101
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Durso DF, Bacalini MG, Sala C, Pirazzini C, Marasco E, Bonafé M, do Valle ÍF, Gentilini D, Castellani G, Faria AMC, Franceschi C, Garagnani P, Nardini C. Acceleration of leukocytes' epigenetic age as an early tumor and sex-specific marker of breast and colorectal cancer. Oncotarget 2017; 8:23237-23245. [PMID: 28423572 PMCID: PMC5410300 DOI: 10.18632/oncotarget.15573] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/12/2017] [Indexed: 01/12/2023] Open
Abstract
Changes in blood epigenetic age have been associated with several pathological conditions and have recently been described to anticipate cancer development. In this work, we analyze a publicly available leukocytes methylation dataset to evaluate the relation between DNA methylation age and the prospective development of specific types of cancer. We calculated DNA methylation age acceleration using five state-of-the-art estimators (three multi-site: Horvath, Hannum, Weidner; and two CpG specific: ELOV2 and FHL2) in a cohort including 845 subjects from the EPIC-Italy project and we compared 424 samples that remained cancer-free over the approximately ten years of follow-up with 235 and 166 subjects who developed breast and colorectal cancer, respectively. We show that the epigenetic age estimated from blood DNA methylation data is statistically significantly associated to future breast and male colorectal cancer development. These results are corroborated by survival analysis that shows significant association between age acceleration and cancer incidence suggesting that the chance of developing age-related diseases may be predicted by circulating epigenetic markers, with a dependence upon tumor type, sex and age estimator. These are encouraging results towards the non-invasive and perspective usage of epigenetic biomarkers.
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Affiliation(s)
- Danielle Fernandes Durso
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- National Counsel of Technological and Scientific Development (CNPq), Ministry of Science Technology and Innovation (MCTI), Brasilia, Brazil
| | | | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Massimiliano Bonafé
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | | | - Davide Gentilini
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Ana Maria Caetano Faria
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna, Italy
- Interdepartmental Center “L. Galvani”, University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Christine Nardini
- Personal Genomics S.r.l., Verona, Italy
- CNR IAC “Mauro Picone”, Rome, Italy
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102
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Raciti GA, Spinelli R, Desiderio A, Longo M, Parrillo L, Nigro C, D'Esposito V, Mirra P, Fiory F, Pilone V, Forestieri P, Formisano P, Pastan I, Miele C, Beguinot F. Specific CpG hyper-methylation leads to Ankrd26 gene down-regulation in white adipose tissue of a mouse model of diet-induced obesity. Sci Rep 2017; 7:43526. [PMID: 28266632 PMCID: PMC5339897 DOI: 10.1038/srep43526] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 01/27/2017] [Indexed: 12/16/2022] Open
Abstract
Epigenetic modifications alter transcriptional activity and contribute to the effects of environment on the individual risk of obesity and Type 2 Diabetes (T2D). Here, we have estimated the in vivo effect of a fat-enriched diet (HFD) on the expression and the epigenetic regulation of the Ankyrin repeat domain 26 (Ankrd26) gene, which is associated with the onset of these disorders. In visceral adipose tissue (VAT), HFD exposure determined a specific hyper-methylation of Ankrd26 promoter at the −436 and −431 bp CpG sites (CpGs) and impaired its expression. Methylation of these 2 CpGs impaired binding of the histone acetyltransferase/transcriptional coactivator p300 to this same region, causing hypo-acetylation of histone H4 at the Ankrd26 promoter and loss of binding of RNA Pol II at the Ankrd26 Transcription Start Site (TSS). In addition, HFD increased binding of DNA methyl-transferases (DNMTs) 3a and 3b and methyl-CpG-binding domain protein 2 (MBD2) to the Ankrd26 promoter. More importantly, Ankrd26 down-regulation enhanced secretion of pro-inflammatory mediators by 3T3-L1 adipocytes as well as in human sera. Thus, in mice, the exposure to HFD induces epigenetic silencing of the Ankrd26 gene, which contributes to the adipose tissue inflammatory secretion profile induced by high-fat regimens.
