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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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García-Calzón S, Schrader S, Perfilyev A, Martinell M, Ahlqvist E, Ling C. DNA methylation partially mediates antidiabetic effects of metformin on HbA1c levels in individuals with type 2 diabetes. Diabetes Res Clin Pract 2023:110807. [PMID: 37356726 DOI: 10.1016/j.diabres.2023.110807] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
AIMS Despite metformin being used as first-line pharmacological therapy for type 2 diabetes, its underlying mechanisms remain unclear. We aimed to determine whether metformin altered DNA methylation in newly-diagnosed individuals with type 2 diabetes. METHODS AND RESULTS We found that metformin therapy is associated with altered methylation of 26 sites in blood from Scandinavian discovery and replication cohorts (FDR<0.05), using MethylationEPIC arrays. The majority (88%) of these 26 sites were hypermethylated in patients taking metformin for ∼3 months compared to controls, who had diabetes but had not taken any diabetes medication. Two of these blood-based methylation markers mirrored the epigenetic pattern in muscle and adipose tissue (FDR<0.05). Four type 2 diabetes-associated SNPs were annotated to genes with differential methylation between metformin cases and controls, e.g., GRB10, RPTOR, SLC22A18AS and TH2LCRR. Methylation correlated with expression in human islets for two of these genes. Three metformin-associated methylation sites (PKNOX2, WDTC1 and MICB) partially mediate effects of metformin on follow-up HbA1c levels. When combining methylation of these three sites into a score, which was used in a causal mediation analysis, methylation was suggested to mediate up to 32% of metformin's effects on HbA1c. CONCLUSION Metformin-associated alterations in DNA methylation partially mediates metformin's antidiabetic effects on HbA1c in newly-diagnosed individuals with type 2 diabetes.
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Affiliation(s)
- Sonia García-Calzón
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, 205 02 Malmö, Sweden; Department of Food Sciences and Physiology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain.
| | - Silja Schrader
- 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
| | - Mats Martinell
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Emma Ahlqvist
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - 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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3
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Jönsson J, Renault KM, Perfilyev A, Vaag A, Carlsen EM, Nørgaard K, Franks PW, Ling C. Gestational weight gain in pregnant women with obesity is associated with cord blood DNA methylation, which partially mediates offspring anthropometrics. Clin Transl Med 2023; 13:e1215. [PMID: 36929108 PMCID: PMC10019770 DOI: 10.1002/ctm2.1215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Affiliation(s)
- Josefine Jönsson
- Department of Clinical SciencesEpigenetics and Diabetes UnitLund University Diabetes CentreScania University HospitalLund UniversityMalmöSweden
| | - Kristina M. Renault
- Department of Obstetrics and GynecologyHvidovre HospitalUniversity of CopenhagenCopenhagenDenmark
- Department of ObstetricsJuliane Marie CentretRigshospitaletUniversity of CopenhagenCopenhagenDenmark
| | - Alexander Perfilyev
- Department of Clinical SciencesEpigenetics and Diabetes UnitLund University Diabetes CentreScania University HospitalLund UniversityMalmöSweden
| | - Allan Vaag
- Steno Diabetes Center CopenhagenGentofteDenmark
| | - Emma Malchau Carlsen
- Department of NutritionExercise and SportsFaculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
- Department of PediatricsCopenhagen University Hospital HvidovreHvidovreDenmark
| | | | - Paul W. Franks
- Department of Clinical SciencesGenetic and Molecular Epidemiology UnitLund University Diabetes CentreLund UniversityMalmöSweden
| | - Charlotte Ling
- Department of Clinical SciencesEpigenetics and Diabetes UnitLund University Diabetes CentreScania University HospitalLund UniversityMalmöSweden
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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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Sehgal R, Perfilyev A, Männistö V, Ågren J, Nilsson E, Käkelä P, Ling C, de Mello VD, Pihlajamäki J. Liver saturated fat content associates with hepatic DNA methylation in obese individuals. Clin Epigenetics 2023; 15:21. [PMID: 36765383 PMCID: PMC9921201 DOI: 10.1186/s13148-023-01431-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 03/14/2022] [Accepted: 01/19/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Accumulation of saturated fatty acids (SFAs) in the liver is known to induce hepatic steatosis and inflammation causing non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH). Although SFAs have been shown to affect the epigenome in whole blood, pancreatic islets, and adipose tissue in humans, and genome-wide DNA methylation studies have linked epigenetic changes to NAFLD and NASH, studies focusing on the association of SFAs and DNA methylation in human liver are missing. We, therefore, investigated whether human liver SFA content associates with DNA methylation and tested if SFA-linked alterations in DNA methylation associate with NAFLD-related clinical phenotypes in obese individuals. RESULTS We identified DNA methylation (Infinium HumanMethylation450 BeadChip) of 3169 CpGs to be associated with liver total SFA content (q-value < 0.05) measured using proton NMR spectroscopy in participants of the Kuopio Obesity Surgery Study (n = 51; mean ± SD:49.3 ± 8.5 years old; BMI:43.7 ± 6.2 kg/m2). Of these 3169 sites, 797 overlapped with previously published NASH-associated CpGs (NASH-SFA), while 2372 CpGs were exclusively associated with SFA (Only-SFA). The corresponding annotated genes of these only-SFA CpGs were found to be enriched in pathways linked to satiety and hunger. Among the 54 genes mapping to these enriched pathways, DNA methylation of CpGs mapping to PRKCA and TSPO correlated with their own mRNA expression (HumanHT-12 Expression BeadChip). In addition, DNA methylation of another ten of these CpGs correlated with the mRNA expression of their neighboring genes (p value < 0.05). The proportion of CpGs demonstrating a correlation of DNA methylation with plasma glucose was higher in NASH-SFA and only-SFA groups, while the proportion of significant correlations with plasma insulin was higher in only-NASH and NASH-SFA groups as compared to all CpGs on the Illumina 450 K array (Illumina, San Diego, CA, USA). CONCLUSIONS Our results suggest that one of the mechanisms how SFA could contribute to metabolic dysregulation in NAFLD is at the level of DNA methylation. We further propose that liver SFA-related DNA methylation profile may contribute more to hyperglycemia, while insulin-related methylation profile is more linked to NAFLD or NASH. Further research is needed to elucidate the molecular mechanisms behind these observations.
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Affiliation(s)
- Ratika Sehgal
- grid.9668.10000 0001 0726 2490Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Alexander Perfilyev
- grid.411843.b0000 0004 0623 9987Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Ville Männistö
- grid.9668.10000 0001 0726 2490Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Jyrki Ågren
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Emma Nilsson
- grid.411843.b0000 0004 0623 9987Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Pirjo Käkelä
- grid.9668.10000 0001 0726 2490Department of Surgery, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Charlotte Ling
- grid.411843.b0000 0004 0623 9987Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Vanessa D. de Mello
- grid.9668.10000 0001 0726 2490Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Jussi Pihlajamäki
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland. .,Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland.
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6
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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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Schrader S, Perfilyev A, Ahlqvist E, Groop L, Vaag A, Martinell M, García-Calzón S, Ling C. Novel Subgroups of Type 2 Diabetes Display Different Epigenetic Patterns That Associate With Future Diabetic Complications. Diabetes Care 2022; 45:1621-1630. [PMID: 35607770 PMCID: PMC9274219 DOI: 10.2337/dc21-2489] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 11/30/2021] [Accepted: 04/05/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Type 2 diabetes (T2D) was recently reclassified into severe insulin-deficient diabetes (SIDD), severe insulin-resistant diabetes (SIRD), mild obesity-related diabetes (MOD), and mild age-related diabetes (MARD), which have different risk of complications. We explored whether DNA methylation differs between these subgroups and whether subgroup-unique methylation risk scores (MRSs) predict diabetic complications. RESEARCH DESIGN AND METHODS Genome-wide DNA methylation was analyzed in blood from subjects with newly diagnosed T2D in discovery and replication cohorts. Subgroup-unique MRSs were built, including top subgroup-unique DNA methylation sites. Regression models examined whether MRSs associated with subgroups and future complications. RESULTS We found epigenetic differences between the T2D subgroups. Subgroup-unique MRSs were significantly different in those patients allocated to each respective subgroup compared with the combined group of all other subgroups. These associations were validated in an independent replication cohort, showing that subgroup-unique MRSs associate with individual subgroups (odds ratios 1.6-6.1 per 1-SD increase, P < 0.01). Subgroup-unique MRSs were also associated with future complications. Higher MOD-MRS was associated with lower risk of cardiovascular (hazard ratio [HR] 0.65, P = 0.001) and renal (HR 0.50, P < 0.001) disease, whereas higher SIRD-MRS and MARD-MRS were associated with an increased risk of these complications (HR 1.4-1.9 per 1-SD increase, P < 0.01). Of 95 methylation sites included in subgroup-unique MRSs, 39 were annotated to genes previously linked to diabetes-related traits, including TXNIP and ELOVL2. Methylation in the blood of 18 subgroup-unique sites mirrors epigenetic patterns in tissues relevant for T2D, muscle and adipose tissue. CONCLUSIONS We identified differential epigenetic patterns between T2D subgroups that associated with future diabetic complications. These data support a reclassification of diabetes and the need for precision medicine in T2D subgroups.
