMC10716521 DOI: 10.1038/s41467-023-43719-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Epigenetic dysregulation may influence disease progression. Here we explore whether epigenetic alterations in human pancreatic islets impact insulin secretion and type 2 diabetes (T2D). In islets, 5,584 DNA methylation sites exhibit alterations in T2D cases versus controls and are associated with HbA1c in individuals not diagnosed with T2D. T2D-associated methylation changes are found in enhancers and regions bound by β-cell-specific transcription factors and associated with reduced expression of e.g. CABLES1, FOXP1, GABRA2, GLR1A, RHOT1, and TBC1D4. We find RHOT1 (MIRO1) to be a key regulator of insulin secretion in human islets. Rhot1-deficiency in β-cells leads to reduced insulin secretion, ATP/ADP ratio, mitochondrial mass, Ca2+, and respiration. Regulators of mitochondrial dynamics and metabolites, including L-proline, glycine, GABA, and carnitines, are altered in Rhot1-deficient β-cells. Islets from diabetic GK rats present Rhot1-deficiency. Finally, RHOT1methylation in blood is associated with future T2D. Together, individuals with T2D exhibit epigenetic alterations linked to mitochondrial dysfunction in pancreatic islets.
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Affiliation(s)
- Tina Rönn
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Jones K Ofori
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Alexander Perfilyev
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Alexander Hamilton
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
- Department of Biology, University of Copenhagen, København, Denmark
| | - Karolina Pircs
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
- HCEMM-Su, Neurobiology and Neurodegenerative Diseases Research Group, Budapest, Hungary
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Fabian Eichelmann
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Sonia Garcia-Calzon
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
- Department of Food Science and Physiology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain
| | - Alexandros Karagiannopoulos
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Hans Stenlund
- Swedish Metabolomics Centre, Umeå University, Umeå, Sweden
| | - Anna Wendt
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Petr Volkov
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Hindrik Mulder
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Lena Eliasson
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Sabrina Ruhrmann
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Karl Bacos
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Charlotte Ling
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden.
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Bacos K, Perfilyev A, Karagiannopoulos A, Cowan E, Ofori JK, Bertonnier-Brouty L, Rönn T, Lindqvist A, Luan C, Ruhrmann S, Ngara M, Nilsson Å, Gheibi S, Lyons CL, Lagerstedt JO, Barghouth M, Esguerra JL, Volkov P, Fex M, Mulder H, Wierup N, Krus U, Artner I, Eliasson L, Prasad RB, Cataldo LR, Ling C. Type 2 diabetes candidate genes, including PAX5, cause impaired insulin secretion in human pancreatic islets. J Clin Invest 2023; 133:163612. [PMID: 36656641 PMCID: PMC9927941 DOI: 10.1172/jci163612] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
Type 2 diabetes (T2D) is caused by insufficient insulin secretion from pancreatic β cells. To identify candidate genes contributing to T2D pathophysiology, we studied human pancreatic islets from approximately 300 individuals. We found 395 differentially expressed genes (DEGs) in islets from individuals with T2D, including, to our knowledge, novel (OPRD1, PAX5, TET1) and previously identified (CHL1, GLRA1, IAPP) candidates. A third of the identified expression changes in islets may predispose to diabetes, as expression of these genes associated with HbA1c in individuals not previously diagnosed with T2D. Most DEGs were expressed in human β cells, based on single-cell RNA-Seq data. Additionally, DEGs displayed alterations in open chromatin and associated with T2D SNPs. Mouse KO strains demonstrated that the identified T2D-associated candidate genes regulate glucose homeostasis and body composition in vivo. Functional validation showed that mimicking T2D-associated changes for OPRD1, PAX5, and SLC2A2 impaired insulin secretion. Impairments in Pax5-overexpressing β cells were due to severe mitochondrial dysfunction. Finally, we discovered PAX5 as a potential transcriptional regulator of many T2D-associated DEGs in human islets. Overall, we have identified molecular alterations in human pancreatic islets that contribute to β cell dysfunction in T2D pathophysiology.
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Affiliation(s)
- Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | | | - Alexandros Karagiannopoulos
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Elaine Cowan
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Jones K. Ofori
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Ludivine Bertonnier-Brouty
- Endocrine Cell Differentiation, Department of Laboratory Medicine, Lund Stem Cell Center, Malmö, Scania, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Andreas Lindqvist
- Neuroendocrine Cell Biology, Department of Experimental Medical Science
| | - Cheng Luan
- Unit of Islet Pathophysiology, Department of Clinical Sciences
| | - Sabrina Ruhrmann
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Mtakai Ngara
- Neuroendocrine Cell Biology, Department of Experimental Medical Science
| | - Åsa Nilsson
- Human Tissue Lab, Department of Clinical Sciences
| | - Sevda Gheibi
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Claire L. Lyons
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Jens O. Lagerstedt
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | | | - Jonathan L.S. Esguerra
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Malin Fex
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Hindrik Mulder
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Nils Wierup
- Neuroendocrine Cell Biology, Department of Experimental Medical Science
| | - Ulrika Krus
- Human Tissue Lab, Department of Clinical Sciences
| | - Isabella Artner
- Endocrine Cell Differentiation, Department of Laboratory Medicine, Lund Stem Cell Center, Malmö, Scania, Sweden
| | - Lena Eliasson
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Rashmi B. Prasad
- Genomics, Diabetes and Endocrinology, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden.,Institute of Molecular Medicine (FIMM), Helsinki University, Helsinki, Finland
| | - Luis Rodrigo Cataldo
- Molecular Metabolism Unit, Department of Clinical Sciences, and,The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
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Rönn T, Perfilyev A, Jönsson J, Eriksson KF, Jørgensen SW, Brøns C, Gillberg L, Vaag A, Stener-Victorin E, Ling C. Circulating triglycerides are associated with human adipose tissue DNA methylation of genes linked to metabolic disease. Hum Mol Genet 2023; 32:1875-1887. [PMID: 36752523 DOI: 10.1093/hmg/ddad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Dysregulation of circulating lipids is a central element for the metabolic syndrome. However, it is not well established whether human subcutaneous adipose tissue is affected by or affect circulating lipids through epigenetic mechanisms. Hence, our aim was to investigate the association between circulating lipids and DNA methylation levels in human adipose tissue. METHODS DNA methylation and gene expression were analyzed genome-wide in subcutaneous adipose tissue from two different cohorts, including 85 men and 93 women, respectively. Associations between DNA methylation and circulating levels of triglycerides, LDL, HDL and total cholesterol were analysed. Causal mediation analyses tested if adipose tissue DNA methylation mediates the effects of triglycerides on gene expression or insulin resistance. RESULTS We found 115 novel associations between triglycerides and adipose tissue DNA methylation, e.g. in the promoter of RFS1, ARID2, and HOXA5 in the male cohort (p ≤ 1.1x10-7), and 63 associations e.g. within the gene body of PTPRN2 and COL6A3 in the female cohort. We further connected these findings to altered mRNA expression levels in adipose tissue (e.g. HOXA5, IL11 and FAM45B). Interestingly, there was no overlap between methylation sites associated with triglycerides in men and the sites found in women, which points towards sex-specific effects of triglycerides on the epigenome. Finally, a causal mediation analysis provided support for adipose tissue DNA methylation as a partial mediating factor between circulating triglycerides and insulin resistance. CONCLUSIONS This study identified novel epigenetic alterations in adipose tissue associated with circulating lipids. Identified epigenetic changes seem to mediate effects of triglycerides on insulin resistance.
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Affiliation(s)
- Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, 205 02 Malmö, Sweden
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, 205 02 Malmö, Sweden
| | - Josefine Jönsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, 205 02 Malmö, Sweden
| | - Karl-Fredrik Eriksson
- Department of Clinical Sciences, Vascular Diseases, Lund University, 205 02 Malmö, Sweden
| | - Sine W Jørgensen
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Charlotte Brøns
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Linn Gillberg
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Vaag
- Steno Diabetes Center Copenhagen, DK-2820, Gentofte, Denmark
| | | | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, 205 02 Malmö, Sweden
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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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Ouni M, Saussenthaler S, Eichelmann F, Jähnert M, Stadion M, Wittenbecher C, Rönn T, Zellner L, Gottmann P, Ling C, Schulze MB, Schürmann A. Epigenetic Changes in Islets of Langerhans Preceding the Onset of Diabetes. Diabetes 2020; 69:2503-2517. [PMID: 32816961 PMCID: PMC7576562 DOI: 10.2337/db20-0204] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/09/2020] [Indexed: 12/19/2022]
Abstract
The identification of individuals with a high risk of developing type 2 diabetes (T2D) is fundamental for prevention. Here, we used a translational approach and prediction criteria to identify changes in DNA methylation visible before the development of T2D. Islets of Langerhans were isolated from genetically identical 10-week-old female New Zealand Obese mice, which differ in their degree of hyperglycemia and in liver fat content. The application of a semiexplorative approach identified 497 differentially expressed and methylated genes (P = 6.42e-09, hypergeometric test) enriched in pathways linked to insulin secretion and extracellular matrix-receptor interaction. The comparison of mouse data with DNA methylation levels of incident T2D cases from the prospective European Prospective Investigation of Cancer (EPIC)-Potsdam cohort, revealed 105 genes with altered DNA methylation at 605 cytosine-phosphate-guanine (CpG) sites, which were associated with future T2D. AKAP13, TENM2, CTDSPL, PTPRN2, and PTPRS showed the strongest predictive potential (area under the receiver operating characteristic curve values 0.62-0.73). Among the new candidates identified in blood cells, 655 CpG sites, located in 99 genes, were differentially methylated in islets of humans with T2D. Using correction for multiple testing detected 236 genes with an altered DNA methylation in blood cells and 201 genes in diabetic islets. Thus, the introduced translational approach identified novel putative biomarkers for early pancreatic islet aberrations preceding T2D.
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Affiliation(s)
- Meriem Ouni
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Sophie Saussenthaler
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Fabian Eichelmann
- German Center for Diabetes Research, München-Neuherberg, Germany
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
| | - Markus Jähnert
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Mandy Stadion
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Clemens Wittenbecher
- German Center for Diabetes Research, München-Neuherberg, Germany
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Tina Rönn
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Lisa Zellner
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Pascal Gottmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Matthias B Schulze
- German Center for Diabetes Research, München-Neuherberg, Germany
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Annette Schürmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Brandenburg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
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Bysani M, Agren R, Davegårdh C, Volkov P, Rönn T, Unneberg P, Bacos K, Ling C. Author Correction: ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes. Sci Rep 2020; 10:1744. [PMID: 31996742 PMCID: PMC6989682 DOI: 10.1038/s41598-020-58485-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Madhusudhan Bysani
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Rasmus Agren
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Göteborg, Sweden
| | - Cajsa Davegårdh
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Petr Volkov
- 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
| | - Per Unneberg
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden.
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Gillberg L, Rönn T, Jørgensen SW, Perfilyev A, Hjort L, Nilsson E, Brøns C, Vaag A, Ling C. Fasting unmasks differential fat and muscle transcriptional regulation of metabolic gene sets in low versus normal birth weight men. EBioMedicine 2019; 47:341-351. [PMID: 31439477 PMCID: PMC6796584 DOI: 10.1016/j.ebiom.2019.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/19/2019] [Accepted: 08/06/2019] [Indexed: 12/17/2022] Open
Abstract
Background Individuals born with low birth weight (LBW) have an increased risk of metabolic diseases when exposed to diets rich in calories and fat but may respond to fasting in a metabolically preferential manner. We hypothesized that impaired foetal growth is associated with differential regulation of gene expression and epigenetics in metabolic tissues in response to fasting in young adulthood. Methods Genome-wide expression and DNA methylation were analysed in subcutaneous adipose tissue (SAT) and skeletal muscle from LBW and normal birth weight (NBW) men after 36 h fasting and after an isocaloric control study using microarrays. Findings Transcriptome analyses revealed that expression of genes involved in oxidative phosphorylation (OXPHOS) and other key metabolic pathways were lower in SAT from LBW vs NBW men after the control study, but paradoxically higher in LBW vs NBW men after 36 h fasting. Thus, fasting was associated with downregulated OXPHOS and metabolic gene sets in NBW men only. Likewise, in skeletal muscle only NBW men downregulated OXPHOS genes with fasting. Few epigenetic changes were observed in SAT and muscle between the groups. Interpretation Our results provide insights into the molecular mechanisms in muscle and adipose tissue governing a differential metabolic response in subjects with impaired foetal growth when exposed to fasting in adulthood. The results support the concept of developmental programming of metabolic diseases including type 2 diabetes. Fund The Swedish Research Council, the Danish Council for Strategic Research, the Novo Nordisk foundation, the Swedish Foundation for Strategic Research, The European Foundation for the Study of Diabetes, The EU 6th Framework EXGENESIS grant and Rigshospitalet.
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Affiliation(s)
- Linn Gillberg
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Tina Rönn
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | | | - Alexander Perfilyev
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Line Hjort
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Emma Nilsson
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Charlotte Brøns
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Allan Vaag
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Cardiovascular, Renal and Metabolism (CVRM), Translational Medical Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden
| | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden.