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Affiliation(s)
- Gregory A Raciti
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
| | - Rosa Spinelli
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
| | - Antonella Desiderio
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
| | - Michele Longo
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
| | - Luca Parrillo
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
| | - Cecilia Nigro
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
| | - Vittoria D'Esposito
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
| | - Paola Mirra
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
| | - Francesca Fiory
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
| | - Vincenzo Pilone
- Bariatric and Metabolic Surgery Unit, University of Salerno, Salerno, 84084, Italy
| | - Pietro Forestieri
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, 80131, Italy
| | - Pietro Formisano
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
| | - Ira Pastan
- Laboratory of Molecular Biology (LMB), National Cancer Institute (NCI), National Institute of Health (NIH), Bethesda, MD 20892, USA
| | - Claudia Miele
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
| | - Francesco Beguinot
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, 80131, Italy.,Department of Translational Medical Sciences, University of Naples "Federico II", Naples, 80131, Italy
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103
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Ambele MA, Pepper MS. Identification of transcription factors potentially involved in human adipogenesis in vitro. Mol Genet Genomic Med 2017; 5:210-222. [PMID: 28546992 PMCID: PMC5441431 DOI: 10.1002/mgg3.269] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/26/2016] [Accepted: 12/09/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Increased adiposity in humans leads to obesity, which is a major risk factor for cardiovascular disease, type 2 diabetes, and cancer. We previously conducted an extensive unbiased in vitro transcriptomic analysis of adipogenesis, using human adipose-derived stromal cells (ASCs). Here, we have applied computational methods to these data to identify transcription factors (TFs) that constitute the upstream gene regulatory networks potentially, driving adipocyte formation in human ASCs. METHODS We used Affymetrix Transcription Analysis Console™ v3.0 for calculating differentially expressed genes. MATCH™ and F-MATCH™ algorithms for TF identification. STRING v10 to predict protein-protein interactions between TFs. RESULTS A number of TFs that were reported to have a significant role in adipogenesis, as well as novel TFs that have not previously been described in this context, were identified. Thus, 32 upstream TFs were identified, with most belonging to the C2H2-type zinc finger and HOX families, which are potentially involved in regulating most of the differentially expressed genes observed during adipocyte differentiation. Furthermore, 17 important upstream TFs were found to have increased regulatory effects on their downstream target genes and were consistently up-regulated during the differentiation process. A strong hypothetical functional interaction was observed among these TFs, which supports their common role in the downstream regulation of gene expression during adipogenesis. CONCLUSION Our results support several previous findings on TFs involved in adipogenesis and thereby validate the comprehensive and systematic in silico approach described in this study. In silico analysis also allowed for the identification of novel regulators of adipocyte differentiation.
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Affiliation(s)
- Melvin Anyasi Ambele
- Department of Immunology and Institute for Cellular and Molecular MedicineSAMRC Extramural Unit for Stem Cell Research and TherapyFaculty of Health SciencesUniversity of PretoriaPretoriaSouth Africa
| | - Michael Sean Pepper
- Department of Immunology and Institute for Cellular and Molecular MedicineSAMRC Extramural Unit for Stem Cell Research and TherapyFaculty of Health SciencesUniversity of PretoriaPretoriaSouth Africa
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104
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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] [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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105
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DNA methylation map in circulating leukocytes mirrors subcutaneous adipose tissue methylation pattern: a genome-wide analysis from non-obese and obese patients. Sci Rep 2017; 7:41903. [PMID: 28211912 PMCID: PMC5314866 DOI: 10.1038/srep41903] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 12/09/2016] [Indexed: 02/07/2023] Open
Abstract
The characterization of the epigenetic changes within the obesity-related adipose tissue will provide new insights to understand this metabolic disorder, but adipose tissue is not easy to sample in population-based studies. We aimed to evaluate the capacity of circulating leukocytes to reflect the adipose tissue-specific DNA methylation status of obesity susceptibility. DNA samples isolated from subcutaneous adipose tissue and circulating leukocytes were hybridized in the Infinium HumanMethylation 450 BeadChip. Data were compared between samples from obese (n = 45) and non-obese (n = 8–10) patients by Wilcoxon-rank test, unadjusted for cell type distributions. A global hypomethylation of the differentially methylated CpG sites (DMCpGs) was observed in the obese subcutaneous adipose tissue and leukocytes. The overlap analysis yielded a number of genes mapped by the common DMCpGs that were identified to reflect the obesity state in the leukocytes. Specifically, the methylation levels of FGFRL1, NCAPH2, PNKD and SMAD3 exhibited excellent and statistically significant efficiencies in the discrimination of obesity from non-obesity status (AUC > 0.80; p < 0.05) and a great correlation between both tissues. Therefore, the current study provided new and valuable DNA methylation biomarkers of obesity-related adipose tissue pathogenesis through peripheral blood analysis, an easily accessible and minimally invasive biological material instead of adipose tissue.