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Affiliation(s)
- Silja Schrader
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Emma Ahlqvist
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Leif Groop
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Allan Vaag
- Type 2 Diabetes Biology Research, Steno Diabetes Center, Copenhagen, Denmark
| | - Mats Martinell
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden.,Academic Primary Care Centre, Uppsala, Sweden
| | - Sonia García-Calzón
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden.,Department of Food Science and Physiology, University of Navarra, Pamplona, Spain
| | - 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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8
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dos Santos C, Karagiannopoulos A, Rafacho A, Perfilyev A, Eliasson L, Ling C, Bacos K. Glucocorticoids and glucolipotoxicity alter the DNA methylome and function of human EndoC-βH1 cells. Life Sci 2022; 307:120854. [DOI: 10.1016/j.lfs.2022.120854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 10/16/2022]
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9
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Nilsson E, Vavakova M, Perfilyev A, Säll J, Jansson PA, Poulsen P, Esguerra JLS, Eliasson L, Vaag A, Göransson O, Ling C. Differential DNA Methylation and Expression of miRNAs in Adipose Tissue From Twin Pairs Discordant for Type 2 Diabetes. Diabetes 2021; 70:2402-2418. [PMID: 34315727 DOI: 10.2337/db20-0324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/03/2020] [Accepted: 07/21/2021] [Indexed: 11/13/2022]
Abstract
The prevalence of type 2 diabetes (T2D) is increasing worldwide, but current treatments have limitations. miRNAs may play a key role in the development of T2D and can be targets for novel therapies. Here, we examined whether T2D is associated with altered expression and DNA methylation of miRNAs using adipose tissue from 14 monozygotic twin pairs discordant for T2D. Four members each of the miR-30 and let-7-families were downregulated in adipose tissue of subjects with T2D versus control subjects, which was confirmed in an independent T2D case-control cohort. Further, DNA methylation of five CpG sites annotated to gene promoters of differentially expressed miRNAs, including miR-30a and let-7a-3, was increased in T2D versus control subjects. Luciferase experiments showed that increased DNA methylation of the miR-30a promoter reduced its transcription in vitro. Silencing of miR-30 in adipocytes resulted in reduced glucose uptake and TBC1D4 phosphorylation; downregulation of genes involved in demethylation and carbohydrate/lipid/amino acid metabolism; and upregulation of immune system genes. In conclusion, T2D is associated with differential DNA methylation and expression of miRNAs in adipose tissue. Downregulation of the miR-30 family may lead to reduced glucose uptake and altered expression of key genes associated with T2D.
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MESH Headings
- 3T3-L1 Cells
- Adipose Tissue/metabolism
- Adipose Tissue/pathology
- Aged
- Animals
- Arrhythmias, Cardiac/genetics
- Arrhythmias, Cardiac/pathology
- Case-Control Studies
- Cells, Cultured
- Cohort Studies
- DNA Methylation
- Denmark
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Diseases in Twins/genetics
- Female
- Gene Expression
- Genetic Diseases, X-Linked/genetics
- Genetic Diseases, X-Linked/pathology
- Gigantism/genetics
- Gigantism/pathology
- Heart Defects, Congenital/genetics
- Heart Defects, Congenital/pathology
- Humans
- Intellectual Disability/genetics
- Intellectual Disability/pathology
- Male
- Mice
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Middle Aged
- Sweden
- Twins, Monozygotic/genetics
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Affiliation(s)
- Emma Nilsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Magdalena Vavakova
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
- Diabetes, Metabolism and Endocrinology, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Johanna Säll
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Per-Anders Jansson
- Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Jonathan Lou S Esguerra
- Islet Cell Exocytosis Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Lena Eliasson
- Islet Cell Exocytosis Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Allan Vaag
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Olga Göransson
- Diabetes, Metabolism and Endocrinology, Department of Experimental Medical Science, Lund University, Lund, 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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10
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Schrader S, Perfilyev A, Martinell M, García-Calzón S, Ling C. Statin therapy is associated with epigenetic modifications in individuals with Type 2 diabetes. Epigenomics 2021; 13:919-925. [PMID: 33947200 DOI: 10.2217/epi-2020-0442] [Citation(s) in RCA: 4] [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] [Indexed: 11/21/2022] Open
Abstract
Aim: Statins lower cholesterol and reduce the risk of cardiovascular disease. However, the exact mechanisms of statins remain unknown. We investigated whether statin therapy associates with epigenetics in Type 2 diabetes (T2D) patients. Materials & methods: DNA methylation was analyzed in blood from newly diagnosed T2D patients in All New Diabetics in Scania (ANDIS) and a replication cohort All New Diabetics in Uppsala County (ANDiU). Results: Seventy-nine sites were differentially methylated between cases on statins and controls (false discovery rate <5%) in ANDIS. These include previously statin-associated methylation sites annotated to DHCR24 (cg17901584), ABCG1 (cg27243685) and SC4MOL (cg05119988). Differential methylation of two sites related to cholesterol biosynthesis and immune response, cg17901584 (DHCR24) and cg23011663 (ARIH2), were replicated in ANDiU. Conclusion: Statin therapy associates with epigenetic modifications in T2D patients.
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Affiliation(s)
- Silja Schrader
- Department of Clinical Sciences, Epigenetics & Diabetes Unit, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö 205 02, Sweden
| | - Alexander Perfilyev
- Department of Clinical Sciences, Epigenetics & Diabetes Unit, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö 205 02, Sweden
| | - Mats Martinell
- Department of Public Health & Caring Sciences, Uppsala University, Uppsala 75122, Sweden
| | - Sonia García-Calzón
- Department of Clinical Sciences, Epigenetics & Diabetes Unit, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö 205 02, Sweden.,Department of Nutrition, Food Sciences & Physiology, University of Navarra, Pamplona 31008, Spain
| | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics & Diabetes Unit, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö 205 02, Sweden
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11
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Davegårdh C, Säll J, Benrick A, Broholm C, Volkov P, Perfilyev A, Henriksen TI, Wu Y, Hjort L, Brøns C, Hansson O, Pedersen M, Würthner JU, Pfeffer K, Nilsson E, Vaag A, Stener-Victorin E, Pircs K, Scheele C, Ling C. VPS39-deficiency observed in type 2 diabetes impairs muscle stem cell differentiation via altered autophagy and epigenetics. Nat Commun 2021; 12:2431. [PMID: 33893273 PMCID: PMC8065135 DOI: 10.1038/s41467-021-22068-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/25/2021] [Indexed: 02/02/2023] Open
Abstract
Insulin resistance and lower muscle quality (strength divided by mass) are hallmarks of type 2 diabetes (T2D). Here, we explore whether alterations in muscle stem cells (myoblasts) from individuals with T2D contribute to these phenotypes. We identify VPS39 as an important regulator of myoblast differentiation and muscle glucose uptake, and VPS39 is downregulated in myoblasts and myotubes from individuals with T2D. We discover a pathway connecting VPS39-deficiency in human myoblasts to impaired autophagy, abnormal epigenetic reprogramming, dysregulation of myogenic regulators, and perturbed differentiation. VPS39 knockdown in human myoblasts has profound effects on autophagic flux, insulin signaling, epigenetic enzymes, DNA methylation and expression of myogenic regulators, and gene sets related to the cell cycle, muscle structure and apoptosis. These data mimic what is observed in myoblasts from individuals with T2D. Furthermore, the muscle of Vps39+/- mice display reduced glucose uptake and altered expression of genes regulating autophagy, epigenetic programming, and myogenesis. Overall, VPS39-deficiency contributes to impaired muscle differentiation and reduced glucose uptake. VPS39 thereby offers a therapeutic target for T2D.