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Bysani M, Agren R, Davegårdh C, Volkov P, Rönn T, Unneberg P, Bacos K, Ling C. ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes. Sci Rep 2019; 9:7785. [PMID: 31123324 PMCID: PMC6533306 DOI: 10.1038/s41598-019-44076-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 05/08/2019] [Indexed: 01/08/2023] Open
Abstract
Impaired insulin secretion from pancreatic islets is a hallmark of type 2 diabetes (T2D). Altered chromatin structure may contribute to the disease. We therefore studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified 57,105 and 53,284 ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors, respectively. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific transcription factors (TFs), e.g. FOXA2, MAFB, NKX2.2, NKX6.1 and PDX1, bind. Islet ATAC-seq peaks overlap with 13 SNPs associated with T2D (e.g. rs7903146, rs2237897, rs757209, rs11708067 and rs878521 near TCF7L2, KCNQ1, HNF1B, ADCY5 and GCK, respectively) and with additional 67 SNPs in LD with known T2D SNPs (e.g. SNPs annotated to GIPR, KCNJ11, GLIS3, IGF2BP2, FTO and PPARG). There was enrichment of open chromatin regions near highly expressed genes in human islets. Moreover, 1,078 open chromatin peaks, annotated to 898 genes, differed in prevalence between diabetic and non-diabetic islet donors. Some of these peaks are annotated to candidate genes for T2D and islet dysfunction (e.g. HHEX, HMGA2, GLIS3, MTNR1B and PARK2) and some overlap with SNPs associated with T2D (e.g. rs3821943 near WFS1 and rs508419 near ANK1). Enhancer regions and motifs specific to key TFs including BACH2, FOXO1, FOXA2, NEUROD1, MAFA and PDX1 were enriched in differential islet ATAC-seq peaks of T2D versus non-diabetic donors. Our study provides new understanding into how T2D alters the chromatin landscape, and thereby accessibility for TFs and gene expression, in human pancreatic islets.
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Affiliation(s)
- Madhusudhan Bysani
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Rasmus Agren
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Göteborg, Sweden
| | - Cajsa Davegårdh
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Petr Volkov
- 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
| | - Per Unneberg
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden.
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Abstract
Epigenetic mechanisms control gene activity and the development of an organism. The epigenome includes DNA methylation, histone modifications, and RNA-mediated processes, and disruption of this balance may cause several pathologies and contribute to obesity and type 2 diabetes (T2D). This Review summarizes epigenetic signatures obtained from human tissues of relevance for metabolism-i.e., adipose tissue, skeletal muscle, pancreatic islets, liver, and blood-in relation to obesity and T2D. Although this research field is still young, these comprehensive data support not only a role for epigenetics in disease development, but also epigenetic alterations as a response to disease. Genetic predisposition, as well as aging, contribute to epigenetic variability, and several environmental factors, including exercise and diet, further interact with the human epigenome. The reversible nature of epigenetic modifications holds promise for future therapeutic strategies in obesity and T2D.
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Affiliation(s)
- Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden.
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
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Volkov P, Bacos K, Ofori JK, Esguerra JLS, Eliasson L, Rönn T, Ling C. Whole-Genome Bisulfite Sequencing of Human Pancreatic Islets Reveals Novel Differentially Methylated Regions in Type 2 Diabetes Pathogenesis. Diabetes 2017; 66:1074-1085. [PMID: 28052964 DOI: 10.2337/db16-0996] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/28/2016] [Indexed: 11/13/2022]
Abstract
Current knowledge about the role of epigenetics in type 2 diabetes (T2D) remains limited. Only a few studies have investigated DNA methylation of selected candidate genes or a very small fraction of genomic CpG sites in human pancreatic islets, the tissue of primary pathogenic importance for diabetes. Our aim was to characterize the whole-genome DNA methylation landscape in human pancreatic islets, to identify differentially methylated regions (DMRs) in diabetic islets, and to investigate the function of DMRs in islet biology. Here, we performed whole-genome bisulfite sequencing, which is a comprehensive and unbiased method to study DNA methylation throughout the genome at a single nucleotide resolution, in pancreatic islets from donors with T2D and control subjects without diabetes. We identified 25,820 DMRs in islets from individuals with T2D. These DMRs cover loci with known islet function, e.g., PDX1, TCF7L2, and ADCY5 Importantly, binding sites previously identified by ChIP-seq for islet-specific transcription factors, enhancer regions, and different histone marks were enriched in the T2D-associated DMRs. We also identified 457 genes, including NR4A3, PARK2, PID1, SLC2A2, and SOCS2, that had both DMRs and significant expression changes in T2D islets. To mimic the situation in T2D islets, candidate genes were overexpressed or silenced in cultured β-cells. This resulted in impaired insulin secretion, thereby connecting differential methylation to islet dysfunction. We further explored the islet methylome and found a strong link between methylation levels and histone marks. Additionally, DNA methylation in different genomic regions and of different transcript types (i.e., protein coding, noncoding, and pseudogenes) was associated with islet expression levels. Our study provides a comprehensive picture of the islet DNA methylome in individuals with and without diabetes and highlights the importance of epigenetic dysregulation in pancreatic islets and T2D pathogenesis.
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Affiliation(s)
- Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Jones K Ofori
- Islet Cell Exocytosis Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Jonathan Lou S Esguerra
- Islet Cell Exocytosis Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Lena Eliasson
- Islet Cell Exocytosis Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
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de Mello VD, Matte A, Perfilyev A, Männistö V, Rönn T, Nilsson E, Käkelä P, Ling C, Pihlajamäki J. Human liver epigenetic alterations in non-alcoholic steatohepatitis are related to insulin action. Epigenetics 2017; 12:287-295. [PMID: 28277977 DOI: 10.1080/15592294.2017.1294305] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Both genetic and lifestyle factors contribute to the risk of non-alcoholic steatohepatitis (NASH). Additionally, epigenetic modifications may also play a key role in the pathogenesis of NASH. We therefore investigated liver DNA methylation, as a marker for epigenetic alterations, in individuals with simple steatosis and NASH, and further tested if these alterations were associated with clinical phenotypes. Liver biopsies obtained from 95 obese individuals (age: 49.5 ± 7.7 years, BMI: 43 ± 5.7 kg/m2, type 2 diabetes [T2D]: 35) as a wedge biopsy during a Roux-en-Y gastric bypass operation were investigated. Thirty-four individuals had a normal liver phenotype, 35 had simple steatosis, and 26 had NASH. Genome-wide DNA methylation pattern was analyzed using the Infinium HumanMethylation450 BeadChip. mRNA expression was analyzed from 42 individuals using the HumanHT-12 Expression BeadChip. We identified 1,292 CpG sites representing 677 unique genes differentially methylated in liver of individuals with NASH (q < 0.001), independently of T2D, age, sex, and BMI. Focusing on the top-ranking 30 and another 37 CpG sites mapped to genes enriched in pathways of metabolism (q = 0.0036) and cancer (q = 0.0001) all together, 59 NASH-associated CpG sites correlated with fasting insulin levels independently of age, fasting glucose, or T2D. From these, we identified 30 correlations between DNA methylation and mRNA expression, for example LDHB (r = -0.45, P = 0.003). We demonstrated that NASH, more than simple steatosis, associates with differential DNA methylation in the human liver. These epigenetic alterations in NASH are linked with insulin metabolism.
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Affiliation(s)
- Vanessa D de Mello
- a Institute of Public Health and Clinical Nutrition, Clinical Nutrition, University of Eastern Finland , Kuopio , Finland
| | - Ashok Matte
- a Institute of Public Health and Clinical Nutrition, Clinical Nutrition, University of Eastern Finland , Kuopio , Finland
| | - Alexander Perfilyev
- b Epigenetics and Diabetes Unit, Department of Clinical Sciences , Lund University Diabetes Centre , Malmö , Sweden
| | - Ville Männistö
- a Institute of Public Health and Clinical Nutrition, Clinical Nutrition, University of Eastern Finland , Kuopio , Finland
| | - Tina Rönn
- b Epigenetics and Diabetes Unit, Department of Clinical Sciences , Lund University Diabetes Centre , Malmö , Sweden
| | - Emma Nilsson
- b Epigenetics and Diabetes Unit, Department of Clinical Sciences , Lund University Diabetes Centre , Malmö , Sweden
| | - Pirjo Käkelä
- c Department of Surgery , University of Eastern Finland and Kuopio University Hospital , Kuopio , Finland
| | - Charlotte Ling
- b Epigenetics and Diabetes Unit, Department of Clinical Sciences , Lund University Diabetes Centre , Malmö , Sweden
| | - Jussi Pihlajamäki
- a Institute of Public Health and Clinical Nutrition, Clinical Nutrition, University of Eastern Finland , Kuopio , Finland.,d Clinical Nutrition and Obesity Center , Kuopio University Hospital , Kuopio , Finland
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12
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Bysani M, Perfilyev A, de Mello VD, Rönn T, Nilsson E, Pihlajamäki J, Ling C. Epigenetic alterations in blood mirror age-associated DNA methylation and gene expression changes in human liver. Epigenomics 2016; 9:105-122. [PMID: 27911095 DOI: 10.2217/epi-2016-0087] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
AIM To study the impact of aging on DNA methylation and mRNA expression in human liver. EXPERIMENTAL PROCEDURES We analysed genome-wide DNA methylation and gene expression in human liver samples using Illumina 450K and HumanHT12 expression BeadChip arrays. RESULTS DNA methylation analysis of ∼455,000 CpG sites in human liver revealed that age was significantly associated with altered DNA methylation of 20,396 CpG sites. Comparison of liver methylation data with published methylation data in other tissues showed that vast majority of the age-associated significant CpG sites overlapped between liver and blood, whereas a smaller overlap was found between liver and pancreatic islets or adipose tissue, respectively. We identified 151 genes whose liver expression also correlated with age. CONCLUSIONS We identified age-associated DNA methylation and expression changes in human liver that are partly reflected by epigenetic alterations in blood.
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Affiliation(s)
- Madhusudhan Bysani
- Epigenetics & Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Alexander Perfilyev
- Epigenetics & Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Vanessa D de Mello
- Department of Clinical Nutrition, Institute of Public Health & Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Tina Rönn
- Epigenetics & Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Emma Nilsson
- Epigenetics & Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Jussi Pihlajamäki
- Department of Clinical Nutrition, Institute of Public Health & Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.,Clinical Nutrition & Obesity Center, Kuopio University Hospital, Kuopio, Finland
| | - Charlotte Ling
- Epigenetics & Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
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Abstract
Epigenetic variation in human adipose tissue has been linked to type 2 diabetes and its related risk factors including age and obesity. Insulin resistance, a key risk factor for type 2 diabetes, may also be associated with altered DNA methylation in visceral and subcutaneous adipose tissue. Furthermore, linking epigenetic variation in target tissues to similar changes in blood cells may identify new blood-based biomarkers. In this issue of Diabetologia, Arner et al studied the transcriptome and methylome in subcutaneous and visceral adipose tissue of 80 obese women who were either insulin-sensitive or -resistant (DOI 10.1007/s00125-016-4074-5 ). While they found differences in gene expression between the two groups, no alterations in DNA methylation were found after correction for multiple testing. Nevertheless, based on nominal p values, their methylation data overlapped with methylation differences identified in adipose tissue of individuals with type 2 diabetes compared with healthy individuals. Differential methylation of these overlapping CpG sites may predispose to diabetes by occurring already in the insulin-resistant state. Furthermore, some methylation changes may contribute to an inflammatory process in adipose tissue since the identified CpG sites were annotated to genes encoding proteins involved in inflammation. Finally, the methylation pattern in circulating leucocytes did not mirror the adipose tissue methylome of these 80 women. Together, identifying novel molecular mechanisms contributing to insulin resistance and type 2 diabetes may help advance the search for new therapeutic alternatives.
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Affiliation(s)
- Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Jan Waldenströms gata 35, 205 02, Malmö, Sweden.