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106
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Day SE, Coletta RL, Kim JY, Garcia LA, Campbell LE, Benjamin TR, Roust LR, De Filippis EA, Mandarino LJ, Coletta DK. Potential epigenetic biomarkers of obesity-related insulin resistance in human whole-blood. Epigenetics 2017; 12:254-263. [PMID: 28106509 DOI: 10.1080/15592294.2017.1281501] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Obesity can increase the risk of complex metabolic diseases, including insulin resistance. Moreover, obesity can be caused by environmental and genetic factors. However, the epigenetic mechanisms of obesity are not well defined. Therefore, the identification of novel epigenetic biomarkers of obesity allows for a more complete understanding of the disease and its underlying insulin resistance. The aim of our study was to identify DNA methylation changes in whole-blood that were strongly associated with obesity and insulin resistance. Whole-blood was obtained from lean (n = 10; BMI = 23.6 ± 0.7 kg/m2) and obese (n = 10; BMI = 34.4 ± 1.3 kg/m2) participants in combination with euglycemic hyperinsulinemic clamps to assess insulin sensitivity. We performed reduced representation bisulfite sequencing on genomic DNA isolated from the blood. We identified 49 differentially methylated cytosines (DMCs; q < 0.05) that were altered in obese compared with lean participants. We identified 2 sites (Chr.21:46,957,981 and Chr.21:46,957,915) in the 5' untranslated region of solute carrier family 19 member 1 (SLC19A1) with decreased methylation in obese participants (lean 0.73 ± 0.11 vs. obese 0.09 ± 0.05; lean 0.68 ± 0.10 vs. obese 0.09 ± 0.05, respectively). These 2 DMCs identified by obesity were also significantly predicted by insulin sensitivity (r = 0.68, P = 0.003; r = 0.66; P = 0.004). In addition, we performed a differentially methylated region (DMR) analysis and demonstrated a decrease in methylation of Chr.21:46,957,915-46,958,001 in SLC19A1 of -34.9% (70.4% lean vs. 35.5% obese). The decrease in whole-blood SLC19A1 methylation in our obese participants was similar to the change observed in skeletal muscle (Chr.21:46,957,981, lean 0.70 ± 0.09 vs. obese 0.31 ± 0.11 and Chr.21:46,957,915, lean 0.72 ± 0.11 vs. obese 0.31 ± 0.13). Pyrosequencing analysis further demonstrated a decrease in methylation at Chr.21:46,957,915 in both whole-blood (lean 0.71 ± 0.10 vs. obese 0.18 ± 0.06) and skeletal muscle (lean 0.71 ± 0.10 vs. obese 0.30 ± 0.11). Our findings demonstrate a new potential epigenetic biomarker, SLC19A1, for obesity and its underlying insulin resistance.