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Affiliation(s)
- Cajsa Davegårdh
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Johanna Säll
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Anna Benrick
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- School of Health Sciences, University of Skövde, Skövde, Sweden
| | - Christa Broholm
- Diabetes and Bone-metabolic Research Unit, Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Tora Ida Henriksen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Yanling Wu
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Line Hjort
- Diabetes and Bone-metabolic Research Unit, Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
- Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
| | - Charlotte Brøns
- Diabetes and Bone-metabolic Research Unit, Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Ola Hansson
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden
- Finnish Institute of Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - Maria Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Emma Nilsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Allan Vaag
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | | | - Karolina Pircs
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Camilla Scheele
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center 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, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden.
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12
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de Mello VD, Sehgal R, Männistö V, Klåvus A, Nilsson E, Perfilyev A, Kaminska D, Miao Z, Pajukanta P, Ling C, Hanhineva K, Pihlajamäki J. Serum aromatic and branched-chain amino acids associated with NASH demonstrate divergent associations with serum lipids. Liver Int 2021; 41:754-763. [PMID: 33219609 PMCID: PMC8048463 DOI: 10.1111/liv.14743] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 06/17/2020] [Revised: 11/04/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Non-alcoholic fatty liver disease (NAFLD) has been associated with multiple metabolic abnormalities. By applying a non-targeted metabolomics approach, we aimed at investigating whether serum metabolite profile that associates with NAFLD would differ in its association with NAFLD-related metabolic risk factors. METHODS & RESULTS A total of 233 subjects (mean ± SD: 48.3 ± 9.3 years old; BMI: 43.1 ± 5.4 kg/m2 ; 64 male) undergoing bariatric surgery were studied. Of these participants, 164 with liver histology could be classified as normal liver (n = 79), simple steatosis (SS, n = 40) or non-alcoholic steatohepatitis (NASH, n = 45). Among the identified fasting serum metabolites with higher levels in those with NASH when compared to those with normal phenotype were the aromatic amino acids (AAAs: tryptophan, tyrosine and phenylalanine), the branched-chain amino acids (BCAAs: leucine and isoleucine), a phosphatidylcholine (PC(16:0/16:1)) and uridine (all FDRp < 0.05). Only tryptophan was significantly higher in those with NASH compared to those with SS (FDRp < 0.05). Only the AAAs tryptophan and tyrosine correlated positively with serum total and LDL cholesterol (FDRp < 0.1), and accordingly, with liver LDLR at mRNA expression level. In addition, tryptophan was the single AA associated with liver DNA methylation of CpG sites known to be differentially methylated in those with NASH. CONCLUSIONS We found that serum levels of the NASH-related AAAs and BCAAs demonstrate divergent associations with serum lipids. The specific correlation of tryptophan with LDL-c may result from the molecular events affecting LDLR mRNA expression and NASH-associated methylation of genes in the liver.
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Affiliation(s)
- Vanessa D. de Mello
- Institute of Public Health and Clinical NutritionDepartment of Clinical NutritionUniversity of Eastern FinlandKuopioFinland
| | - Ratika Sehgal
- Institute of Public Health and Clinical NutritionDepartment of Clinical NutritionUniversity of Eastern FinlandKuopioFinland
| | - Ville Männistö
- Department of MedicineUniversity of Eastern Finland and Kuopio University HospitalKuopioFinland
| | - Anton Klåvus
- Institute of Public Health and Clinical NutritionDepartment of Clinical NutritionUniversity of Eastern FinlandKuopioFinland
| | - Emma Nilsson
- Epigenetics and Diabetes UnitDepartment of Clinical SciencesLund University Diabetes CentreMalmöSweden
| | - Alexander Perfilyev
- Epigenetics and Diabetes UnitDepartment of Clinical SciencesLund University Diabetes CentreMalmöSweden
| | - Dorota Kaminska
- Institute of Public Health and Clinical NutritionDepartment of Clinical NutritionUniversity of Eastern FinlandKuopioFinland
| | - Zong Miao
- Department of Human GeneticsDavid Geffen School of Medicine at University of California Los Angeles (UCLA)Los AngelesCAUSA
| | - Päivi Pajukanta
- Department of Human GeneticsDavid Geffen School of Medicine at University of California Los Angeles (UCLA)Los AngelesCAUSA,Institute for Precision HealthSchool of MedicineUCLALos AngelesCAUSA
| | - Charlotte Ling
- Epigenetics and Diabetes UnitDepartment of Clinical SciencesLund University Diabetes CentreMalmöSweden
| | - Kati Hanhineva
- Institute of Public Health and Clinical NutritionDepartment of Clinical NutritionUniversity of Eastern FinlandKuopioFinland,Department of BiochemistryFood Chemistry and Food Development UnitUniversity of TurkuTurkuFinland
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical NutritionDepartment of Clinical NutritionUniversity of Eastern FinlandKuopioFinland,Department of Medicine, Endocrinology and Clinical NutritionKuopio University HospitalKuopioFinland
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13
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Jönsson J, Renault KM, García-Calzón S, Perfilyev A, Estampador AC, Nørgaard K, Lind MV, Vaag A, Hjort L, Michaelsen KF, Carlsen EM, Franks PW, Ling C. Lifestyle Intervention in Pregnant Women With Obesity Impacts Cord Blood DNA Methylation, Which Associates With Body Composition in the Offspring. Diabetes 2021; 70:854-866. [PMID: 33431374 PMCID: PMC7980200 DOI: 10.2337/db20-0487] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 05/11/2020] [Accepted: 01/01/2021] [Indexed: 02/06/2023]
Abstract
Maternal obesity may lead to epigenetic alterations in the offspring and might thereby contribute to disease later in life. We investigated whether a lifestyle intervention in pregnant women with obesity is associated with epigenetic variation in cord blood and body composition in the offspring. Genome-wide DNA methylation was analyzed in cord blood from 208 offspring from the Treatment of Obese Pregnant women (TOP)-study, which includes pregnant women with obesity randomized to lifestyle interventions comprised of physical activity with or without dietary advice versus control subjects (standard of care). DNA methylation was altered at 379 sites, annotated to 370 genes, in cord blood from offspring of mothers following a lifestyle intervention versus control subjects (false discovery rate [FDR] <5%) when using the Houseman reference-free method to correct for cell composition, and three of these sites were significant based on Bonferroni correction. These 370 genes are overrepresented in gene ontology terms, including response to fatty acids and adipose tissue development. Offspring of mothers included in a lifestyle intervention were born with more lean mass compared with control subjects. Methylation at 17 sites, annotated to, for example, DISC1, GBX2, HERC2, and HUWE1, partially mediates the effect of the lifestyle intervention on lean mass in the offspring (FDR <5%). Moreover, 22 methylation sites were associated with offspring BMI z scores during the first 3 years of life (P < 0.05). Overall, lifestyle interventions in pregnant women with obesity are associated with epigenetic changes in offspring, potentially influencing the offspring's lean mass and early growth.