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Jan Waldenströms gata 35, 205 02, Malmö, Sweden
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14
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Gillberg L, Perfilyev A, Brøns C, Thomasen M, Grunnet LG, Volkov P, Rosqvist F, Iggman D, Dahlman I, Risérus U, Rönn T, Nilsson E, Vaag A, Ling C. Adipose tissue transcriptomics and epigenomics in low birthweight men and controls: role of high-fat overfeeding. Diabetologia 2016; 59:799-812. [PMID: 26750116 DOI: 10.1007/s00125-015-3852-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/09/2015] [Indexed: 02/07/2023]
Abstract
AIMS/HYPOTHESIS Individuals who had a low birthweight (LBW) are at an increased risk of insulin resistance and type 2 diabetes when exposed to high-fat overfeeding (HFO). We studied genome-wide mRNA expression and DNA methylation in subcutaneous adipose tissue (SAT) after 5 days of HFO and after a control diet in 40 young men, of whom 16 had LBW. METHODS mRNA expression was analysed using Affymetrix Human Gene 1.0 ST arrays and DNA methylation using Illumina 450K BeadChip arrays. RESULTS We found differential DNA methylation at 53 sites in SAT from LBW vs normal birthweight (NBW) men (false discovery rate <5%), including sites in the FADS2 and CPLX1 genes previously associated with type 2 diabetes. When we used reference-free cell mixture adjustments to potentially adjust for cell composition, 4,323 sites had differential methylation in LBW vs NBW men. However, no differences in SAT gene expression levels were identified between LBW and NBW men. In the combined group of all 40 participants, 3,276 genes (16.5%) were differentially expressed in SAT after HFO (false discovery rate <5%) and there was no difference between LBW men and controls. The most strongly upregulated genes were ELOVL6, FADS2 and NNAT; in contrast, INSR, IRS2 and the SLC27A2 fatty acid transporter showed decreased expression after HFO. Interestingly, SLC27A2 expression correlated negatively with diabetes- and obesity-related traits in a replication cohort of 142 individuals. DNA methylation at 652 CpG sites (including in CDK5, IGFBP5 and SLC2A4) was altered in SAT after overfeeding in this and in another cohort. CONCLUSIONS/INTERPRETATION Young men who had a LBW exhibit epigenetic alterations in their adipose tissue that potentially influence insulin resistance and risk of type 2 diabetes. Short-term overfeeding influences gene transcription and, to some extent, DNA methylation in adipose tissue; there was no major difference in this response between LBW and control participants.
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Affiliation(s)
- Linn Gillberg
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200, Copenhagen N, Denmark.
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University, Jan Waldenströms gata 35, SE-20502, Malmö, Sweden
| | - Charlotte Brøns
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200, Copenhagen N, Denmark
| | - Martin Thomasen
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200, Copenhagen N, Denmark
| | - Louise G Grunnet
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200, Copenhagen N, Denmark
| | - Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University, Jan Waldenströms gata 35, SE-20502, Malmö, Sweden
| | - Fredrik Rosqvist
- Clinical Nutrition and Metabolism, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - David Iggman
- Clinical Nutrition and Metabolism, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
- Center for Clinical Research Dalarna, Falun, Sweden
| | - Ingrid Dahlman
- Department of Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Ulf Risérus
- Clinical Nutrition and Metabolism, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University, Jan Waldenströms gata 35, SE-20502, Malmö, Sweden
| | - Emma Nilsson
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200, Copenhagen N, Denmark
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University, Jan Waldenströms gata 35, SE-20502, Malmö, Sweden
| | - Allan Vaag
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200, Copenhagen N, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University, Jan Waldenströms gata 35, SE-20502, Malmö, Sweden.
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15
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Ekman C, Elgzyri T, Ström K, Almgren P, Parikh H, Dekker Nitert M, Rönn T, Manderson Koivula F, Ling C, Tornberg ÅB, Wollmer P, Eriksson KF, Groop L, Hansson O. Less pronounced response to exercise in healthy relatives to type 2 diabetic subjects compared with controls. J Appl Physiol (1985) 2015; 119:953-60. [PMID: 26338460 DOI: 10.1152/japplphysiol.01067.2014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 08/27/2015] [Indexed: 01/03/2023] Open
Abstract
Healthy first-degree relatives with heredity of type 2 diabetes (FH+) are known to have metabolic inflexibility compared with subjects without heredity for diabetes (FH-). In this study, we aimed to test the hypothesis that FH+ individuals have an impaired response to exercise compared with FH-. Sixteen FH+ and 19 FH- insulin-sensitive men similar in age, peak oxygen consumption (V̇o2 peak), and body mass index completed an exercise intervention with heart rate monitored during exercise for 7 mo. Before and after the exercise intervention, the participants underwent a physical examination and tests for glucose tolerance and exercise capacity, and muscle biopsies were taken for expression analysis. The participants attended, on average, 39 training sessions during the intervention and spent 18.8 MJ on exercise. V̇o2 peak/kg increased by 14%, and the participants lost 1.2 kg of weight and 3 cm waist circumference. Given that the FH+ group expended 61% more energy during the intervention, we used regression analysis to analyze the response in the FH+ and FH- groups separately. Exercise volume had a significant effect on V̇o2 peak, weight, and waist circumference in the FH- group, but not in the FH+ group. After exercise, expression of genes involved in metabolism, oxidative phosphorylation, and cellular respiration increased more in the FH- compared with the FH+ group. This suggests that healthy, insulin-sensitive FH+ and FH- participants with similar age, V̇o2 peak, and body mass index may respond differently to an exercise intervention. The FH+ background might limit muscle adaptation to exercise, which may contribute to the increased susceptibility to type 2 diabetes in FH+ individuals.
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Affiliation(s)
- C Ekman
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - T Elgzyri
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - K Ström
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden; Swedish Winter Sports Research Centre, Department of Health Sciences, Mid Sweden University, Östersund, Sweden
| | - P Almgren
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - H Parikh
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden; Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Marloes Dekker Nitert
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - T Rönn
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | | | - C Ling
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - Å B Tornberg
- Department of Health Sciences, Division of Physiotherapy, Lund University, Lund, Sweden; Genetic Molecular Epidemiology Unit, Lund University Diabetes Center, Clinical Research Centre, Malmö, Sweden; and
| | - P Wollmer
- Department of Health Sciences, Division of Physiotherapy, Lund University, Lund, Sweden; Department of Clinical Sciences, Clinical Physiology and Nuclear Medicine Unit, Lund University, Malmö, Sweden
| | - K F Eriksson
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - L Groop
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - O Hansson
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden;
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16
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Agardh E, Lundstig A, Perfilyev A, Volkov P, Freiburghaus T, Lindholm E, Rönn T, Agardh CD, Ling C. Genome-wide analysis of DNA methylation in subjects with type 1 diabetes identifies epigenetic modifications associated with proliferative diabetic retinopathy. BMC Med 2015; 13:182. [PMID: 26248552 PMCID: PMC4527111 DOI: 10.1186/s12916-015-0421-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 07/15/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Epigenetic variation has been linked to several human diseases. Proliferative diabetic retinopathy (PDR) is a major cause of vision loss in subjects with diabetes. However, studies examining the association between PDR and the genome-wide DNA methylation pattern are lacking. Our aim was to identify epigenetic modifications that associate with and predict PDR in subjects with type 1 diabetes (T1D). METHODS DNA methylation was analyzed genome-wide in 485,577 sites in blood from cases with PDR (n = 28), controls (n = 30), and in a prospective cohort (n = 7). False discovery rate analysis was used to correct the data for multiple testing. Study participants with T1D diagnosed before 30 years of age and insulin treatment within 1 year from diagnosis were selected based on 1) subjects classified as having PDR (cases) and 2) subjects with T1D who had had diabetes for at least 10 years when blood DNA was sampled and classified as having no/mild diabetic retinopathy also after an 8.7-year follow-up (controls). DNA methylation was also analyzed in a prospective cohort including seven subjects with T1D who had no/mild diabetic retinopathy when blood samples were taken, but who developed PDR within 6.3 years (converters). The retinopathy level was classified by fundus photography. RESULTS We identified differential DNA methylation of 349 CpG sites representing 233 unique genes including TNF, CHI3L1 (also known as YKL-40), CHN2, GIPR, GLRA1, GPX1, AHRR, and BCOR in cases with PDR compared with controls. The majority of these sites (79 %) showed decreased DNA methylation in cases with PDR. The Natural Killer cell-mediated cytotoxicity pathway was found to be significantly (P = 0.006) enriched among differentially methylated genes in cases with PDR. We also identified differential DNA methylation of 28 CpG sites representing 17 genes (e.g. AHRR, GIPR, GLRA1, and BCOR) with P <0.05 in the prospective cohort, which is more than expected by chance (P = 0.0096). CONCLUSIONS Subjects with T1D and PDR exhibit altered DNA methylation patterns in blood. Some of these epigenetic changes may predict the development of PDR, suggesting that DNA methylation may be used as a prospective marker of PDR.
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Affiliation(s)
- Elisabet Agardh
- Department of Clinical Sciences, Ophthalmology, Lund University, Scania University Hospital, 205 02, Malmö, Sweden.
| | - Annika Lundstig
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden.
| | - Alexander Perfilyev
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden.
| | - Petr Volkov
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden.
| | - Tove Freiburghaus
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden.
| | - Eero Lindholm
- Department of Clinical Sciences, Endocrinology, Lund University, Scania University Hospital, 205 02, Malmö, Sweden.
| | - Tina Rönn
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden.
| | - Carl-David Agardh
- Department of Clinical Sciences, Endocrinology, Lund University, Scania University Hospital, 205 02, Malmö, Sweden.
| | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02, Malmö, Sweden.
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Abstract
Type 2 diabetes (T2D) develops due to insulin resistance and impaired insulin secretion, predominantly in genetically predisposed subjects exposed to nongenetic risk factors like obesity, physical inactivity and ageing. Emerging data suggest that epigenetics also play a key role in the pathogenesis of T2D. Genome-wide studies have identified altered DNA methylation patterns in pancreatic islets, skeletal muscle and adipose tissue from subjects with T2D compared with nondiabetic controls. Environmental factors known to affect T2D, including obesity, exercise and diet, have also been found to alter the human epigenome. Additionally, ageing and the intrauterine environment are associated with differential DNA methylation. Together, these data highlight a key role for epigenetics and particularly DNA methylation in the growing incidence of T2D.
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Affiliation(s)
- Tina Rönn
- Epigenetics & Diabetes, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, CRC, Jan Waldenströms gata 35, 205 02 Malmö, Sweden
| | - Charlotte Ling
- Epigenetics & Diabetes, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, CRC, Jan Waldenströms gata 35, 205 02 Malmö, Sweden
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18
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Rönn T, Volkov P, Gillberg L, Kokosar M, Perfilyev A, Jacobsen AL, Jørgensen SW, Brøns C, Jansson PA, Eriksson KF, Pedersen O, Hansen T, Groop L, Stener-Victorin E, Vaag A, Nilsson E, Ling C. Impact of age, BMI and HbA1c levels on the genome-wide DNA methylation and mRNA expression patterns in human adipose tissue and identification of epigenetic biomarkers in blood. Hum Mol Genet 2015; 24:3792-813. [PMID: 25861810 DOI: 10.1093/hmg/ddv124] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/07/2015] [Indexed: 01/03/2023] Open
Abstract
Increased age, BMI and HbA1c levels are risk factors for several non-communicable diseases. However, the impact of these factors on the genome-wide DNA methylation pattern in human adipose tissue remains unknown. We analyzed the DNA methylation of ∼480 000 sites in human adipose tissue from 96 males and 94 females and related methylation to age, BMI and HbA1c. We also compared epigenetic signatures in adipose tissue and blood. Age was significantly associated with both altered DNA methylation and expression of 1050 genes (e.g. FHL2, NOX4 and PLG). Interestingly, many reported epigenetic biomarkers of aging in blood, including ELOVL2, FHL2, KLF14 and GLRA1, also showed significant correlations between adipose tissue DNA methylation and age in our study. The most significant association between age and adipose tissue DNA methylation was found upstream of ELOVL2. We identified 2825 genes (e.g. FTO, ITIH5, CCL18, MTCH2, IRS1 and SPP1) where both DNA methylation and expression correlated with BMI. Methylation at previously reported HIF3A sites correlated significantly with BMI in females only. HbA1c (range 28-46 mmol/mol) correlated significantly with the methylation of 711 sites, annotated to, for example, RAB37, TICAM1 and HLA-DPB1. Pathway analyses demonstrated that methylation levels associated with age and BMI are overrepresented among genes involved in cancer, type 2 diabetes and cardiovascular disease. Our results highlight the impact of age, BMI and HbA1c on epigenetic variation of candidate genes for obesity, type 2 diabetes and cancer in human adipose tissue. Importantly, we demonstrate that epigenetic biomarkers in blood can mirror age-related epigenetic signatures in target tissues for metabolic diseases such as adipose tissue.