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Affiliation(s)
- Samantha E Day
- a School of Life Sciences , Arizona State University , Tempe , AZ , USA
| | - Richard L Coletta
- b School for the Science of Health Care Delivery , Arizona State University , Phoenix , AZ , USA
| | - Joon Young Kim
- c Division of Weight Management and Wellness , Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center , Pittsburgh , PA , USA
| | - Luis A Garcia
- b School for the Science of Health Care Delivery , Arizona State University , Phoenix , AZ , USA
| | - Latoya E Campbell
- a School of Life Sciences , Arizona State University , Tempe , AZ , USA
| | - Tonya R Benjamin
- d Endocrinology Department , Mayo Clinic in Arizona , Scottsdale , AZ , USA
| | - Lori R Roust
- d Endocrinology Department , Mayo Clinic in Arizona , Scottsdale , AZ , USA
| | | | - Lawrence J Mandarino
- e Department of Medicine , The University of Arizona College of Medicine , Tucson , AZ , USA
| | - Dawn K Coletta
- e Department of Medicine , The University of Arizona College of Medicine , Tucson , AZ , USA.,f Department of Basic Medical Sciences , The University of Arizona College of Medicine , Phoenix , AZ , USA
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107
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Mendelson MM, Marioni RE, Joehanes R, Liu C, Hedman ÅK, Aslibekyan S, Demerath EW, Guan W, Zhi D, Yao C, Huan T, Willinger C, Chen B, Courchesne P, Multhaup M, Irvin MR, Cohain A, Schadt EE, Grove ML, Bressler J, North K, Sundström J, Gustafsson S, Shah S, McRae AF, Harris SE, Gibson J, Redmond P, Corley J, Murphy L, Starr JM, Kleinbrink E, Lipovich L, Visscher PM, Wray NR, Krauss RM, Fallin D, Feinberg A, Absher DM, Fornage M, Pankow JS, Lind L, Fox C, Ingelsson E, Arnett DK, Boerwinkle E, Liang L, Levy D, Deary IJ. Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach. PLoS Med 2017; 14:e1002215. [PMID: 28095459 PMCID: PMC5240936 DOI: 10.1371/journal.pmed.1002215] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 12/08/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The link between DNA methylation, obesity, and adiposity-related diseases in the general population remains uncertain. METHODS AND FINDINGS We conducted an association study of body mass index (BMI) and differential methylation for over 400,000 CpGs assayed by microarray in whole-blood-derived DNA from 3,743 participants in the Framingham Heart Study and the Lothian Birth Cohorts, with independent replication in three external cohorts of 4,055 participants. We examined variations in whole blood gene expression and conducted Mendelian randomization analyses to investigate the functional and clinical relevance of the findings. We identified novel and previously reported BMI-related differential methylation at 83 CpGs that replicated across cohorts; BMI-related differential methylation was associated with concurrent changes in the expression of genes in lipid metabolism pathways. Genetic instrumental variable analysis of alterations in methylation at one of the 83 replicated CpGs, cg11024682 (intronic to sterol regulatory element binding transcription factor 1 [SREBF1]), demonstrated links to BMI, adiposity-related traits, and coronary artery disease. Independent genetic instruments for expression of SREBF1 supported the findings linking methylation to adiposity and cardiometabolic disease. Methylation at a substantial proportion (16 of 83) of the identified loci was found to be secondary to differences in BMI. However, the cross-sectional nature of the data limits definitive causal determination. CONCLUSIONS We present robust associations of BMI with differential DNA methylation at numerous loci in blood cells. BMI-related DNA methylation and gene expression provide mechanistic insights into the relationship between DNA methylation, obesity, and adiposity-related diseases.
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Affiliation(s)
- Michael M. Mendelson
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Cardiology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Riccardo E. Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Roby Joehanes
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Hebrew SeniorLife, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chunyu Liu
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Biostatistics, Boston University, Boston, Massachusetts, United States of America
| | - Åsa K. Hedman
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Stella Aslibekyan
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ellen W. Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Degui Zhi
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Chen Yao
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tianxiao Huan
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christine Willinger
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brian Chen
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Paul Courchesne
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Multhaup
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Marguerite R. Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ariella Cohain
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Eric E. Schadt
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Megan L. Grove
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Kari North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Johan Sundström
- Cardiovascular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Stefan Gustafsson
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Sonia Shah
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Allan F. McRae
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jude Gibson
- Wellcome Trust Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Redmond
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Janie Corley