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Affiliation(s)
- Josefine Jönsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Kristina M Renault
- Department of Obstetrics and Gynecology, Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics, Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sonia García-Calzón
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
- Department of Nutrition, Food Sciences and Physiology, University of Navarra, Pamplona, Spain
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Angela C Estampador
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | | | - Mads Vendelbo Lind
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Allan Vaag
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Line Hjort
- Department of Obstetrics, Center for Pregnant Women with Diabetes, Rigshospitalet, Copenhagen, Denmark
| | - Kim F Michaelsen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Emma Malchau Carlsen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
- Department of Pediatrics, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, 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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14
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García-Calzón S, Perfilyev A, Martinell M, Ustinova M, Kalamajski S, Franks PW, Bacos K, Elbere I, Pihlajamäki J, Volkov P, Vaag A, Groop L, Maziarz M, Klovins J, Ahlqvist E, Ling C. Epigenetic markers associated with metformin response and intolerance in drug-naïve patients with type 2 diabetes. Sci Transl Med 2020; 12:12/561/eaaz1803. [DOI: 10.1126/scitranslmed.aaz1803] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/27/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Abstract
Metformin is the first-line pharmacotherapy for managing type 2 diabetes (T2D). However, many patients with T2D do not respond to or tolerate metformin well. Currently, there are no phenotypes that successfully predict glycemic response to, or tolerance of, metformin. We explored whether blood-based epigenetic markers could discriminate metformin response and tolerance by analyzing genome-wide DNA methylation in drug-naïve patients with T2D at the time of their diagnosis. DNA methylation of 11 and 4 sites differed between glycemic responders/nonresponders and metformin-tolerant/intolerant patients, respectively, in discovery and replication cohorts. Greater methylation at these sites associated with a higher risk of not responding to or not tolerating metformin with odds ratios between 1.43 and 3.09 per 1-SD methylation increase. Methylation risk scores (MRSs) of the 11 identified sites differed between glycemic responders and nonresponders with areas under the curve (AUCs) of 0.80 to 0.98. MRSs of the 4 sites associated with future metformin intolerance generated AUCs of 0.85 to 0.93. Some of these blood-based methylation markers mirrored the epigenetic pattern in adipose tissue, a key tissue in diabetes pathogenesis, and genes to which these markers were annotated to had biological functions in hepatocytes that altered metformin-related phenotypes. Overall, we could discriminate between glycemic responders/nonresponders and participants tolerant/intolerant to metformin at diagnosis by measuring blood-based epigenetic markers in drug-naïve patients with T2D. This epigenetics-based tool may be further developed to help patients with T2D receive optimal therapy.
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Affiliation(s)
- Sonia García-Calzón
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
- Department of Nutrition, Food Science and Physiology, University of Navarra, 31008 Pamplona, Spain
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Mats Martinell
- Department of Public Health and Caring Sciences, Uppsala University, 751 22 Uppsala, Sweden
| | - Monta Ustinova
- Latvian Biomedical Research and Study Centre, Rātsupītes Street 1, k-1, Riga LV-1067, Latvia
| | - Sebastian Kalamajski
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, 214 28 Malmö, Sweden
| | - Paul W. Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, 214 28 Malmö, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Ilze Elbere
- Latvian Biomedical Research and Study Centre, Rātsupītes Street 1, k-1, Riga LV-1067, Latvia
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, Internal Medicine, University of Eastern Finland, 70211 Kuopio, Finland
- Clinical Nutrition and Obesity Center, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Allan Vaag
- Type 2 Diabetes Biology Research, Steno Diabetes Center, 2820 Gentofte, Denmark
| | - Leif Groop
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Marlena Maziarz
- Bioinformatics Unit, Department of Clinical Sciences, Lund University Diabetes Centre, 214 28 Malmö, Sweden
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Rātsupītes Street 1, k-1, Riga LV-1067, Latvia
- Faculty of Biology, University of Latvia, Riga LV-1004, Latvia
| | - Emma Ahlqvist
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
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15
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Broholm C, Ribel-Madsen R, Hjort L, Olsson AH, Ahlers JMD, Hansen NS, Schrölkamp M, Gillberg L, Perfilyev A, Volkov P, Ling C, Jørgensen SW, Mortensen B, Hingst J, Wojtaszewski J, Scheele C, Brøns C, Pedersen BK, Vaag A. Epigenome- and Transcriptome-wide Changes in Muscle Stem Cells from Low Birth Weight Men. Endocr Res 2020; 45:58-71. [PMID: 31566019 DOI: 10.1080/07435800.2019.1669160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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] [Indexed: 12/31/2022]
Abstract
Background: Being born with low birth weight (LBW) is a risk factor for muscle insulin resistance and type 2 diabetes (T2D), which may be mediated by epigenetic mechanisms programmed by the intrauterine environment. Epigenetic mechanisms exert their prime effects in developing cells. We hypothesized that muscle insulin resistance in LBW subjects may be due to early differential epigenomic and transcriptomic alterations in their immature muscle progenitor cells.Results: Muscle progenitor cells were obtained from 23 healthy young adult men born at term with LBW, and 15 BMI-matched normal birth weight (NBW) controls. The cells were subsequently cultured and differentiated into myotubes. DNA and RNA were harvested before and after differentiation for genome-wide DNA methylation and RNA expression measurements.After correcting for multiple comparisons (q ≤ 0.05), 56 CpG sites were found to be significantly, differentially methylated in myoblasts from LBW compared with NBW men, of which the top five gene-annotated CpG sites (SKI, ARMCX3, NR5A2, NEUROG, ESRRG) previously have been associated to regulation of cholesterol, fatty acid and glucose metabolism and muscle development or hypertrophy. LBW men displayed markedly decreased myotube gene expression levels of the AMPK-repressing tyrosine kinase gene FYN and the histone deacetylase gene HDAC7. Silencing of FYN and HDAC7 was associated with impaired myotube formation, which for HDAC7 reduced muscle glucose uptake.Conclusions: The data provides evidence of impaired muscle development predisposing LBW individuals to T2D is linked to and potentially caused by distinct DNA methylation and transcriptional changes including down regulation of HDAC7 and FYN in their immature myoblast stem cells.
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Affiliation(s)
- Christa Broholm
- Department of Endocrinology, Diabetes and Bone-metabolic Research Unit, Copenhagen, Denmark
| | - Rasmus Ribel-Madsen
- Department of Endocrinology, Diabetes and Bone-metabolic Research Unit, Copenhagen, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | - Line Hjort
- Department of Endocrinology, Diabetes and Bone-metabolic Research Unit, Copenhagen, Denmark
- Danish Diabetes Academy, Odense, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Henrik Olsson
- Department of Endocrinology, Diabetes and Bone-metabolic Research Unit, Copenhagen, Denmark
| | | | - Ninna Schiøler Hansen
- Department of Endocrinology, Diabetes and Bone-metabolic Research Unit, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish PhD School of Molecular Metabolism, Odense, Denmark
| | - Maren Schrölkamp
- Department of Endocrinology, Diabetes and Bone-metabolic Research Unit, Copenhagen, Denmark
| | - Linn Gillberg
- Department of Endocrinology, Diabetes and Bone-metabolic Research Unit, Copenhagen, Denmark
| | - Alexander Perfilyev
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Malmo, Sweden
| | - Petr Volkov
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Malmo, Sweden
| | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, CRC, Malmo, Sweden
| | | | | | - Janne Hingst
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sport, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen Wojtaszewski
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sport, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Scheele
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Brøns
- Department of Endocrinology, Diabetes and Bone-metabolic Research Unit, Copenhagen, Denmark
| | - Bente Klarlund Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Allan Vaag
- Department of Endocrinology, Diabetes and Bone-metabolic Research Unit, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Cardiovascular and Metabolic Disease (CVMD) Translational Medicine Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
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16
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Cardona A, Day FR, Perry JRB, Loh M, Chu AY, Lehne B, Paul DS, Lotta LA, Stewart ID, Kerrison ND, Scott RA, Khaw KT, Forouhi NG, Langenberg C, Liu C, Mendelson MM, Levy D, Beck S, Leslie RD, Dupuis J, Meigs JB, Kooner JS, Pihlajamäki J, Vaag A, Perfilyev A, Ling C, Hivert MF, Chambers JC, Wareham NJ, Ong KK. Epigenome-Wide Association Study of Incident Type 2 Diabetes in a British Population: EPIC-Norfolk Study. Diabetes 2019; 68:2315-2326. [PMID: 31506343 PMCID: PMC6868468 DOI: 10.2337/db18-0290] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [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: 03/12/2018] [Accepted: 08/25/2019] [Indexed: 12/28/2022]
Abstract
Epigenetic changes may contribute substantially to risks of diseases of aging. Previous studies reported seven methylation variable positions (MVPs) robustly associated with incident type 2 diabetes mellitus (T2DM). However, their causal roles in T2DM are unclear. In an incident T2DM case-cohort study nested within the population-based European Prospective Investigation into Cancer and Nutrition (EPIC)-Norfolk cohort, we used whole blood DNA collected at baseline, up to 11 years before T2DM onset, to investigate the role of methylation in the etiology of T2DM. We identified 15 novel MVPs with robust associations with incident T2DM and robustly confirmed three MVPs identified previously (near to TXNIP, ABCG1, and SREBF1). All 18 MVPs showed directionally consistent associations with incident and prevalent T2DM in independent studies. Further conditional analyses suggested that the identified epigenetic signals appear related to T2DM via glucose and obesity-related pathways acting before the collection of baseline samples. We integrated genome-wide genetic data to identify methylation-associated quantitative trait loci robustly associated with 16 of the 18 MVPs and found one MVP, cg00574958 at CPT1A, with a possible direct causal role in T2DM. None of the implicated genes were previously highlighted by genetic association studies, suggesting that DNA methylation studies may reveal novel biological mechanisms involved in tissue responses to glycemia.