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Affiliation(s)
- Tina Rönn
- Department of Clinical Sciences, Epigenetics and Diabetes and
| | - Petr Volkov
- Department of Clinical Sciences, Epigenetics and Diabetes and
| | - Linn Gillberg
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Milana Kokosar
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 11, Box 434, 405 30 Gothenburg, Sweden
| | | | - Anna Louisa Jacobsen
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark
| | - Sine W Jørgensen
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark, Steno Diabetes Center, Niels Steensensvej 2, DK-2820 Gentofte, Denmark
| | - Charlotte Brøns
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark
| | - Per-Anders Jansson
- Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Karl-Fredrik Eriksson
- Department of Clinical Sciences, Vascular Diseases, Lund University, 205 02 Malmö, Sweden
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen, Denmark and
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen, Denmark and
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, CRC, 205 02 Malmö, Sweden
| | - Elisabet Stener-Victorin
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 11, Box 434, 405 30 Gothenburg, Sweden, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Allan Vaag
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Emma Nilsson
- Department of Clinical Sciences, Epigenetics and Diabetes and Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark
| | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes and
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Hall E, Volkov P, Dayeh T, Esguerra JLS, Salö S, Eliasson L, Rönn T, Bacos K, Ling C. Sex differences in the genome-wide DNA methylation pattern and impact on gene expression, microRNA levels and insulin secretion in human pancreatic islets. Genome Biol 2014; 15:522. [PMID: 25517766 PMCID: PMC4256841 DOI: 10.1186/s13059-014-0522-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 10/30/2014] [Indexed: 12/19/2022] Open
Abstract
Background Epigenetic factors regulate tissue-specific expression and X-chromosome inactivation. Previous studies have identified epigenetic differences between sexes in some human tissues. However, it is unclear whether epigenetic modifications contribute to sex-specific differences in insulin secretion and metabolism. Here, we investigate the impact of sex on the genome-wide DNA methylation pattern in human pancreatic islets from 53 males and 34 females, and relate the methylome to changes in expression and insulin secretion. Results Glucose-stimulated insulin secretion is higher in female versus male islets. Genome-wide DNA methylation data in human islets clusters based on sex. While the chromosome-wide DNA methylation level on the X-chromosome is higher in female versus male islets, the autosomes do not display a global methylation difference between sexes. Methylation of 8,140 individual X-chromosome sites and 470 autosomal sites shows sex-specific differences in human islets. These include sites in/near AR, DUSP9, HNF4A, BCL11A and CDKN2B. 61 X-chromosome genes and 18 autosomal genes display sex-specific differences in both DNA methylation and expression. These include NKAP, SPESP1 and APLN, which exhibited lower expression in females. Functional analyses demonstrate that methylation of NKAP and SPESP1 promoters in vitro suppresses their transcriptional activity. Silencing of Nkap or Apln in clonal beta-cells results in increased insulin secretion. Differential methylation between sexes is associated with altered levels of microRNAs miR-660 and miR-532 and related target genes. Conclusions Chromosome-wide and gene-specific sex differences in DNA methylation associate with altered expression and insulin secretion in human islets. Our data demonstrate that epigenetics contribute to sex-specific metabolic phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0522-z) contains supplementary material, which is available to authorized users.
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Olsson AH, Volkov P, Bacos K, Dayeh T, Hall E, Nilsson EA, Ladenvall C, Rönn T, Ling C. Genome-wide associations between genetic and epigenetic variation influence mRNA expression and insulin secretion in human pancreatic islets. PLoS Genet 2014; 10:e1004735. [PMID: 25375650 PMCID: PMC4222689 DOI: 10.1371/journal.pgen.1004735] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 09/05/2014] [Indexed: 12/29/2022] Open
Abstract
Genetic and epigenetic mechanisms may interact and together affect biological processes and disease development. However, most previous studies have investigated genetic and epigenetic mechanisms independently, and studies examining their interactions throughout the human genome are lacking. To identify genetic loci that interact with the epigenome, we performed the first genome-wide DNA methylation quantitative trait locus (mQTL) analysis in human pancreatic islets. We related 574,553 single nucleotide polymorphisms (SNPs) with genome-wide DNA methylation data of 468,787 CpG sites targeting 99% of RefSeq genes in islets from 89 donors. We identified 67,438 SNP-CpG pairs in cis, corresponding to 36,783 SNPs (6.4% of tested SNPs) and 11,735 CpG sites (2.5% of tested CpGs), and 2,562 significant SNP-CpG pairs in trans, corresponding to 1,465 SNPs (0.3% of tested SNPs) and 383 CpG sites (0.08% of tested CpGs), showing significant associations after correction for multiple testing. These include reported diabetes loci, e.g. ADCY5, KCNJ11, HLA-DQA1, INS, PDX1 and GRB10. CpGs of significant cis-mQTLs were overrepresented in the gene body and outside of CpG islands. Follow-up analyses further identified mQTLs associated with gene expression and insulin secretion in human islets. Causal inference test (CIT) identified SNP-CpG pairs where DNA methylation in human islets is the potential mediator of the genetic association with gene expression or insulin secretion. Functional analyses further demonstrated that identified candidate genes (GPX7, GSTT1 and SNX19) directly affect key biological processes such as proliferation and apoptosis in pancreatic β-cells. Finally, we found direct correlations between DNA methylation of 22,773 (4.9%) CpGs with mRNA expression of 4,876 genes, where 90% of the correlations were negative when CpGs were located in the region surrounding transcription start site. Our study demonstrates for the first time how genome-wide genetic and epigenetic variation interacts to influence gene expression, islet function and potential diabetes risk in humans. Inter-individual variation in genetics and epigenetics affects biological processes and disease susceptibility. However, most studies have investigated genetic and epigenetic mechanisms independently and to uncover novel mechanisms affecting disease susceptibility there is a highlighted need to study interactions between these factors on a genome-wide scale. To identify novel loci affecting islet function and potentially diabetes, we performed the first genome-wide methylation quantitative trait locus (mQTL) analysis in human pancreatic islets including DNA methylation of 468,787 CpG sites located throughout the genome. Our results showed that DNA methylation of 11,735 CpGs in 4,504 unique genes is regulated by genetic factors located in cis (67,438 SNP-CpG pairs). Furthermore, significant mQTLs cover previously reported diabetes loci including KCNJ11, INS, HLA, PDX1 and GRB10. We also found mQTLs associated with gene expression and insulin secretion in human islets. By performing causality inference tests (CIT), we identified CpGs where DNA methylation potentially mediates the genetic impact on gene expression and insulin secretion. Our functional follow-up experiments further demonstrated that identified mQTLs/genes (GPX7, GSTT1 and SNX19) directly affect pancreatic β-cell function. Together, our study provides a detailed map of genome-wide associations between genetic and epigenetic variation, which affect gene expression and insulin secretion in human pancreatic islets.
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Affiliation(s)
- Anders H. Olsson
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Malmö, Sweden
| | - Petr Volkov
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Malmö, Sweden
| | - Karl Bacos
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Malmö, Sweden
| | - Tasnim Dayeh
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Malmö, Sweden
| | - Elin Hall
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Malmö, Sweden
| | - Emma A. Nilsson
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Malmö, Sweden
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Clinical Research Centre, Malmö, Sweden
| | - Tina Rönn
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Malmö, Sweden
| | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Malmö, Sweden
- * E-mail:
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21
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Affiliation(s)
- Tina Rönn
- Epigenetics & Diabetes Unit, Lund University Diabetes Centre, Malmö, Sweden.
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22
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Nilsson E, Jansson PA, Perfilyev A, Volkov P, Pedersen M, Svensson MK, Poulsen P, Ribel-Madsen R, Pedersen NL, Almgren P, Fadista J, Rönn T, Klarlund Pedersen B, Scheele C, Vaag A, Ling C. Altered DNA methylation and differential expression of genes influencing metabolism and inflammation in adipose tissue from subjects with type 2 diabetes. Diabetes 2014; 63:2962-76. [PMID: 24812430 DOI: 10.2337/db13-1459] [Citation(s) in RCA: 279] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genetics, epigenetics, and environment may together affect the susceptibility for type 2 diabetes (T2D). Our aim was to dissect molecular mechanisms underlying T2D using genome-wide expression and DNA methylation data in adipose tissue from monozygotic twin pairs discordant for T2D and independent case-control cohorts. In adipose tissue from diabetic twins, we found decreased expression of genes involved in oxidative phosphorylation; carbohydrate, amino acid, and lipid metabolism; and increased expression of genes involved in inflammation and glycan degradation. The most differentially expressed genes included ELOVL6, GYS2, FADS1, SPP1 (OPN), CCL18, and IL1RN. We replicated these results in adipose tissue from an independent case-control cohort. Several candidate genes for obesity and T2D (e.g., IRS1 and VEGFA) were differentially expressed in discordant twins. We found a heritable contribution to the genome-wide DNA methylation variability in twins. Differences in methylation between monozygotic twin pairs discordant for T2D were subsequently modest. However, 15,627 sites, representing 7,046 genes including PPARG, KCNQ1, TCF7L2, and IRS1, showed differential DNA methylation in adipose tissue from unrelated subjects with T2D compared with control subjects. A total of 1,410 of these sites also showed differential DNA methylation in the twins discordant for T2D. For the differentially methylated sites, the heritability estimate was 0.28. We also identified copy number variants (CNVs) in monozygotic twin pairs discordant for T2D. Taken together, subjects with T2D exhibit multiple transcriptional and epigenetic changes in adipose tissue relevant to the development of the disease.
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Affiliation(s)
- Emma Nilsson
- Epigenetics and Diabetes, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Clinical Research Centre, Malmö, Sweden Department of Endocrinology, Diabetes and Metabolism, Rigshospitalet, Copenhagen, Denmark
| | - Per Anders Jansson
- Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Alexander Perfilyev
- Epigenetics and Diabetes, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Clinical Research Centre, Malmö, Sweden
| | - Petr Volkov
- Epigenetics and Diabetes, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Clinical Research Centre, Malmö, Sweden
| | - Maria Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Maria K Svensson
- Institute of Medicine, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | | | - Rasmus Ribel-Madsen
- Department of Endocrinology, Diabetes and Metabolism, Rigshospitalet, Copenhagen, Denmark
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Almgren
- Diabetes and Endocrinology, Department of Clinical Sciences, Lund University Diabetes Centre, Clinical Research Centre, Lund University, Malmö, Sweden
| | - João Fadista
- Diabetes and Endocrinology, Department of Clinical Sciences, Lund University Diabetes Centre, Clinical Research Centre, Lund University, Malmö, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Clinical Research Centre, Malmö, Sweden
| | - Bente Klarlund Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Scheele
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Allan Vaag
- Department of Endocrinology, Diabetes and Metabolism, Rigshospitalet, Copenhagen, Denmark
| | - Charlotte Ling
- Epigenetics and Diabetes, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Clinical Research Centre, Malmö, Sweden
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Hall E, Volkov P, Dayeh T, Bacos K, Rönn T, Nitert MD, Ling C. Effects of palmitate on genome-wide mRNA expression and DNA methylation patterns in human pancreatic islets. BMC Med 2014; 12:103. [PMID: 24953961 PMCID: PMC4065864 DOI: 10.1186/1741-7015-12-103] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/25/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Circulating free fatty acids are often elevated in patients with type 2 diabetes (T2D) and obese individuals. Chronic exposure to high levels of saturated fatty acids has detrimental effects on islet function and insulin secretion. Altered gene expression and epigenetics may contribute to T2D and obesity. However, there is limited information on whether fatty acids alter the genome-wide transcriptome profile in conjunction with DNA methylation patterns in human pancreatic islets. To dissect the molecular mechanisms linking lipotoxicity to impaired insulin secretion, we investigated the effects of a 48 h palmitate treatment in vitro on genome-wide mRNA expression and DNA methylation patterns in human pancreatic islets. METHODS Genome-wide mRNA expression was analyzed using Affymetrix GeneChip(®) Human Gene 1.0 ST whole transcript-based array (n = 13) and genome-wide DNA methylation was analyzed using Infinium HumanMethylation450K BeadChip (n = 13) in human pancreatic islets exposed to palmitate or control media for 48 h. A non-parametric paired Wilcoxon statistical test was used to analyze mRNA expression. Apoptosis was measured using Apo-ONE(®) Homogeneous Caspase-3/7 Assay (n = 4). RESULTS While glucose-stimulated insulin secretion was decreased, there was no significant effect on apoptosis in human islets exposed to palmitate. We identified 1,860 differentially expressed genes in palmitate-treated human islets. These include candidate genes for T2D, such as TCF7L2, GLIS3, HNF1B and SLC30A8. Additionally, genes in glycolysis/gluconeogenesis, pyruvate metabolism, fatty acid metabolism, glutathione metabolism and one carbon pool by folate were differentially expressed in palmitate-treated human islets. Palmitate treatment altered the global DNA methylation level and DNA methylation levels of CpG island shelves and shores, 5'UTR, 3'UTR and gene body regions in human islets. Moreover, 290 genes with differential expression had a corresponding change in DNA methylation, for example, TCF7L2 and GLIS3. Importantly, out of the genes differentially expressed due to palmitate treatment in human islets, 67 were also associated with BMI and 37 were differentially expressed in islets from T2D patients. CONCLUSION Our study demonstrates that palmitate treatment of human pancreatic islets gives rise to epigenetic modifications that together with altered gene expression may contribute to impaired insulin secretion and T2D.
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Affiliation(s)
| | | | | | | | | | | | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, CRC, Lund University, Scania University Hospital, Malmö, Sweden.