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Lee Murphy
- Wellcome Trust Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Erica Kleinbrink
- Center for Molecular Medicine and Genetics and Department of Neurology, Wayne State University, Detroit, Michigan, United States of America
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics and Department of Neurology, Wayne State University, Detroit, Michigan, United States of America
| | - Peter M. Visscher
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Naomi R. Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Ronald M. Krauss
- Children’s Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Daniele Fallin
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Andrew Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Devin M. Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Myriam Fornage
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Brown Foundation Institute of Molecular Medicine, University of Texas, Houston, Texas, United States of America
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lars Lind
- Cardiovascular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Caroline Fox
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Erik Ingelsson
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Donna K. Arnett
- College of Public Health, University of Kentucky, Lexington, Kentucky, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Liming Liang
- Departments of Epidemiology and Biostatistics, School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Daniel Levy
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
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Keller M, Hopp L, Liu X, Wohland T, Rohde K, Cancello R, Klös M, Bacos K, Kern M, Eichelmann F, Dietrich A, Schön MR, Gärtner D, Lohmann T, Dreßler M, Stumvoll M, Kovacs P, DiBlasio AM, Ling C, Binder H, Blüher M, Böttcher Y. Genome-wide DNA promoter methylation and transcriptome analysis in human adipose tissue unravels novel candidate genes for obesity. Mol Metab 2016; 6:86-100. [PMID: 28123940 PMCID: PMC5220399 DOI: 10.1016/j.molmet.2016.11.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/03/2016] [Accepted: 11/10/2016] [Indexed: 02/04/2023] Open
Abstract
Objective/methods DNA methylation plays an important role in obesity and related metabolic complications. We examined genome-wide DNA promoter methylation along with mRNA profiles in paired samples of human subcutaneous adipose tissue (SAT) and omental visceral adipose tissue (OVAT) from non-obese vs. obese individuals. Results We identified negatively correlated methylation and expression of several obesity-associated genes in our discovery dataset and in silico replicated ETV6 in two independent cohorts. Further, we identified six adipose tissue depot-specific genes (HAND2, HOXC6, PPARG, SORBS2, CD36, and CLDN1). The effects were further supported in additional independent cohorts. Our top hits might play a role in adipogenesis and differentiation, obesity, lipid metabolism, and adipose tissue expandability. Finally, we show that in vitro methylation of SORBS2 directly represses gene expression. Conclusions Taken together, our data show distinct tissue specific epigenetic alterations which associate with obesity. Obesity-associated differences in DNA promoter methylation and transcriptome in human adipose tissue (ETV6). Depot-specific analyses revealed novel/known genes (HAND2, HOXC6, PPARG, SORBS2, CD36, CLDN1). EWAS revealed SSPN and CCDC125 associated to BMI in SAT or OVAT, respectively. Differentially methylated genes overlap in part with GWAS hits for obesity and fat distribution.
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Affiliation(s)
- Maria Keller
- IFB Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany
| | - Lydia Hopp
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, 04103, Germany
| | - Xuanshi Liu
- IFB Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany; Bioinformatics Group, Department of Computer Science, University of Leipzig, 04107, Leipzig, Germany
| | - Tobias Wohland
- IFB Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany
| | - Kerstin Rohde
- IFB Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany
| | - Raffaella Cancello
- Molecular Biology Laboratory, Istituto Auxologico Italiano IRCCS, Milan, 20149, Italy
| | - Matthias Klös
- IFB Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 205 02, Malmoe, Sweden
| | - Matthias Kern
- Department of Medicine, University of Leipzig, Leipzig, 04103, Germany
| | - Fabian Eichelmann
- IFB Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany
| | - Arne Dietrich
- IFB Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany; Department of Surgery, University of Leipzig, Leipzig, 04103, Germany
| | - Michael R Schön
- Städtisches Klinikum Karlsruhe, Clinic of Visceral Surgery, Karlsruhe, 76133, Germany
| | - Daniel Gärtner
- Städtisches Klinikum Karlsruhe, Clinic of Visceral Surgery, Karlsruhe, 76133, Germany
| | - Tobias Lohmann
- Municipal Clinic Dresden-Neustadt, Dresden, 01129, Germany
| | - Miriam Dreßler
- Municipal Clinic Dresden-Neustadt, Dresden, 01129, Germany
| | - Michael Stumvoll
- IFB Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany; Department of Medicine, University of Leipzig, Leipzig, 04103, Germany
| | - Peter Kovacs
- IFB Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany
| | - Anna-Maria DiBlasio
- Molecular Biology Laboratory, Istituto Auxologico Italiano IRCCS, Milan, 20149, Italy
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 205 02, Malmoe, Sweden
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, 04103, Germany
| | - Matthias Blüher
- IFB Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany; Department of Medicine, University of Leipzig, Leipzig, 04103, Germany.
| | - Yvonne Böttcher
- IFB Adiposity Diseases, University of Leipzig, Leipzig, 04103, Germany.