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Affiliation(s)
- Alexia Cardona
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, U.K.
- Department of Genetics, University of Cambridge, Cambridge, U.K
| | - Felix R Day
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, U.K
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, U.K
| | - Marie Loh
- Department of Epidemiology and Biostatistics, Imperial College London, London, U.K
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research, Singapore
- Department of Biochemistry, National University of Singapore, Singapore
| | - Audrey Y Chu
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, Imperial College London, London, U.K
| | - Dirk S Paul
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, U.K
| | - Luca A Lotta
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, U.K
| | - Isobel D Stewart
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, U.K
| | - Nicola D Kerrison
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, U.K
| | - Robert A Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, U.K
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, U.K
| | - Nita G Forouhi
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, U.K
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, U.K
| | - Chunyu Liu
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA
| | - Michael M Mendelson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA
- Department of Cardiology, Boston Children's Hospital, Boston, MA
| | - Daniel Levy
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London, U.K
| | - R David Leslie
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, U.K
| | - Josée Dupuis
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, Middlesex, U.K
- Imperial College Healthcare NHS Trust, London, U.K
- MRC-PHE Centre for Environment and Health, Imperial College London, London, U.K
- National Heart and Lung Institute, Imperial College London, London, U.K
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Joensuu, Finland
- Clinical Nutrition and Obesity Center, Kuopio University Hospital, Kuopio, Finland
| | - Allan Vaag
- Cardiovascular and Metabolic Disease Translational Medicine Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Alexander Perfilyev
- 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
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA
- Massachusetts General Hospital, Boston, MA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, U.K
- Department of Cardiology, Ealing Hospital, Middlesex, U.K
- Imperial College Healthcare NHS Trust, London, U.K
- MRC-PHE Centre for Environment and Health, Imperial College London, London, U.K
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, U.K
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, School of Clinical Medicine, University of Cambridge, Cambridge, U.K.
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Hall E, Jönsson J, Ofori JK, Volkov P, Perfilyev A, Dekker Nitert M, Eliasson L, Ling C, Bacos K. Glucolipotoxicity Alters Insulin Secretion via Epigenetic Changes in Human Islets. Diabetes 2019; 68:1965-1974. [PMID: 31420409 DOI: 10.2337/db18-0900] [Citation(s) in RCA: 24] [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: 08/21/2018] [Accepted: 07/24/2019] [Indexed: 11/13/2022]
Abstract
Type 2 diabetes (T2D) is characterized by insufficient insulin secretion and elevated glucose levels, often in combination with high levels of circulating fatty acids. Long-term exposure to high levels of glucose or fatty acids impair insulin secretion in pancreatic islets, which could partly be due to epigenetic alterations. We studied the effects of high concentrations of glucose and palmitate combined for 48 h (glucolipotoxicity) on the transcriptome, the epigenome, and cell function in human islets. Glucolipotoxicity impaired insulin secretion, increased apoptosis, and significantly (false discovery rate <5%) altered the expression of 1,855 genes, including 35 genes previously implicated in T2D by genome-wide association studies (e.g., TCF7L2 and CDKN2B). Additionally, metabolic pathways were enriched for downregulated genes. Of the differentially expressed genes, 1,469 also exhibited altered DNA methylation (e.g., CDK1, FICD, TPX2, and TYMS). A luciferase assay showed that increased methylation of CDK1 directly reduces its transcription in pancreatic β-cells, supporting the idea that DNA methylation underlies altered expression after glucolipotoxicity. Follow-up experiments in clonal β-cells showed that knockdown of FICD and TPX2 alters insulin secretion. Together, our novel data demonstrate that glucolipotoxicity changes the epigenome in human islets, thereby altering gene expression and possibly exacerbating the secretory defect in T2D.
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Affiliation(s)
- Elin Hall
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Josefine Jönsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Jones K Ofori
- Islet Cell Exocytosis 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
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Marloes Dekker Nitert
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Lena Eliasson
- Islet Cell Exocytosis 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
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
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18
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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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19
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Walle P, Männistö V, de Mello VD, Vaittinen M, Perfilyev A, Hanhineva K, Ling C, Pihlajamäki J. Correction to: Liver DNA methylation of FADS2 associates with FADS2 genotype. Clin Epigenetics 2019; 11:47. [PMID: 30867039 PMCID: PMC6416962 DOI: 10.1186/s13148-019-0625-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 11/10/2022] Open
Abstract
Following publication of the original article [1], the author reported the title of this article has been misspelled.
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Affiliation(s)
- Paula Walle
- 0000 0001 0726 2490grid.9668.1Department of Clinical Nutrition, Faculty of Health Sciences, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70210 Kuopio, Finland
| | - Ville Männistö
- Department of Medicine, University of Eastern Finland, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Vanessa Derenji de Mello
- 0000 0001 0726 2490grid.9668.1Department of Clinical Nutrition, Faculty of Health Sciences, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70210 Kuopio, Finland
| | - Maija Vaittinen
- 0000 0001 0726 2490grid.9668.1Department of Clinical Nutrition, Faculty of Health Sciences, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70210 Kuopio, Finland
| | - Alexander Perfilyev
- 0000 0001 0930 2361grid.4514.4Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, 20502 Malmö, Sweden
| | - Kati Hanhineva
- 0000 0001 0726 2490grid.9668.1Department of Clinical Nutrition, Faculty of Health Sciences, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70210 Kuopio, Finland
| | - Charlotte Ling
- 0000 0001 0930 2361grid.4514.4Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, 20502 Malmö, Sweden
| | - Jussi Pihlajamäki
- 0000 0001 0726 2490grid.9668.1Department of Clinical Nutrition, Faculty of Health Sciences, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70210 Kuopio, Finland ,0000 0004 0628 207Xgrid.410705.7Clinical Nutrition and Obesity Center, Kuopio University Hospital, 70211 Kuopio, Finland
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García-Calzón S, Perfilyev A, de Mello VD, Pihlajamäki J, Ling C. Sex Differences in the Methylome and Transcriptome of the Human Liver and Circulating HDL-Cholesterol Levels. J Clin Endocrinol Metab 2018; 103:4395-4408. [PMID: 29846646 PMCID: PMC6212806 DOI: 10.1210/jc.2018-00423] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022]
Abstract
Context Epigenetics may contribute to sex-specific differences in human liver metabolism. Objective To study the impact of sex on DNA methylation and gene expression in human liver. Design/Setting Cross-sectional, Kuopio Obesity Surgery Study. Participants/Intervention We analyzed DNA methylation with the Infinium HumanMethylation450 BeadChip in liver of an obese population (34 males, 61 females). Females had a higher high-density lipoprotein (HDL)-cholesterol levels compared with males. Gene expression was measured with the HumanHT-12 Expression BeadChip in a subset of 42 participants. Results Females displayed higher average methylation in the X-chromosome, whereas males presented higher methylation in autosomes. We found 9455 CpG sites in the X-chromosome and 33,205 sites in autosomes with significant methylation differences in liver between sexes (q < 0.05). When comparing our findings with published studies, 95% of the sex-specific differences in liver methylation in the X-chromosome were also found in pancreatic islets and brain, and 26 autosomal sites showed sex-specific methylation differences in the liver as well as in other human tissues. Furthermore, this sex-specific methylation profile in liver was associated with hepatic gene expression changes between males and females. Notably, females showed higher HDL-cholesterol levels, which were associated with higher KDM6A expression and epigenetic differences in human liver. Accordingly, silencing of KDM6A in cultured liver cells reduced HDL-cholesterol levels and APOA1 expression, which is a major component of HDL particles. Conclusions Human liver has a sex-specific methylation profile in both the X-chromosome and autosomes, which associates with hepatic gene expression changes and HDL-cholesterol. We identified KDM6A as a novel target that regulates HDL-cholesterol levels.