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Rönn T, Volkov P, Tornberg Å, Elgzyri T, Hansson O, Eriksson KF, Groop L, Ling C. Extensive changes in the transcriptional profile of human adipose tissue including genes involved in oxidative phosphorylation after a 6-month exercise intervention. Acta Physiol (Oxf) 2014; 211:188-200. [PMID: 24495239 DOI: 10.1111/apha.12247] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/21/2013] [Accepted: 01/28/2014] [Indexed: 12/21/2022]
Abstract
AIM Adipose tissue has an important function in total energy homeostasis, and its dysregulation may contribute to lifestyle-related diseases such as type 2 diabetes, cancer and cardiovascular diseases. The aim of this study was to investigate genome-wide mRNA expression in adipose tissue in healthy men before and after an exercise intervention to identify genes or pathways that mediate the beneficial effect of regular exercise. We also investigated the difference in adipose tissue mRNA expression between individuals with or without a family history of type 2 diabetes. METHODS The 6-month supervised exercise intervention was conducted in 47 healthy men (age 37.8 ± 4.3 years, BMI 28.5 ± 3.6 kg m(-2) ) with a previous low level of physical activity. RNA was analysed using GeneChip Human Gene 1.0 ST arrays (Affymetrix) before and after the exercise. RESULTS We identified 2,560 significant transcripts differentially expressed before vs. after exercise with a false discovery rate (FDR) < 0.1%, including genes encoding the respiratory chain, histone subunits, small nucleolar RNAs and ribosomal proteins. Additionally, pathways enriched in response to exercise include the ribosome, oxidative phosphorylation, proteasome and many metabolic pathways, whereas the WNT and MAPK signalling pathways were down-regulated (FDR < 5%) after exercise. There were no significant differences in mRNA expression between individuals with or without a family history of type 2 diabetes. CONCLUSION Exercise increased the expression of genes involved in oxidative phosphorylation, which is the opposite of what has been seen in adipose tissue from elderly or obese individuals with low physical fitness, and our study thereby demonstrates a mechanism for the beneficial effect of exercise.
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Affiliation(s)
- T. Rönn
- Department of Clinical Sciences, Epigenetics and Diabetes; Lund University Diabetes Centre; CRC; Malmö Sweden
| | - P. Volkov
- Department of Clinical Sciences, Epigenetics and Diabetes; Lund University Diabetes Centre; CRC; Malmö Sweden
| | - Å. Tornberg
- Genetic & Molecular Epidemiology Unit; Lund University Diabetes Centre; CRC; Malmö Sweden
- Department of Health Sciences; Division of Physiotherapy; Lund University; Lund Sweden
| | - T. Elgzyri
- Department of Clinical Sciences, Diabetes and Endocrinology; Lund University Diabetes Centre; CRC; Malmö Sweden
| | - O. Hansson
- Department of Clinical Sciences, Diabetes and Endocrinology; Lund University Diabetes Centre; CRC; Malmö Sweden
| | - K.-F. Eriksson
- Department of Clinical Sciences, Vascular Diseases; Lund University; Malmö Sweden
| | - L. Groop
- Department of Clinical Sciences, Diabetes and Endocrinology; Lund University Diabetes Centre; CRC; Malmö Sweden
| | - C. Ling
- Department of Clinical Sciences, Epigenetics and Diabetes; Lund University Diabetes Centre; CRC; Malmö Sweden
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25
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Claussnitzer M, Dankel SN, Klocke B, Grallert H, Glunk V, Berulava T, Lee H, Oskolkov N, Fadista J, Ehlers K, Wahl S, Hoffmann C, Qian K, Rönn T, Riess H, Müller-Nurasyid M, Bretschneider N, Schroeder T, Skurk T, Horsthemke B, Spieler D, Klingenspor M, Seifert M, Kern MJ, Mejhert N, Dahlman I, Hansson O, Hauck SM, Blüher M, Arner P, Groop L, Illig T, Suhre K, Hsu YH, Mellgren G, Hauner H, Laumen H. Leveraging cross-species transcription factor binding site patterns: from diabetes risk loci to disease mechanisms. Cell 2014; 156:343-58. [PMID: 24439387 DOI: 10.1016/j.cell.2013.10.058] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 09/05/2013] [Accepted: 10/30/2013] [Indexed: 10/25/2022]
Abstract
Genome-wide association studies have revealed numerous risk loci associated with diverse diseases. However, identification of disease-causing variants within association loci remains a major challenge. Divergence in gene expression due to cis-regulatory variants in noncoding regions is central to disease susceptibility. We show that integrative computational analysis of phylogenetic conservation with a complexity assessment of co-occurring transcription factor binding sites (TFBS) can identify cis-regulatory variants and elucidate their mechanistic role in disease. Analysis of established type 2 diabetes risk loci revealed a striking clustering of distinct homeobox TFBS. We identified the PRRX1 homeobox factor as a repressor of PPARG2 expression in adipose cells and demonstrate its adverse effect on lipid metabolism and systemic insulin sensitivity, dependent on the rs4684847 risk allele that triggers PRRX1 binding. Thus, cross-species conservation analysis at the level of co-occurring TFBS provides a valuable contribution to the translation of genetic association signals to disease-related molecular mechanisms.
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Affiliation(s)
- Melina Claussnitzer
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany; Hebrew SeniorLife Institute for Aging Research, Harvard Medical School, Boston, MA 02131, USA.
| | - Simon N Dankel
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; Hormone Laboratory, Haukeland University Hospital, 5021 Bergen, Norway
| | | | - Harald Grallert
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Viktoria Glunk
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Tea Berulava
- Institut für Humangenetik, Universitätsklinikum Essen, Universität-Duisburg-Essen, 45147 Essen, Germany
| | - Heekyoung Lee
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Nikolay Oskolkov
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden
| | - Joao Fadista
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden
| | - Kerstin Ehlers
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Simone Wahl
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Christoph Hoffmann
- Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; Chair of Molecular Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany
| | - Kun Qian
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Tina Rönn
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden
| | - Helene Riess
- Department of Internal Medicine II-Cardiology, University of Ulm Medical Center, 89081 Ulm, Germany; Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany; Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, 81377 Munich, Germany; Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | | | - Timm Schroeder
- Research Unit Stem Cell Dynamics, Helmholtz Center Munich-German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany; Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, 4058 Basel, Switzerland
| | - Thomas Skurk
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; Else Kröner-Fresenius-Center for Nutritional Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Bernhard Horsthemke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität-Duisburg-Essen, 45147 Essen, Germany
| | | | - Derek Spieler
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, German Research Center for Environmental Health, Germany; Department of Neurology, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Martin Klingenspor
- Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; Chair of Molecular Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany
| | | | - Michael J Kern
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Niklas Mejhert
- Department of Medicine, Karolinska Institutet, Center for Endocrinology and Metabolism, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Ingrid Dahlman
- Department of Medicine, Karolinska Institutet, Center for Endocrinology and Metabolism, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Ola Hansson
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden
| | - Stefanie M Hauck
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Peter Arner
- Department of Medicine, Karolinska Institutet, Center for Endocrinology and Metabolism, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Leif Groop
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Hanover Unified Biobank, Hanover Medical School, 30625 Hanover, Germany
| | - Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, Qatar Foundation, PO Box 24144, Doha, Qatar
| | - Yi-Hsiang Hsu
- Hebrew SeniorLife Institute for Aging Research, Harvard Medical School, Boston, MA 02131, USA; Molecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, MA 02115, USA
| | - Gunnar Mellgren
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; Hormone Laboratory, Haukeland University Hospital, 5021 Bergen, Norway
| | - Hans Hauner
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany; Else Kröner-Fresenius-Center for Nutritional Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Helmut Laumen
- Chair of Nutritional Medicine, Technische Universität München, Else Kröner-Fresenius-Center for Nutritional Medicine, 85350 Freising-Weihenstephan, Germany; Nutritional Medicine Unit, ZIEL-Research Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany and Technische Universität München, 85350 Freising-Weihenstephan, Germany; Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg 85764, Germany.
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Abstract
Regular exercise has numerous health benefits, for example, it reduces the risk of cardiovascular disease and cancer. It has also been shown that the risk of type 2 diabetes can be halved in high-risk groups through nonpharmacological lifestyle interventions involving exercise and diet. Nevertheless, the number of people living a sedentary life is dramatically increasing worldwide. Researchers have searched for molecular mechanisms explaining the health benefits of regular exercise for decades and it is well established that exercise alters the gene expression pattern in multiple tissues. However, until recently it was unknown that regular exercise can modify the genome-wide DNA methylation pattern in humans. This review will focus on recent progress in the field of regular exercise and epigenetics.
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Affiliation(s)
- Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02 Malmö, Sweden.
| | - Tina Rönn
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02 Malmö, Sweden
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Keildson S, Fadista J, Ladenvall C, Hedman ÅK, Elgzyri T, Small KS, Grundberg E, Nica AC, Glass D, Richards JB, Barrett A, Nisbet J, Zheng HF, Rönn T, Ström K, Eriksson KF, Prokopenko I, Spector TD, Dermitzakis ET, Deloukas P, McCarthy MI, Rung J, Groop L, Franks PW, Lindgren CM, Hansson O. Expression of phosphofructokinase in skeletal muscle is influenced by genetic variation and associated with insulin sensitivity. Diabetes 2014; 63:1154-65. [PMID: 24306210 PMCID: PMC3931395 DOI: 10.2337/db13-1301] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Using an integrative approach in which genetic variation, gene expression, and clinical phenotypes are assessed in relevant tissues may help functionally characterize the contribution of genetics to disease susceptibility. We sought to identify genetic variation influencing skeletal muscle gene expression (expression quantitative trait loci [eQTLs]) as well as expression associated with measures of insulin sensitivity. We investigated associations of 3,799,401 genetic variants in expression of >7,000 genes from three cohorts (n = 104). We identified 287 genes with cis-acting eQTLs (false discovery rate [FDR] <5%; P < 1.96 × 10(-5)) and 49 expression-insulin sensitivity phenotype associations (i.e., fasting insulin, homeostasis model assessment-insulin resistance, and BMI) (FDR <5%; P = 1.34 × 10(-4)). One of these associations, fasting insulin/phosphofructokinase (PFKM), overlaps with an eQTL. Furthermore, the expression of PFKM, a rate-limiting enzyme in glycolysis, was nominally associated with glucose uptake in skeletal muscle (P = 0.026; n = 42) and overexpressed (Bonferroni-corrected P = 0.03) in skeletal muscle of patients with T2D (n = 102) compared with normoglycemic controls (n = 87). The PFKM eQTL (rs4547172; P = 7.69 × 10(-6)) was nominally associated with glucose uptake, glucose oxidation rate, intramuscular triglyceride content, and metabolic flexibility (P = 0.016-0.048; n = 178). We explored eQTL results using published data from genome-wide association studies (DIAGRAM and MAGIC), and a proxy for the PFKM eQTL (rs11168327; r(2) = 0.75) was nominally associated with T2D (DIAGRAM P = 2.7 × 10(-3)). Taken together, our analysis highlights PFKM as a potential regulator of skeletal muscle insulin sensitivity.
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Affiliation(s)
- Sarah Keildson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Joao Fadista
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Åsa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Targ Elgzyri
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, U.K
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
| | - Elin Grundberg
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, U.K
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
| | - Alexandra C. Nica
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Daniel Glass
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, U.K
| | - J. Brent Richards
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, U.K
- Department of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Churchill Hospital, Oxford, U.K
| | - James Nisbet
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
| | - Hou-Feng Zheng
- Department of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Tina Rönn
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Kristoffer Ström
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
- Swedish Winter Sports Research Centre, Department of Health Sciences, Mid Sweden University, Östersund, Sweden
| | - Karl-Fredrik Eriksson
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | | | | | | | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, U.K
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Churchill Hospital, Oxford, U.K
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - Johan Rung
- European Molecular Biology Laboratory–European Bioinformatics Institute, Cambridge, U.K
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Paul W. Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Ola Hansson
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
- Corresponding author: Ola Hansson,
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Gillberg L, Jacobsen SC, Rönn T, Brøns C, Vaag A. PPARGC1A DNA methylation in subcutaneous adipose tissue in low birth weight subjects--impact of 5 days of high-fat overfeeding. Metabolism 2014; 63:263-71. [PMID: 24262291 DOI: 10.1016/j.metabol.2013.10.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/16/2013] [Accepted: 10/15/2013] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Increased DNA methylation of the metabolic regulator peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A) has been reported in skeletal muscle from type 2 diabetes (T2D) subjects and from low birth weight (LBW) subjects with an increased risk of T2D. High-fat overfeeding increases PPARGC1A DNA methylation in muscle in a birth weight dependent manner. However, PPARGC1A DNA methylation in subcutaneous adipose tissue (SAT) in LBW subjects has not previously been investigated. Our objective was to determine PPARGC1A DNA methylation and mRNA expression in basal and insulin-stimulated SAT from LBW and matched normal birth weight (NBW) subjects during control and high-fat overfeeding. MATERIALS/METHODS Nineteen young healthy men with LBW and 26 NBW controls were studied after both a 5-day high-fat overfeeding and a control diet in a randomized crossover setting. DNA methylation was assessed with bisulfite sequencing and mRNA expression with quantitative real-time PCR. RESULTS Following high-fat overfeeding, increased SAT PPARGC1A DNA methylation was observed in LBW subjects but not in NBW controls. Basal SAT PPARGC1A mRNA expression was unaffected by diet and similar in the two groups. However, LBW subjects showed an increased SAT PPARGC1A mRNA expression during insulin-stimulation. SAT PPARGC1A methylation correlated inversely with mRNA expression during insulin-stimulation. CONCLUSIONS The study adds to the increasing awareness of PPARGC1A DNA methylation being flexible and influenced by high-fat overfeeding in a birth weight dependent manner with muscle and fat responding differently. Further data are needed to understand the role of PPARGC1A DNA methylation in insulin resistance and developmental programming of T2D.