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Arner P, Sahlqvist AS, Sinha I, Xu H, Yao X, Waterworth D, Rajpal D, Loomis AK, Freudenberg JM, Johnson T, Thorell A, Näslund E, Ryden M, Dahlman I. The epigenetic signature of systemic insulin resistance in obese women. Diabetologia 2016; 59:2393-2405. [PMID: 27535281 PMCID: PMC5506095 DOI: 10.1007/s00125-016-4074-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/13/2016] [Indexed: 02/07/2023]
Abstract
AIMS/HYPOTHESIS Insulin resistance (IR) links obesity to type 2 diabetes. The aim of this study was to explore whether white adipose tissue (WAT) epigenetic dysregulation is associated with systemic IR by genome-wide CG dinucleotide (CpG) methylation and gene expression profiling in WAT from insulin-resistant and insulin-sensitive women. A secondary aim was to determine whether the DNA methylation signature in peripheral blood mononuclear cells (PBMCs) reflects WAT methylation and, if so, can be used as a marker for systemic IR. METHODS From 220 obese women, we selected a total of 80 individuals from either of the extreme ends of the distribution curve of HOMA-IR, an indirect measure of systemic insulin sensitivity. Genome-wide transcriptome and DNA CpG methylation profiling by array was performed on subcutaneous (SAT) and visceral (omental) adipose tissue (VAT). CpG methylation in PBMCs was assayed in the same cohort. RESULTS There were 647 differentially expressed genes (false discovery rate [FDR] 10%) in SAT, all of which displayed directionally consistent associations in VAT. This suggests that IR is associated with dysregulated expression of a common set of genes in SAT and VAT. The average degree of DNA methylation did not differ between the insulin-resistant and insulin-sensitive group in any of the analysed tissues/cells. There were 223 IR-associated genes in SAT containing a total of 336 nominally significant differentially methylated sites (DMS). The 223 IR-associated genes were over-represented in pathways related to integrin cell surface interactions and insulin signalling and included COL5A1, GAB1, IRS2, PFKFB3 and PTPRJ. In VAT there were a total of 51 differentially expressed genes (FDR 10%); 18 IR-associated genes contained a total of 29 DMS. CONCLUSIONS/INTERPRETATION In individuals discordant for insulin sensitivity, the average DNA CpG methylation in SAT and VAT is similar, although specific genes, particularly in SAT, display significantly altered expression and DMS in IR, possibly indicating that epigenetic regulation of these genes influences metabolism.
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Affiliation(s)
- Peter Arner
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital, C2:94, Huddinge, S-141 86, Stockholm, Sweden
| | | | - Indranil Sinha
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Huan Xu
- GlaxoSmithKline R&D, Research Triangle Park, NC, USA
| | - Xiang Yao
- Computational and Systems Biology, Discovery Sciences, Janssen Pharmaceutical, Research & Development, LLC, San Diego, CA, USA
| | | | | | | | | | | | - Anders Thorell
- Department of Surgery, Ersta Hospital, Stockholm, Sweden
- Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Danderyd, Sweden
| | - Erik Näslund
- Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Danderyd, Sweden
| | - Mikael Ryden
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital, C2:94, Huddinge, S-141 86, Stockholm, Sweden
| | - Ingrid Dahlman
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital, C2:94, Huddinge, S-141 86, Stockholm, Sweden.
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110
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Ling C, Rönn T. Epigenetic markers to further understand insulin resistance. Diabetologia 2016; 59:2295-2297. [PMID: 27650286 DOI: 10.1007/s00125-016-4109-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 08/31/2016] [Indexed: 12/19/2022]
Abstract
Epigenetic variation in human adipose tissue has been linked to type 2 diabetes and its related risk factors including age and obesity. Insulin resistance, a key risk factor for type 2 diabetes, may also be associated with altered DNA methylation in visceral and subcutaneous adipose tissue. Furthermore, linking epigenetic variation in target tissues to similar changes in blood cells may identify new blood-based biomarkers. In this issue of Diabetologia, Arner et al studied the transcriptome and methylome in subcutaneous and visceral adipose tissue of 80 obese women who were either insulin-sensitive or -resistant (DOI 10.1007/s00125-016-4074-5 ). While they found differences in gene expression between the two groups, no alterations in DNA methylation were found after correction for multiple testing. Nevertheless, based on nominal p values, their methylation data overlapped with methylation differences identified in adipose tissue of individuals with type 2 diabetes compared with healthy individuals. Differential methylation of these overlapping CpG sites may predispose to diabetes by occurring already in the insulin-resistant state. Furthermore, some methylation changes may contribute to an inflammatory process in adipose tissue since the identified CpG sites were annotated to genes encoding proteins involved in inflammation. Finally, the methylation pattern in circulating leucocytes did not mirror the adipose tissue methylome of these 80 women. Together, identifying novel molecular mechanisms contributing to insulin resistance and type 2 diabetes may help advance the search for new therapeutic alternatives.