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Affiliation(s)
- Sonia García-Calzón
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Vanessa D de Mello
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Clinical Nutrition and Obesity Center, Kuopio University Hospital, Kuopio, Finland
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
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Kokosar M, Benrick A, Perfilyev A, Nilsson E, Källman T, Ohlsson C, Ling C, Stener-Victorin E. A Single Bout of Electroacupuncture Remodels Epigenetic and Transcriptional Changes in Adipose Tissue in Polycystic Ovary Syndrome. Sci Rep 2018; 8:1878. [PMID: 29382850 PMCID: PMC5790004 DOI: 10.1038/s41598-017-17919-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [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: 08/30/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022] Open
Abstract
A single bout of electroacupuncture results in muscle contractions and increased whole body glucose uptake in women with polycystic ovary syndrome (PCOS). Women with PCOS have transcriptional and epigenetic alterations in the adipose tissue and we hypothesized that electroacupuncture induces epigenetic and transcriptional changes to restore metabolic alterations. Twenty-one women with PCOS received a single bout of electroacupuncture, which increased the whole body glucose uptake. In subcutaneous adipose tissue biopsies, we identified treatment-induced expression changes of 2369 genes (Q < 0.05) and DNA methylation changes of 7055 individual genes (Q = 0.11). The largest increase in expression was observed for FOSB (2405%), and the largest decrease for LOC100128899 (54%). The most enriched pathways included Acute phase response signaling and LXR/RXR activation. The DNA methylation changes ranged from 1-16%, and 407 methylation sites correlated with gene expression. Among genes known to be differentially expressed in PCOS, electroacupuncture reversed the expression of 80 genes, including PPARγ and ADIPOR2. Changes in the expression of Nr4a2 and Junb are reversed by adrenergic blockers in rats demonstrating that changes in gene expression, in part, is due to activation of the sympathetic nervous system. In conclusion, low-frequency electroacupuncture with muscle contractions remodels epigenetic and transcriptional changes that elicit metabolic improvement.
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Affiliation(s)
- Milana Kokosar
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Benrick
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- School of Health and Education, University of Skövde, Skövde, Sweden
| | - Alexander Perfilyev
- Epigenetics and Diabetes, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Clinical Research Centre, Scania University Hospital, Malmö, Sweden
| | - Emma Nilsson
- Epigenetics and Diabetes, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Clinical Research Centre, Scania University Hospital, Malmö, Sweden
| | - Thomas Källman
- Department of Medical Biochemistry and Microbiology, NBIS - National Bioinformatics Infrastructure Sweden, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Clinical Research Centre, Scania University Hospital, Malmö, Sweden
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García-Calzón S, Perfilyev A, Männistö V, de Mello VD, Nilsson E, Pihlajamäki J, Ling C. Diabetes medication associates with DNA methylation of metformin transporter genes in the human liver. Clin Epigenetics 2017; 9:102. [PMID: 28947922 PMCID: PMC5609005 DOI: 10.1186/s13148-017-0400-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [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: 07/27/2017] [Accepted: 09/04/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Given that metformin is the most common pharmacological therapy for type 2 diabetes, understanding the function of this drug is of great importance. Hepatic metformin transporters are responsible for the pharmacologic action of metformin. However, epigenetics in genes encoding metformin transporters has not been fully elucidated. We examined the DNA methylation of these genes in the liver of subjects with type 2 diabetes and tested whether epigenetic alterations associate with diabetes medication, i.e., metformin or insulin plus metformin treatment. RESULTS DNA methylation in OCT1 encoded by SLC22A1, OCT3 encoded by SLC22A3, and MATE1 encoded by SLC47A1 was assessed in the human liver. Lower average and promoter DNA methylation of SLC22A1, SLC22A3, and SLC47A1 was found in diabetic subjects receiving just metformin, compared to those who took insulin plus metformin or no diabetes medication. Moreover, diabetic subjects receiving just metformin had a similar DNA methylation pattern in these genes compared to non-diabetic subjects. Notably, DNA methylation was also associated with gene expression, glucose levels, and body mass index, i.e., higher SLC22A3 methylation was related to lower SLC22A3 expression and to insulin plus metformin treatment, higher fasting glucose levels and higher body mass index. Importantly, metformin treatment did also directly decrease DNA methylation of SLC22A1 in hepatocytes cultured in vitro. CONCLUSIONS Our study supports that metformin decreases DNA methylation of metformin transporter genes in the human liver. Moreover, higher methylation levels in these genes associate with hyperglycaemia and obesity.
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Affiliation(s)
- Sonia García-Calzón
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden
| | - Alexander Perfilyev
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden
| | - Ville Männistö
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Vanessa D de Mello
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 80100 Joensuu, Finland
| | - Emma Nilsson
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 80100 Joensuu, Finland.,Clinical Nutrition and Obesity Center, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden
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23
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Perfilyev A, Dahlman I, Gillberg L, Rosqvist F, Iggman D, Volkov P, Nilsson E, Risérus U, Ling C. Impact of polyunsaturated and saturated fat overfeeding on the DNA-methylation pattern in human adipose tissue: a randomized controlled trial. Am J Clin Nutr 2017; 105:991-1000. [PMID: 28275132 DOI: 10.3945/ajcn.116.143164] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [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: 08/23/2016] [Accepted: 01/19/2017] [Indexed: 11/14/2022] Open
Abstract
Background: Dietary fat composition can affect ectopic lipid accumulation and, thereby, insulin resistance. Diets that are high in saturated fatty acids (SFAs) or polyunsaturated fatty acids (PUFAs) have different metabolic responses.Objective: We investigated whether the epigenome of human adipose tissue is affected differently by dietary fat composition and general overfeeding in a randomized trial.Design: We studied the effects of 7 wk of excessive SFA (n = 17) or PUFA (n = 14) intake (+750 kcal/d) on the DNA methylation of ∼450,000 sites in human subcutaneous adipose tissue. Both diets resulted in similar body weight increases. We also combined the data from the 2 groups to examine the overall effect of overfeeding on the DNA methylation in adipose tissue.Results: The DNA methylation of 4875 Cytosine-phosphate-guanine (CpG) sites was affected differently between the 2 diets. Furthermore, both the SFA and PUFA diets increased the mean degree of DNA methylation in adipose tissue, particularly in promoter regions. However, although the mean methylation was changed in 1797 genes [e.g., alpha-ketoglutarate dependent dioxygenase (FTO), interleukin 6 (IL6), insulin receptor (INSR), neuronal growth regulator 1 (NEGR1), and proopiomelanocortin (POMC)] by PUFAs, only 125 genes [e.g., adiponectin, C1Q and collagen domain containing (ADIPOQ)] were changed by SFA overfeeding. In addition, the SFA diet significantly altered the expression of 28 transcripts [e.g., acyl-CoA oxidase 1 (ACOX1) and FAT atypical cadherin 1 (FAT1)], whereas the PUFA diet did not significantly affect gene expression. When the data from the 2 diet groups were combined, the mean methylation of 1444 genes, including fatty acid binding protein 1 (FABP1), fatty acid binding protein 2 (FABP2), melanocortin 2 receptor (MC2R), MC3R, PPARG coactivator 1 α (PPARGC1A), and tumor necrosis factor (TNF), was changed in adipose tissue by overfeeding. Moreover, the baseline DNA methylation of 12 CpG sites that was annotated to 9 genes [e.g., mitogen-activated protein kinase 7 (MAPK7), melanin concentrating hormone receptor 1 (MCHR1), and splicing factor SWAP homolog (SFRS8)] was associated with the degree of weight increase in response to extra energy intake.Conclusions: SFA overfeeding and PUFA overfeeding induce distinct epigenetic changes in human adipose tissue. In addition, we present data that suggest that baseline DNA methylation can predict weight increase in response to overfeeding in humans. This trial was registered at clinicaltrials.gov as NCT01427140.