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Affiliation(s)
- Linn Gillberg
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark; Steno Diabetes Center, Niels Steensensvej 2, DK-2820 Gentofte, Denmark.
| | - Stine C Jacobsen
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark; Steno Diabetes Center, Niels Steensensvej 2, DK-2820 Gentofte, Denmark
| | - Tina Rönn
- Department of Clinical Sciences, Lund University, Skåne University Hospital, SE-205 02 Malmö, Sweden
| | - Charlotte Brøns
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark; Steno Diabetes Center, Niels Steensensvej 2, DK-2820 Gentofte, Denmark
| | - Allan Vaag
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark; Steno Diabetes Center, Niels Steensensvej 2, DK-2820 Gentofte, Denmark; Department of Clinical Sciences, Lund University, Skåne University Hospital, SE-205 02 Malmö, Sweden; Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
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29
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Dayeh TA, Olsson AH, Volkov P, Almgren P, Rönn T, Ling C. Identification of CpG-SNPs associated with type 2 diabetes and differential DNA methylation in human pancreatic islets. Diabetologia 2013; 56:1036-46. [PMID: 23462794 PMCID: PMC3622750 DOI: 10.1007/s00125-012-2815-7] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 12/06/2012] [Indexed: 12/22/2022]
Abstract
AIMS/HYPOTHESIS To date, the molecular function of most of the reported type 2 diabetes-associated loci remains unknown. The introduction or removal of cytosine-phosphate-guanine (CpG) dinucleotides, which are possible sites of DNA methylation, has been suggested as a potential mechanism through which single-nucleotide polymorphisms (SNPs) can affect gene function via epigenetics. The aim of this study was to examine if any of 40 SNPs previously associated with type 2 diabetes introduce or remove a CpG site and if these CpG-SNPs are associated with differential DNA methylation in pancreatic islets of 84 human donors. METHODS DNA methylation was analysed using pyrosequencing. RESULTS We found that 19 of 40 (48%) type 2 diabetes-associated SNPs introduce or remove a CpG site. Successful DNA methylation data were generated for 16 of these 19 CpG-SNP loci, representing the candidate genes TCF7L2, KCNQ1, PPARG, HHEX, CDKN2A, SLC30A8, DUSP9, CDKAL1, ADCY5, SRR, WFS1, IRS1, DUSP8, HMGA2, TSPAN8 and CHCHD9. All analysed CpG-SNPs were associated with differential DNA methylation of the CpG-SNP site in human islets. Moreover, six CpG-SNPs, representing TCF7L2, KCNQ1, CDKN2A, ADCY5, WFS1 and HMGA2, were also associated with DNA methylation of surrounding CpG sites. Some of the type 2 diabetes CpG-SNP sites that exhibit differential DNA methylation were further associated with gene expression, alternative splicing events determined by splice index, and hormone secretion in the human islets. The 19 type 2 diabetes-associated CpG-SNPs are in strong linkage disequilibrium (r² > 0.8) with a total of 295 SNPs, including 91 CpG-SNPs. CONCLUSIONS/INTERPRETATION Our results suggest that the introduction or removal of a CpG site may be a molecular mechanism through which some of the type 2 diabetes SNPs affect gene function via differential DNA methylation and consequently contributes to the phenotype of the disease.
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Affiliation(s)
- T. A. Dayeh
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Scania University Hospital, Jan Waldenströmsgata 35, 205 02 Malmö, Sweden
| | - A. H. Olsson
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Scania University Hospital, Jan Waldenströmsgata 35, 205 02 Malmö, Sweden
| | - P. Volkov
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Scania University Hospital, Jan Waldenströmsgata 35, 205 02 Malmö, Sweden
| | - P. Almgren
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Clinical Research Centre, Scania University Hospital, Jan Waldenströmsgata 35, 205 02 Malmö, Sweden
| | - T. Rönn
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Scania University Hospital, Jan Waldenströmsgata 35, 205 02 Malmö, Sweden
| | - C. Ling
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, Clinical Research Centre, Scania University Hospital, Jan Waldenströmsgata 35, 205 02 Malmö, Sweden
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30
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Nitert MD, Dayeh T, Volkov P, Elgzyri T, Hall E, Nilsson E, Yang BT, Lang S, Parikh H, Wessman Y, Weishaupt H, Attema J, Abels M, Wierup N, Almgren P, Jansson PA, Rönn T, Hansson O, Eriksson KF, Groop L, Ling C. Impact of an exercise intervention on DNA methylation in skeletal muscle from first-degree relatives of patients with type 2 diabetes. Diabetes 2012; 61:3322-32. [PMID: 23028138 PMCID: PMC3501844 DOI: 10.2337/db11-1653] [Citation(s) in RCA: 267] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To identify epigenetic patterns, which may predispose to type 2 diabetes (T2D) due to a family history (FH) of the disease, we analyzed DNA methylation genome-wide in skeletal muscle from individuals with (FH(+)) or without (FH(-)) an FH of T2D. We found differential DNA methylation of genes in biological pathways including mitogen-activated protein kinase (MAPK), insulin, and calcium signaling (P ≤ 0.007) and of individual genes with known function in muscle, including MAPK1, MYO18B, HOXC6, and the AMP-activated protein kinase subunit PRKAB1 in skeletal muscle of FH(+) compared with FH(-) men. We further validated our findings from FH(+) men in monozygotic twin pairs discordant for T2D, and 40% of 65 analyzed genes exhibited differential DNA methylation in muscle of both FH(+) men and diabetic twins. We further examined if a 6-month exercise intervention modifies the genome-wide DNA methylation pattern in skeletal muscle of the FH(+) and FH(-) individuals. DNA methylation of genes in retinol metabolism and calcium signaling pathways (P < 3 × 10(-6)) and with known functions in muscle and T2D including MEF2A, RUNX1, NDUFC2, and THADA decreased after exercise. Methylation of these human promoter regions suppressed reporter gene expression in vitro. In addition, both expression and methylation of several genes, i.e., ADIPOR1, BDKRB2, and TRIB1, changed after exercise. These findings provide new insights into how genetic background and environment can alter the human epigenome.
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Affiliation(s)
- Marloes Dekker Nitert
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Tasnim Dayeh
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Peter Volkov
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Targ Elgzyri
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Elin Hall
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Emma Nilsson
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Beatrice T. Yang
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Stefan Lang
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Hemang Parikh
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ylva Wessman
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Holger Weishaupt
- Immunology Unit, Institute for Experimental Medical Science, Lund University, Lund, Sweden
| | - Joanne Attema
- Immunology Unit, Institute for Experimental Medical Science, Lund University, Lund, Sweden
| | - Mia Abels
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Nils Wierup
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Peter Almgren
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Per-Anders Jansson
- Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Tina Rönn
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Ola Hansson
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Karl-Fredrik Eriksson
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Leif Groop
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
- Corresponding author: Charlotte Ling,
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Ahmad S, Heraclides A, Sun Q, Elgzyri T, Rönn T, Ling C, Isomaa B, Eriksson KF, Groop L, Franks PW, Hansson O. Telomere length in blood and skeletal muscle in relation to measures of glycaemia and insulinaemia. Diabet Med 2012; 29:e377-81. [PMID: 22747879 PMCID: PMC3698879 DOI: 10.1111/j.1464-5491.2012.03737.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS Skeletal muscle is a major metabolic organ and plays important roles in glucose metabolism, insulin sensitivity and insulin action. Muscle telomere length reflects the myocyte's exposure to harmful environmental factors. Leukocyte telomere length is considered a marker of muscle telomere length and is used in epidemiologic studies to assess associations with ageing-related diseases where muscle physiology is important. However, the extent to which leucocyte and muscle telomere length are correlated is unknown, as are their relative correlations with glucose and insulin concentrations. The purpose of this study was to determine the extent of these relationships. METHODS Leucocyte and muscle telomere length were measured by quantitative real-time polymerase chain reaction in participants from the Malmö Exercise Intervention (n = 27) and the Prevalence, Prediction and Prevention of Diabetes-Botnia studies (n = 31). Participants in both studies were free from Type 2 diabetes. We assessed the association between leucocyte telomere length, muscle telomere length and metabolic traits using Spearmen correlations and multivariate linear regression. Bland-Altman analysis was used to assess agreement between leucocyte and muscle telomere length. RESULTS In age-, study-, diabetes family history- and sex-adjusted models, leucocyte and muscle telomere length were positively correlated (r = 0.39, 95% CI 0.15-0.59). Leucocyte telomere length was inversely associated with 2-h glucose concentrations (r = -0.58, 95% CI -1.0 to -0.16), but there was no correlation between muscle telomere length and 2-h glucose concentrations (r = 0.05, 95% CI -0.35 to 0.46) or between leucocyte or muscle telomere length with other metabolic traits. CONCLUSIONS In summary, the current study supports the use of leucocyte telomere length as a proxy for muscle telomere length in epidemiological studies of Type 2 diabetes aetiology.
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Affiliation(s)
- Shafqat Ahmad
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Center, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Alexandros Heraclides
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Center, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Qi Sun
- Department of Nutrition, Harvard School of Public Health, Boston, MA
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Targ Elgzyri
- Diabetes and Endocrinology Unit, Lund University Diabetes Center, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Tina Rönn
- Epigenetics Unit, Lund University Diabetes Center, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Charlotte Ling
- Epigenetics Unit, Lund University Diabetes Center, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Bo Isomaa
- Folkhälsan Research Center, Östanpävagen 32, 68660 Jakobstad, Finland
- Department of Social Services and Health Care, PB 111, 68601 Jakobstad, Finland
| | - Karl-Fredrik Eriksson
- Diabetes and Endocrinology Unit, Lund University Diabetes Center, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Leif Groop
- Diabetes and Endocrinology Unit, Lund University Diabetes Center, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Paul W. Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Center, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - Ola Hansson
- Diabetes and Endocrinology Unit, Lund University Diabetes Center, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
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Elgzyri T, Parikh H, Zhou Y, Dekker Nitert M, Rönn T, Segerström ÅB, Ling C, Franks PW, Wollmer P, Eriksson KF, Groop L, Hansson O. First-degree relatives of type 2 diabetic patients have reduced expression of genes involved in fatty acid metabolism in skeletal muscle. J Clin Endocrinol Metab 2012; 97:E1332-7. [PMID: 22547424 DOI: 10.1210/jc.2011-3037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
CONTEXT First-degree relatives of patients with type 2 diabetes (FH+) have been shown to have decreased energy expenditure and decreased expression of mitochondrial genes in skeletal muscle. In previous studies, it has been difficult to distinguish whether mitochondrial dysfunction and differential regulation of genes are primary (genetic) or due to reduced physical activity, obesity, or other correlated factors. OBJECTIVE The aim of this study was to investigate whether mitochondrial dysfunction is a primary defect or results from an altered metabolic state. DESIGN We compared gene expression in skeletal muscle from 24 male subjects with FH and 26 without FH matched for age, glucose tolerance, VO(2peak) (peak oxygen uptake), and body mass index using microarrays. Additionally, type fiber composition, mitochondrial DNA content, and citrate synthase activity were measured. The results were followed up in an additional cohort with measurements of in vivo metabolism. RESULTS FH+ vs. FH- subjects showed reduced expression of mitochondrial genes (P = 2.75 × 10(-6)), particularly genes involved in fatty acid metabolism (P = 4.08 × 10(-7)), despite similar mitochondrial DNA content. Strikingly, a 70% reduced expression of the monoamine oxidase A (MAOA) gene was found in FH+ vs. FH- individuals (P = 0.0009). Down-regulation of the genes involved in fat metabolism was associated with decreased in vivo fat oxidation and increased glucose oxidation examined in an additional cohort of elderly men. CONCLUSIONS These results suggest that genetically altered fatty acid metabolism predisposes to type 2 diabetes and propose a role for catecholamine-metabolizing enzymes like MAOA in the regulation of energy metabolism.