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Affiliation(s)
- Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Center, Lund University, Clinical Research Center, Malmö, Sweden
| | - Ingrid Dahlman
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Linn Gillberg
- Diabetes and Metabolism, Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark; and
| | - 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
| | - Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Center, Lund University, Clinical Research Center, Malmö, Sweden
| | - Emma Nilsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Center, Lund University, Clinical Research Center, Malmö, Sweden
| | - Ulf Risérus
- Clinical Nutrition and Metabolism, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Center, Lund University, Clinical Research Center, Malmö, Sweden;
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24
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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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Davegårdh C, Broholm C, Perfilyev A, Henriksen T, García-Calzón S, Peijs L, Hansen NS, Volkov P, Kjøbsted R, Wojtaszewski JFP, Pedersen M, Pedersen BK, Ballak DB, Dinarello CA, Heinhuis B, Joosten LAB, Nilsson E, Vaag A, Scheele C, Ling C. Abnormal epigenetic changes during differentiation of human skeletal muscle stem cells from obese subjects. BMC Med 2017; 15:39. [PMID: 28222718 PMCID: PMC5320752 DOI: 10.1186/s12916-017-0792-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 10/12/2016] [Accepted: 01/11/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Human skeletal muscle stem cells are important for muscle regeneration. However, the combined genome-wide DNA methylation and expression changes taking place during adult myogenesis have not been described in detail and novel myogenic factors may be discovered. Additionally, obesity is associated with low relative muscle mass and diminished metabolism. Epigenetic alterations taking place during myogenesis might contribute to these defects. METHODS We used Infinium HumanMethylation450 BeadChip Kit (Illumina) and HumanHT-12 Expression BeadChip (Illumina) to analyze genome-wide DNA methylation and transcription before versus after differentiation of primary human myoblasts from 14 non-obese and 14 obese individuals. Functional follow-up experiments were performed using siRNA mediated gene silencing in primary human myoblasts and a transgenic mouse model. RESULTS We observed genome-wide changes in DNA methylation and expression patterns during differentiation of primary human muscle stem cells (myoblasts). We identified epigenetic and transcriptional changes of myogenic transcription factors (MYOD1, MYOG, MYF5, MYF6, PAX7, MEF2A, MEF2C, and MEF2D), cell cycle regulators, metabolic enzymes and genes previously not linked to myogenesis, including IL32, metallothioneins, and pregnancy-specific beta-1-glycoproteins. Functional studies demonstrated IL-32 as a novel target that regulates human myogenesis, insulin sensitivity and ATP levels in muscle cells. Furthermore, IL32 transgenic mice had reduced insulin response and muscle weight. Remarkably, approximately 3.7 times more methylation changes (147,161 versus 39,572) were observed during differentiation of myoblasts from obese versus non-obese subjects. In accordance, DNMT1 expression increased during myogenesis only in obese subjects. Interestingly, numerous genes implicated in metabolic diseases and epigenetic regulation showed differential methylation and expression during differentiation only in obese subjects. CONCLUSIONS Our study identifies IL-32 as a novel myogenic regulator, provides a comprehensive map of the dynamic epigenome during differentiation of human muscle stem cells and reveals abnormal epigenetic changes in obesity.
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Affiliation(s)
- Cajsa Davegårdh
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Christa Broholm
- Department of Endocrinology, Rigshospitalet, Copenhagen, 2100, Denmark
| | - Alexander Perfilyev
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Tora Henriksen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sonia García-Calzón
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Lone Peijs
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Petr Volkov
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Rasmus Kjøbsted
- Department of Exercise and Sports Sciences, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen F P Wojtaszewski
- Department of Exercise and Sports Sciences, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Maria Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Bente Klarlund Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Dov B Ballak
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA.,Department of Medicine, University of Colorado, Aurora, CO, 80045, USA
| | - Charles A Dinarello
- Department of Medicine, University of Colorado, Aurora, CO, 80045, USA.,Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Bas Heinhuis
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Emma Nilsson
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Allan Vaag
- Department of Endocrinology, Rigshospitalet, Copenhagen, 2100, Denmark.,Early Clinical Development, Translational Medical Unit, AstraZeneca, Mölndal, 431 83, Sweden
| | - Camilla Scheele
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden.
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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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Broholm C, Olsson AH, Perfilyev A, Hansen NS, Schrölkamp M, Strasko KS, Scheele C, Ribel-Madsen R, Mortensen B, Jørgensen SW, Ling C, Vaag A. Epigenetic programming of adipose-derived stem cells in low birthweight individuals. Diabetologia 2016; 59:2664-2673. [PMID: 27627980 DOI: 10.1007/s00125-016-4099-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 05/17/2016] [Accepted: 08/09/2016] [Indexed: 12/27/2022]
Abstract
AIMS/HYPOTHESIS Low birthweight (LBW) is associated with dysfunctions of adipose tissue and metabolic disease in adult life. We hypothesised that altered epigenetic and transcriptional regulation of adipose-derived stem cells (ADSCs) could play a role in programming adipose tissue dysfunction in LBW individuals. METHODS ADSCs were isolated from the subcutaneous adipose tissue of 13 normal birthweight (NBW) and 13 LBW adult men. The adipocytes were cultured in vitro, and genome-wide differences in RNA expression and DNA methylation profiles were analysed in ADSCs and differentiated adipocytes. RESULTS We demonstrated that ADSCs from LBW individuals exhibit multiple expression changes as well as genome-wide alterations in methylation pattern. Reduced expression of the transcription factor cyclin T2 encoded by CCNT2 may play a key role in orchestrating several of the gene expression changes in ADSCs from LBW individuals. Indeed, silencing of CCNT2 in human adipocytes decreased leptin secretion as well as the mRNA expression of several genes involved in adipogenesis, including MGLL, LIPE, PPARG, LEP and ADIPOQ. Only subtle genome-wide mRNA expression and DNA methylation changes were seen in mature cultured adipocytes from LBW individuals. CONCLUSIONS/INTERPRETATION Epigenetic and transcriptional changes in LBW individuals are most pronounced in immature ADSCs that in turn may programme physiological characteristics of the mature adipocytes that influence the risk of metabolic diseases. Reduced expression of CCNT2 may play a key role in the developmental programming of adipose tissue.
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Affiliation(s)
- Christa Broholm
- Department of Endocrinology, Diabetes and Metabolism, Rigshospitalet - Section 7652, Tagensvej 20, DK-2200, Copenhagen, Denmark.
| | - Anders H Olsson
- Department of Endocrinology, Diabetes and Metabolism, Rigshospitalet - Section 7652, Tagensvej 20, DK-2200, Copenhagen, Denmark
| | - Alexander Perfilyev
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, CRC, Malmö, Sweden
| | - Ninna S Hansen
- Department of Endocrinology, Diabetes and Metabolism, Rigshospitalet - Section 7652, Tagensvej 20, DK-2200, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maren Schrölkamp
- Department of Endocrinology, Diabetes and Metabolism, Rigshospitalet - Section 7652, Tagensvej 20, DK-2200, Copenhagen, Denmark
| | - Klaudia S Strasko
- Department of Endocrinology, Diabetes and Metabolism, Rigshospitalet - Section 7652, Tagensvej 20, DK-2200, Copenhagen, Denmark
| | - Camilla Scheele
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Centre of Inflammation and Metabolism, Rigshospitalet, Copenhagen, Denmark
| | - Rasmus Ribel-Madsen
- Department of Endocrinology, Diabetes and Metabolism, Rigshospitalet - Section 7652, Tagensvej 20, DK-2200, Copenhagen, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | | | | | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes, Lund University Diabetes Centre, CRC, Malmö, Sweden
| | - Allan Vaag
- Department of Endocrinology, Diabetes and Metabolism, Rigshospitalet - Section 7652, Tagensvej 20, DK-2200, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center A/S, Gentofte, Denmark
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Broholm C, Olsson AH, Perfilyev A, Gillberg L, Hansen NS, Ali A, Mortensen B, Ling C, Vaag A. Human adipogenesis is associated with genome-wide DNA methylation and gene-expression changes. Epigenomics 2016; 8:1601-1617. [PMID: 27854126 DOI: 10.2217/epi-2016-0077] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 01/15/2023] Open
Abstract
AIM To define the genomic distribution and function of DNA methylation changes during human adipogenesis. METHODS We isolated adipocyte-derived stem cells from 13 individuals and analyzed genome-wide DNA methylation and gene expression in cultured adipocyte-derived stem cells and mature adipocytes. RESULTS We observed altered DNA methylation of 11,947 CpG sites and altered expression of 11,830 transcripts after differentiation. De novo methylation was observed across all genomic elements. Co-existence of genes with both altered expression and DNA methylation was found in genes important for cell cycle and adipokine signaling. CONCLUSION Human adipogenesis is associated with significant DNA methylation changes across the entire genome and may impact regulation of cell cycle and adipokine signaling.
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Affiliation(s)
- Christa Broholm
- Department of Endocrinology, Diabetes & Metabolism, Rigshospitalet, Copenhagen, Denmark
| | - Anders Henrik Olsson
- Department of Endocrinology, Diabetes & Metabolism, Rigshospitalet, Copenhagen, Denmark
| | - Alexander Perfilyev
- Department of Clinical Sciences, Epigenetics & Diabetes Unit, Lund University Diabetes Centre, CRC, Malmö, Sweden
| | - Linn Gillberg
- Department of Endocrinology, Diabetes & Metabolism, Rigshospitalet, Copenhagen, Denmark
| | - Ninna Schiøler Hansen
- Department of Endocrinology, Diabetes & Metabolism, Rigshospitalet, Copenhagen, Denmark.,Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ashfaq Ali
- Department of Clinical Sciences, GAME, Lund University Diabetes Centre, CRC, Malmö, Sweden
| | | | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics & Diabetes Unit, Lund University Diabetes Centre, CRC, Malmö, Sweden
| | - Allan Vaag
- Department of Endocrinology, Diabetes & Metabolism, Rigshospitalet, Copenhagen, Denmark.,Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Steno Diabetes Centre A/S, Gentofte, Denmark
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Kokosar M, Benrick A, Perfilyev A, Fornes R, Nilsson E, Maliqueo M, Behre CJ, Sazonova A, Ohlsson C, Ling C, Stener-Victorin E. Erratum: Epigenetic and Transcriptional Alterations in Human Adipose Tissue of Polycystic Ovary Syndrome. Sci Rep 2016; 6:25321. [PMID: 27157924 PMCID: PMC4860789 DOI: 10.1038/srep25321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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30
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Dayeh T, Tuomi T, Almgren P, Perfilyev A, Jansson PA, de Mello VD, Pihlajamäki J, Vaag A, Groop L, Nilsson E, Ling C. DNA methylation of loci within ABCG1 and PHOSPHO1 in blood DNA is associated with future type 2 diabetes risk. Epigenetics 2016; 11:482-8. [PMID: 27148772 PMCID: PMC4939923 DOI: 10.1080/15592294.2016.1178418] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Identification of subjects with a high risk of developing type 2 diabetes (T2D) is fundamental for prevention of the disease. Consequently, it is essential to search for new biomarkers that can improve the prediction of T2D. The aim of this study was to examine whether 5 DNA methylation loci in blood DNA (ABCG1, PHOSPHO1, SOCS3, SREBF1, and TXNIP), recently reported to be associated with T2D, might predict future T2D in subjects from the Botnia prospective study. We also tested if these CpG sites exhibit altered DNA methylation in human pancreatic islets, liver, adipose tissue, and skeletal muscle from diabetic vs. non-diabetic subjects. DNA methylation at the ABCG1 locus cg06500161 in blood DNA was associated with an increased risk for future T2D (OR = 1.09, 95% CI = 1.02–1.16, P-value = 0.007, Q-value = 0.018), while DNA methylation at the PHOSPHO1 locus cg02650017 in blood DNA was associated with a decreased risk for future T2D (OR = 0.85, 95% CI = 0.75–0.95, P-value = 0.006, Q-value = 0.018) after adjustment for age, gender, fasting glucose, and family relation. Furthermore, the level of DNA methylation at the ABCG1 locus cg06500161 in blood DNA correlated positively with BMI, HbA1c, fasting insulin, and triglyceride levels, and was increased in adipose tissue and blood from the diabetic twin among monozygotic twin pairs discordant for T2D. DNA methylation at the PHOSPHO1 locus cg02650017 in blood correlated positively with HDL levels, and was decreased in skeletal muscle from diabetic vs. non-diabetic monozygotic twins. DNA methylation of cg18181703 (SOCS3), cg11024682 (SREBF1), and cg19693031 (TXNIP) was not associated with future T2D risk in subjects from the Botnia prospective study.
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Affiliation(s)
- Tasnim Dayeh
- a Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Center , Malmö , Sweden
| | - Tiinamaija Tuomi
- b Endocrinology, Abdominal Center, Helsinki University Hospital , Helsinki , Finland.,c Folkhälsan Research Center , Helsinki , Finland.,d Diabetes and Obesity Research Program, Research Programs Unit, University of Helsinki , Finland.,e Finnish Institute for Molecular Medicine, University of Helsinki , Helsinki , Finland
| | - Peter Almgren
- f Diabetes and Endocrinology, Department of Clinical Sciences, Lund University Diabetes Center , Malmö , Sweden
| | - Alexander Perfilyev
- a Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Center , Malmö , Sweden
| | - Per-Anders Jansson
- g Wallenberg Laboratory, Sahlgrenska University Hospital , Gothenburg , Sweden
| | - Vanessa D de Mello
- h Department of Clinical Nutrition , Institute of Public Health and Clinical Nutrition, University of Eastern Finland , Kuopio , Finland
| | - Jussi Pihlajamäki
- h Department of Clinical Nutrition , Institute of Public Health and Clinical Nutrition, University of Eastern Finland , Kuopio , Finland.,i Clinical Nutrition and Obesity Center, Kuopio University Hospital , Kuopio , Finland
| | - Allan Vaag
- j Department of Endocrinology , Diabetes and Metabolism , Rigshospitalet , Copenhagen , Denmark
| | - Leif Groop
- f Diabetes and Endocrinology, Department of Clinical Sciences, Lund University Diabetes Center , Malmö , Sweden
| | - Emma Nilsson
- a Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Center , Malmö , Sweden
| | - Charlotte Ling
- a Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Center , Malmö , Sweden
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31
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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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Nilsson E, Matte A, Perfilyev A, de Mello VD, Käkelä P, Pihlajamäki J, Ling C. Epigenetic Alterations in Human Liver From Subjects With Type 2 Diabetes in Parallel With Reduced Folate Levels. J Clin Endocrinol Metab 2015; 100:E1491-501. [PMID: 26418287 PMCID: PMC4702449 DOI: 10.1210/jc.2015-3204] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVE Epigenetic variation may contribute to the development of complex metabolic diseases such as type 2 diabetes (T2D). Hepatic insulin resistance is a hallmark of T2D. However, it remains unknown whether epigenetic alterations take place in the liver from diabetic subjects. Therefore, we investigated the genome-wide DNA methylation pattern in the liver from subjects with T2D and nondiabetic controls and related epigenetic alterations to gene expression and circulating folate levels. RESEARCH DESIGN AND METHODS Liver biopsies were obtained from 35 diabetic and 60 nondiabetic subjects, which are part of the Kuopio Obesity Surgery Study. The genome-wide DNA methylation pattern was analyzed in the liver using the HumanMethylation450 BeadChip. RNA expression was analyzed from a subset of subjects using the HumanHT-12 Expression BeadChip. RESULTS After correction for multiple testing, we identified 251 individual CpG sites that exhibit differential DNA methylation in liver obtained from T2D compared with nondiabetic subjects (Q < .05). These include CpG sites annotated to genes that are biologically relevant to the development of T2D such as GRB10, ABCC3, MOGAT1, and PRDM16. The vast majority of the significant CpG sites (94%) displayed decreased DNA methylation in liver from subjects with T2D. The hypomethylation found in liver from diabetic subjects may be explained by reduced folate levels. Indeed, subjects with T2D had significantly reduced erythrocyte folate levels compared with nondiabetic subjects. We further identified 29 genes that displayed both differential DNA methylation and gene expression in human T2D liver including the imprinted gene H19. CONCLUSIONS Our study highlights the importance of epigenetic and transcriptional changes in the liver from subjects with T2D. Reduced circulating folate levels may provide an explanation for hypomethylation in the human diabetic liver.
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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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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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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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