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Affiliation(s)
- T Elgzyri
- Department of Clinical Sciences, Clinical Research Center, Malmö University Hospital, Lund University, 20502 Malmö, Sweden
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Olsson AH, Rönn T, Elgzyri T, Hansson O, Eriksson KF, Groop L, Vaag A, Poulsen P, Ling C. The expression of myosin heavy chain (MHC) genes in human skeletal muscle is related to metabolic characteristics involved in the pathogenesis of type 2 diabetes. Mol Genet Metab 2011; 103:275-81. [PMID: 21470888 DOI: 10.1016/j.ymgme.2011.03.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 03/16/2011] [Accepted: 03/16/2011] [Indexed: 01/07/2023]
Abstract
Type 2 diabetes patients exhibit a reduction in oxidative muscle fibres and an increase in glycolytic muscle fibres. In this study, we investigated whether both genetic and non-genetic factors influence the mRNA expression levels of three myosin heavy chain (MHC) genes represented in different fibre types. Specifically, we examined the MHC7 (slow-twitch oxidative fibre), MHCIIa (fast-twitch oxidative fibre) and MHCIIx/d (fast-twitch glycolytic fibre) genes in human skeletal muscle. We further investigated the use of MHC mRNA expression as a proxy to determine fibre-type composition, as measured by traditional ATP staining. Two cohorts of age-matched Swedish men were studied to determine the relationship of muscle mRNA expression of MHC7, MHCIIa, and MHCIIx/d with muscle fibre composition. A classical twin approach, including young and elderly Danish twin pairs, was utilised to examine if differences in expression levels were due to genetic or environmental factors. Although MHCIIx/d mRNA expression correlated positively with the level of type IIx/d muscle fibres in the two cohorts (P<0.05), a relatively low magnitude of correlation suggests that mRNA does not fully correlate with fibre-type composition. Heritability estimates and genetic analysis suggest that the levels of MHC7, MHCIIa and MHCIIx/d expression are primarily under non-genetic influence, and MHCIIa indicated an age-related decline. PGC-1α exhibited a positive relationship with the expression of all three MHC genes (P<0.05); meanwhile, PGC-1β related positively with MHCIIa expression and negatively with MHCIIx/d expression (P<0.05). While MHCIIa expression related positively with insulin-stimulated glucose uptake (P<0.01), MHCIIx/d expression related negatively with insulin-stimulated glucose uptake (P<0.05). Our findings suggest that the expression levels of the MHC genes are associated with age and both PGC-1α and PGC-1β and indicate that the MHC genes may to some extent be used to determine fibre-type composition in human skeletal muscle.
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Affiliation(s)
- Anders H Olsson
- Lund University, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden.
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Olsson AH, Rönn T, Ladenvall C, Parikh H, Isomaa B, Groop L, Ling C. Two common genetic variants near nuclear-encoded OXPHOS genes are associated with insulin secretion in vivo. Eur J Endocrinol 2011; 164:765-71. [PMID: 21325017 PMCID: PMC3080761 DOI: 10.1530/eje-10-0995] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
CONTEXT Mitochondrial ATP production is important in the regulation of glucose-stimulated insulin secretion. Genetic factors may modulate the capacity of the β-cells to secrete insulin and thereby contribute to the risk of type 2 diabetes. OBJECTIVE The aim of this study was to identify genetic loci in or adjacent to nuclear-encoded genes of the oxidative phosphorylation (OXPHOS) pathway that are associated with insulin secretion in vivo. DESIGN AND METHODS To find polymorphisms associated with glucose-stimulated insulin secretion, data from a genome-wide association study (GWAS) of 1467 non-diabetic individuals, including the Diabetes Genetic Initiative (DGI), was examined. A total of 413 single nucleotide polymorphisms with a minor allele frequency ≥0.05 located in or adjacent to 76 OXPHOS genes were included in the DGI GWAS. A more extensive population-based study of 4323 non-diabetics, the PPP-Botnia, was used as a replication cohort. Insulinogenic index during an oral glucose tolerance test was used as a surrogate marker of glucose-stimulated insulin secretion. Multivariate linear regression analyses were used to test genotype-phenotype associations. RESULTS Two common variants were identified in the DGI, where the major C-allele of rs606164, adjacent to NADH dehydrogenase (ubiquinone) 1 subunit C2 (NDUFC2), and the minor G-allele of rs1323070, adjacent to cytochrome c oxidase subunit VIIa polypeptide 2 (COX7A2), showed nominal associations with decreased glucose-stimulated insulin secretion (P=0.0009, respective P=0.003). These associations were replicated in PPP-Botnia (P=0.002 and P=0.05). CONCLUSION Our study shows that genetic variation near genes involved in OXPHOS may influence glucose-stimulated insulin secretion in vivo.
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Affiliation(s)
- Anders H Olsson
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
| | - Tina Rönn
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
| | - Claes Ladenvall
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
| | - Hemang Parikh
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and GeneticsNational Cancer Institute, National Institutes of HealthBethesda, MarylandUSA
| | - Bo Isomaa
- Folkhälsan Research CenterHelsinkiFinland
- Department of Social Services and Health CareJakobstadFinland
| | - Leif Groop
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
| | - Charlotte Ling
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
- (Correspondence should be addressed to C Ling; )
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Koeck T, Olsson AH, Nitert MD, Sharoyko VV, Ladenvall C, Kotova O, Reiling E, Rönn T, Parikh H, Taneera J, Eriksson JG, Metodiev MD, Larsson NG, Balhuizen A, Luthman H, Stančáková A, Kuusisto J, Laakso M, Poulsen P, Vaag A, Groop L, Lyssenko V, Mulder H, Ling C. A common variant in TFB1M is associated with reduced insulin secretion and increased future risk of type 2 diabetes. Cell Metab 2011; 13:80-91. [PMID: 21195351 DOI: 10.1016/j.cmet.2010.12.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 06/12/2010] [Accepted: 11/10/2010] [Indexed: 01/07/2023]
Abstract
Type 2 diabetes (T2D) evolves when insulin secretion fails. Insulin release from the pancreatic β cell is controlled by mitochondrial metabolism, which translates fluctuations in blood glucose into metabolic coupling signals. We identified a common variant (rs950994) in the human transcription factor B1 mitochondrial (TFB1M) gene associated with reduced insulin secretion, elevated postprandial glucose levels, and future risk of T2D. Because islet TFB1M mRNA levels were lower in carriers of the risk allele and correlated with insulin secretion, we examined mice heterozygous for Tfb1m deficiency. These mice displayed lower expression of TFB1M in islets and impaired mitochondrial function and released less insulin in response to glucose in vivo and in vitro. Reducing TFB1M mRNA and protein in clonal β cells by RNA interference impaired complexes of the mitochondrial oxidative phosphorylation system. Consequently, nutrient-stimulated ATP generation was reduced, leading to perturbed insulin secretion. We conclude that a deficiency in TFB1M and impaired mitochondrial function contribute to the pathogenesis of T2D.
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Affiliation(s)
- Thomas Koeck
- Department of Clinical Sciences, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02 Malmö, Sweden
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Brøns C, Jacobsen S, Nilsson E, Rönn T, Jensen CB, Storgaard H, Poulsen P, Groop L, Ling C, Astrup A, Vaag A. Deoxyribonucleic acid methylation and gene expression of PPARGC1A in human muscle is influenced by high-fat overfeeding in a birth-weight-dependent manner. J Clin Endocrinol Metab 2010; 95:3048-56. [PMID: 20410232 DOI: 10.1210/jc.2009-2413] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
CONTEXT Low birth weight (LBW) and unhealthy diets are risk factors of metabolic disease including type 2 diabetes (T2D). Genetic, nongenetic, and epigenetic data propose a role of the key metabolic regulator peroxisome proliferator-activated receptor gamma, coactivator 1alpha (PPARGC1A) in the development of T2D. OBJECTIVE Our objective was to investigate gene expression and DNA methylation of PPARGC1A and coregulated oxidative phosphorylation (OXPHOS) genes in LBW and normal birth weight (NBW) subjects during control and high-fat diets. DESIGN, SUBJECTS, AND MAIN OUTCOME MEASURES: Twenty young healthy men with LBW and 26 matched NBW controls were studied after 5 d high-fat overfeeding (+50% calories) and after a control diet in a randomized manner. Hyperinsulinemic-euglycemic clamps were performed and skeletal muscle biopsies excised. DNA methylation and gene expression were measured using bisulfite sequencing and quantitative real-time PCR, respectively. RESULTS When challenged with high-fat overfeeding, LBW subjects developed peripheral insulin resistance and reduced PPARGC1A and OXPHOS (P < 0.05) gene expression. PPARGC1A methylation was significantly higher in LBW subjects (P = 0.0002) during the control diet. However, PPARGC1A methylation increased in only NBW subjects after overfeeding in a reversible manner. DNA methylation of PPARGC1A did not correlate with mRNA expression. CONCLUSIONS LBW subjects developed peripheral insulin resistance and decreased gene expression of PPARGC1A and OXPHOS genes when challenged with fat overfeeding. The extent to which our finding of a constitutively increased DNA methylation in the PPARGC1A promoter in LBW subjects may contribute needs to be determined. We provide the first experimental support in humans that DNA methylation induced by overfeeding is reversible.
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Affiliation(s)
- Charlotte Brøns
- Steno Diabetes Center, Niels Steensensvej 1, 2820 Gentofte, Denmark.
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Wen J, Rönn T, Olsson A, Yang Z, Lu B, Du Y, Groop L, Ling C, Hu R. Investigation of type 2 diabetes risk alleles support CDKN2A/B, CDKAL1, and TCF7L2 as susceptibility genes in a Han Chinese cohort. PLoS One 2010; 5:e9153. [PMID: 20161779 PMCID: PMC2818850 DOI: 10.1371/journal.pone.0009153] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 10/30/2009] [Indexed: 01/15/2023] Open
Abstract
Background Recent genome-wide association studies (GWASs) have reported several genetic variants to be reproducibly associated with type 2 diabetes. Additional variants have also been detected from a metaanalysis of three GWASs, performed in populations of European ancestry. In the present study, we evaluated the influence of 17 genetic variants from 15 candidate loci, identified in type 2 diabetes GWASs and the metaanalysis, in a Han Chinese cohort. Methodology/Principal Findings Selected type 2 diabetes–associated genetic variants were genotyped in 1,165 type 2 diabetic patients and 1,136 normoglycemic control individuals of Southern Han Chinese ancestry. The OR for risk of developing type 2 diabetes was calculated using a logistic regression model adjusted for age, sex, and BMI. Genotype-phenotype associations were tested using a multivariate linear regression model. Genetic variants in CDKN2A/B, CDKAL1, TCF7L2, TCF2, MC4R, and PPARG showed a nominal association with type 2 diabetes (P≤0.05), of whom the three first would stand correction for multiple testing: CDKN2A/B rs10811661, OR: 1.26 (1.12–1.43) P = 1.8*10−4; CDKAL1 rs10946398, OR: 1.23 (1.09–1.39); P = 7.1*10−4, and TCF7L2 rs7903146, OR: 1.61 (1.19–2.18) P = 2.3 * 10−3. Only nominal phenotype associations were observed, notably for rs8050136 in FTO and fasting plasma glucose (P = 0.002), postprandial plasma glucose (P = 0.002), and fasting C-peptide levels (P = 0.006) in the diabetic patients, and with BMI in controls (P = 0.033). Conclusions/Significance We have identified significant association between variants in CDKN2A/B, CDKAL1 and TCF7L2, and type 2 diabetes in a Han Chinese cohort, indicating these genes as strong candidates conferring susceptibility to type 2 diabetes across different ethnicities.
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Affiliation(s)
- Jie Wen
- Department of Endocrinology, Shanghai Medical College Fudan University, Shanghai, China
| | - Tina Rönn
- Department of Clinical Sciences, Lund University Diabetes Center, Malmö, Sweden
| | - Anders Olsson
- Department of Clinical Sciences, Lund University Diabetes Center, Malmö, Sweden
| | - Zhen Yang
- Department of Endocrinology, Shanghai Medical College Fudan University, Shanghai, China
| | - Bin Lu
- Department of Endocrinology, Shanghai Medical College Fudan University, Shanghai, China
| | - Yieping Du
- Department of Endocrinology, Shanghai Medical College Fudan University, Shanghai, China
| | - Leif Groop
- Department of Clinical Sciences, Lund University Diabetes Center, Malmö, Sweden
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University Diabetes Center, Malmö, Sweden
| | - Renming Hu
- Department of Endocrinology, Shanghai Medical College Fudan University, Shanghai, China
- * E-mail:
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Osmark P, Hansson O, Jonsson A, Rönn T, Groop L, Renström E. Unique splicing pattern of the TCF7L2 gene in human pancreatic islets. Diabetologia 2009; 52:850-4. [PMID: 19247628 DOI: 10.1007/s00125-009-1293-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 01/22/2009] [Indexed: 12/01/2022]
Abstract
AIMS/HYPOTHESIS Intronic variation in the TCF7L2 gene exhibits the strongest association to type 2 diabetes observed to date, but the mechanism whereby this genetic variation translates into altered biological function is largely unknown. A possible explanation is a genotype-dependent difference in the complex splicing pattern; however, this has not previously been characterised in pancreatic or insulin target tissues. Here, the detailed TCF7L2 splicing pattern in five human tissues is described and dependence on risk genotype explored. METHODS RT-PCR and quantitative real-time PCR were employed to characterise TCF7L2 splicing in pancreatic islets, blood lymphocytes, skeletal muscle and subcutaneous and visceral adipose tissue from non-diabetic individuals. RESULTS The mapping of TCF7L2 splice variants shows a specific pattern in pancreatic islets, with four predominant transcripts and high usage of the variable exons 4 and 15. The overall concentration of TCF7L2 mRNA is highest in islets and fat and lower in blood and muscle. No significant difference in overall amount or splicing pattern was observed between carriers and non-carriers of the rs7903146 risk (T) allele. However, incorporation of exon 4 in islets correlates positively with plasma HbA(1c) levels (r = 0.758; p = 0.018). CONCLUSIONS/INTERPRETATION There were pronounced tissue-specific differences in the splicing of TCF7L2 with forms containing exon 4 and 15 being most abundant in islets. The incorporation of exon 4 in islets correlated with HbA(1c) levels. Further experiments will be needed to determine the direction of this correlation, and larger cohorts needed to unequivocally resolve whether there is a relationship between genotype and splicing in islets.
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Affiliation(s)
- P Osmark
- Department of Clinical Sciences, CRC Malmö University Hospital, Lund University, Malmö, Sweden
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Rönn T, Wen J, Yang Z, Lu B, Du Y, Groop L, Hu R, Ling C. A common variant in MTNR1B, encoding melatonin receptor 1B, is associated with type 2 diabetes and fasting plasma glucose in Han Chinese individuals. Diabetologia 2009; 52:830-3. [PMID: 19241057 DOI: 10.1007/s00125-009-1297-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 02/05/2009] [Indexed: 12/28/2022]
Abstract
AIMS/HYPOTHESIS Recently, three groups independently reported that variation in MTNR1B, the gene encoding melatonin receptor 1B, was associated with an increased risk of type 2 diabetes, increased fasting plasma glucose and impaired insulin secretion in populations of European ancestry. In the present study, we investigated whether a single MTNR1B polymorphism was associated with type 2 diabetes in Han Chinese individuals, to elucidate whether this is a cross-populational effect. METHODS The MTNR1B variant rs10830963 was genotyped in 1,165 type 2 diabetic patients and 1,105 normoglycaemic control individuals of southern Han Chinese ancestry who were residents of the metropolitan area of Shanghai. The risk of developing type 2 diabetes was calculated using a logistic regression model adjusted for age, sex and BMI. A possible association with fasting plasma glucose was analysed in the normoglycaemic control individuals using a multiple linear regression analysis with adjustments for age, sex and BMI. RESULTS The genetic variant rs10830963 was associated with an increased risk of type 2 diabetes in our Han Chinese cohort (OR 1.16, 95% CI 1.03-1.31, p = 0.015). As previously described, the risk variant was also associated with increased fasting plasma glucose, showing an increase of 0.068 mmol/l (95% CI 0.036-0.100, p = 4 x 10(-5)) per risk allele. CONCLUSIONS/INTERPRETATION A common variant in the MTNR1B gene is associated with an increased risk of type 2 diabetes and increased fasting plasma glucose in Han Chinese, suggesting an important role for this polymorphism in populations of different ethnic and environmental backgrounds.
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Affiliation(s)
- T Rönn
- Department of Clinical Sciences, CRC Malmö University Hospital, Lund University Diabetes Center, Malmö, Sweden
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Rönn T, Poulsen P, Tuomi T, Isomaa B, Groop L, Vaag A, Ling C. Genetic variation in ATP5O is associated with skeletal muscle ATP50 mRNA expression and glucose uptake in young twins. PLoS One 2009; 4:e4793. [PMID: 19274082 PMCID: PMC2651471 DOI: 10.1371/journal.pone.0004793] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2008] [Accepted: 01/22/2009] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Impaired oxidative capacity of skeletal muscle mitochondria contribute to insulin resistance and type 2 diabetes (T2D). Furthermore, mRNA expression of genes involved in oxidative phosphorylation, including ATP5O, is reduced in skeletal muscle from T2D patients. Our aims were to investigate mechanisms regulating ATP5O expression in skeletal muscle and association with glucose metabolism, and the relationship between ATP5O single nucleotide polymorphisms (SNPs) and risk of T2D. METHODOLOGY/PRINCIPAL FINDINGS ATP5O mRNA expression was analyzed in skeletal muscle from young (n = 86) and elderly (n = 68) non-diabetic twins before and after a hyperinsulinemic euglycemic clamp. 11 SNPs from the ATP5O locus were genotyped in the twins and a T2D case-control cohort (n = 1466). DNA methylation of the ATP5O promoter was analyzed in twins (n = 22) using bisulfite sequencing. The mRNA level of ATP5O in skeletal muscle was reduced in elderly compared with young twins, both during basal and insulin-stimulated conditions (p<0.0005). The degree of DNA methylation around the transcription start of ATP5O was <1% in both young and elderly twins and not associated with mRNA expression (p = 0.32). The mRNA level of ATP5O in skeletal muscle was positively related to insulin-stimulated glucose uptake (regression coefficient = 6.6; p = 0.02). Furthermore, two SNPs were associated with both ATP5O mRNA expression (rs12482697: T/T versus T/G; p = 0.02 and rs11088262: A/A versus A/G; p = 0.004) and glucose uptake (rs11088262: A/A versus A/G; p = 0.002 and rs12482697: T/T versus T/G; p = 0.005) in the young twins. However, we could not detect any genetic association with T2D. CONCLUSIONS/SIGNIFICANCE Genetic variation and age are associated with skeletal muscle ATP5O mRNA expression and glucose disposal rate, suggesting that combinations of genetic and non-genetic factors may cause the reduced expression of ATP5O in T2D muscle. These findings propose a role for ATP5O, in cooperation with other OXPHOS genes, in the regulation of in vivo glucose metabolism.
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Affiliation(s)
- Tina Rönn
- Department of Clinical Sciences, Diabetes and Endocrinology Research Unit, CRC Malmö University Hospital, Lund University, Malmö, Sweden.
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Rönn T, Poulsen P, Hansson O, Holmkvist J, Almgren P, Nilsson P, Tuomi T, Isomaa B, Groop L, Vaag A, Ling C. Age influences DNA methylation and gene expression of COX7A1 in human skeletal muscle. Diabetologia 2008; 51:1159-68. [PMID: 18488190 DOI: 10.1007/s00125-008-1018-8] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 03/27/2008] [Indexed: 12/15/2022]
Abstract
AIMS/HYPOTHESIS Reduced oxidative capacity of the mitochondria in skeletal muscle has been suggested to contribute to insulin resistance and type 2 diabetes. Moreover, a set of genes influencing oxidative phosphorylation (OXPHOS) is downregulated in diabetic muscle. Here we studied whether genetic, epigenetic and non-genetic factors influence a component of the respiratory chain, COX7A1, previously shown to be downregulated in skeletal muscle from patients with type 2 diabetes. The specific aims were to: (1) evaluate the impact of genetic (single nucleotide polymorphisms [SNPs]), epigenetic (DNA methylation) and non-genetic (age) factors on the expression of COX7A1 in human skeletal muscle; and (2) investigate whether common variants in the COX7A1 gene are associated with increased risk of type 2 diabetes. METHODS COX7A1 mRNA expression was analysed in muscle biopsies from young (n = 110) and elderly (n = 86) non-diabetic twins and related to measures of in vivo metabolism. Genetic variants (three SNPs) from the COX7A1 locus were genotyped in the twins and in two independent type 2 diabetes case-control cohorts (n = 1466 and 6380, respectively). DNA methylation of the COX7A1 promoter was analysed in a subset of twins (ten young, ten elderly) using bisulphite sequencing. RESULTS While DNA methylation of the COX7A1 promoter was increased in muscle from elderly compared with young twins (19.9 +/- 8.3% vs 1.8 +/- 2.7%; p = 0.035), the opposite was found for COX7A1 mRNA expression (elderly 1.00 +/- 0.05 vs young 1.68 +/- 0.06; p = 0.0005). The heritability of COX7A1 expression was estimated to be 50% in young and 72% in elderly twins. One of the polymorphisms investigated, rs753420, influenced basal COX7A1 expression in muscle of young (p = 0.0001) but not of elderly twins. The transcript level of COX7A1 was associated with increased in vivo glucose uptake and VO(2max) (p = 0.009 and p = 0.001, respectively). We did not observe any genetic association between COX7A1 polymorphisms and type 2 diabetes after correcting for multiple testing. CONCLUSIONS/INTERPRETATION Our results provide further evidence for age as a factor influencing DNA methylation and expression of OXPHOS genes, and thereby in vivo metabolism.
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Affiliation(s)
- T Rönn
- Department of Clinical Sciences, CRC Malmö University Hospital, Lund University, 205 02, Malmö, Sweden
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Ling C, Poulsen P, Simonsson S, Rönn T, Holmkvist J, Almgren P, Hagert P, Nilsson E, Mabey AG, Nilsson P, Vaag A, Groop L. Genetic and epigenetic factors are associated with expression of respiratory chain component NDUFB6 in human skeletal muscle. J Clin Invest 2008; 117:3427-35. [PMID: 17948130 DOI: 10.1172/jci30938] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 07/20/2007] [Indexed: 12/19/2022] Open
Abstract
Insulin resistance and type 2 diabetes are associated with decreased expression of genes that regulate oxidative phosphorylation in skeletal muscle. To determine whether this defect might be inherited or acquired, we investigated the association of genetic, epigenetic, and nongenetic factors with expression of NDUFB6, a component of the respiratory chain that is decreased in muscle from diabetic patients. Expression of NDUFB6 was influenced by age, with lower gene expression in muscle of elderly subjects. Heritability of NDUFB6 expression in muscle was estimated to be approximately 60% in twins. A polymorphism in the NDUFB6 promoter region that creates a possible DNA methylation site (rs629566, A/G) was associated with a decline in muscle NDUFB6 expression with age. Although young subjects with the rs629566 G/G genotype exhibited higher muscle NDUFB6 expression, this genotype was associated with reduced expression in elderly subjects. This was subsequently explained by the finding of increased DNA methylation in the promoter of elderly, but not young, subjects carrying the rs629566 G/G genotype. Furthermore, the degree of DNA methylation correlated negatively with muscle NDUFB6 expression, which in turn was associated with insulin sensitivity. Our results demonstrate that genetic, epigenetic, and nongenetic factors associate with NDUFB6 expression in human muscle and suggest that genetic and epigenetic factors may interact to increase age-dependent susceptibility to insulin resistance.
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Affiliation(s)
- Charlotte Ling
- Department of Clinical Sciences, Lund University, University Hospital MAS, Malmö, Sweden.
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Ling C, Del Guerra S, Lupi R, Rönn T, Granhall C, Luthman H, Masiello P, Marchetti P, Groop L, Del Prato S. Epigenetic regulation of PPARGC1A in human type 2 diabetic islets and effect on insulin secretion. Diabetologia 2008; 51:615-22. [PMID: 18270681 PMCID: PMC2270364 DOI: 10.1007/s00125-007-0916-5] [Citation(s) in RCA: 317] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 12/10/2007] [Indexed: 12/15/2022]
Abstract
AIMS/HYPOTHESIS Insulin secretion in pancreatic islets is dependent upon mitochondrial function and production of ATP. The transcriptional coactivator peroxisome proliferator activated receptor gamma coactivator-1 alpha (protein PGC-1alpha; gene PPARGC1A) is a master regulator of mitochondrial genes and its expression is decreased and related to impaired oxidative phosphorylation in muscle from patients with type 2 diabetes. Whether it plays a similar role in human pancreatic islets is not known. We therefore investigated if PPARGC1A expression is altered in islets from patients with type 2 diabetes and whether this expression is influenced by genetic (PPARGC1A Gly482Ser polymorphism) and epigenetic (DNA methylation) factors. We also tested if experimental downregulation of PPARGC1A expression in human islets influenced insulin secretion. METHODS The PPARGC1A Gly482Ser polymorphism was genotyped in human pancreatic islets from 48 non-diabetic and 12 type 2 diabetic multi-organ donors and related to PPARGC1A mRNA expression. DNA methylation of the PPARGC1A promoter was analysed in pancreatic islets from ten type 2 diabetic and nine control donors. Isolated human islets were transfected with PPARGC1A silencing RNA (siRNA). RESULTS PPARGC1A mRNA expression was reduced by 90% (p<0.005) and correlated with the reduction in insulin secretion in islets from patients with type 2 diabetes. After downregulation of PPARGC1A expression in human islets by siRNA, insulin secretion was reduced by 41% (p <or= 0. 01). We were able to ascribe reduced PPARGC1A expression in islets to both genetic and epigenetic factors, i.e. a common PPARGC1A Gly482Ser polymorphism was associated with reduced PPARGC1A mRNA expression (p<0.00005) and reduced insulin secretion (p<0.05). In support of an epigenetic influence, the PPARGC1A gene promoter showed a twofold increase in DNA methylation in diabetic islets compared with non-diabetic islets (p<0.04). CONCLUSIONS/INTERPRETATION We have shown for the first time that PPARGC1A might be important in human islet insulin secretion and that expression of PPARGC1A in human islets can be regulated by both genetic and epigenetic factors.
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Affiliation(s)
- C Ling
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, CRC, 205 02 Malmö, Sweden.
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