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Affiliation(s)
- Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Jan Waldenströms gata 35, 205 02, Malmö, Sweden.
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Jan Waldenströms gata 35, 205 02, Malmö, Sweden
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Main AM, Gillberg L, Jacobsen AL, Nilsson E, Gjesing AP, Hansen T, Pedersen O, Ribel-Madsen R, Vaag A. DNA methylation and gene expression of HIF3A: cross-tissue validation and associations with BMI and insulin resistance. Clin Epigenetics 2016; 8:89. [PMID: 27594926 PMCID: PMC5010678 DOI: 10.1186/s13148-016-0258-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 08/24/2016] [Indexed: 12/17/2022] Open
Abstract
Background Associations between BMI and DNA methylation of hypoxia-inducible factor 3-alpha (HIF3A) in both blood cells and subcutaneous adipose tissue (SAT) have been reported. In this study, we investigated associations between BMI and HIF3A DNA methylation in the blood and SAT from the same individuals, and whether HIF3A gene expression in SAT and skeletal muscle biopsies showed associations with BMI and insulin resistance. Furthermore, we aimed to investigate gender specificity and heritability of these traits. Methods We studied 137 first-degree relatives of type 2 diabetes (T2D) patients from 48 families, from whom we had SAT and muscle biopsies. DNA methylation of four CpG sites in the HIF3A promoter was analyzed in the blood and SAT by pyrosequencing, and HIF3A gene expression was analyzed in SAT and muscle by qPCR. An index of whole-body insulin sensitivity was estimated from oral glucose tolerance tests. Results BMI was associated with HIF3A methylation at one CpG site in the blood, and there was a positive association between the blood and SAT methylation levels at a different CpG site within the individuals. The SAT methylation level did not correlate with HIF3A gene expression. Interestingly, HIF3A expression in SAT, but not in muscle, associated negatively with BMI and whole-body insulin resistance. We found a significant effect of familiality on HIF3A methylation levels in the blood and HIF3A expression levels in skeletal muscle. Conclusions Our findings are in line with the previously reported link between BMI and DNA methylation of HIF3A in the blood. The tissue-specific results of HIF3A gene expression indicate that SAT is the more functional tissue in which a low expression may adversely affect whole-body insulin sensitivity. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0258-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ailsa Maria Main
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200 Copenhagen, Denmark
| | - Linn Gillberg
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200 Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna Louisa Jacobsen
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200 Copenhagen, Denmark
| | - Emma Nilsson
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200 Copenhagen, Denmark.,Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | - Anette Prior Gjesing
- Section of Metabolic Genetics, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Section of Metabolic Genetics, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Section of Metabolic Genetics, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Ribel-Madsen
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200 Copenhagen, Denmark.,The Danish Diabetes Academy, Odense University Hospital, Odense, Denmark
| | - Allan Vaag
- Department of Endocrinology, Rigshospitalet, Section 7652, Tagensvej 20, DK-2200 Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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112
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Pfeiffer S, Krüger J, Maierhofer A, Böttcher Y, Klöting N, El Hajj N, Schleinitz D, Schön MR, Dietrich A, Fasshauer M, Lohmann T, Dreßler M, Stumvoll M, Haaf T, Blüher M, Kovacs P. Hypoxia-inducible factor 3A gene expression and methylation in adipose tissue is related to adipose tissue dysfunction. Sci Rep 2016; 6:27969. [PMID: 27346320 PMCID: PMC4921806 DOI: 10.1038/srep27969] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 05/26/2016] [Indexed: 12/17/2022] Open
Abstract
Recently, a genome-wide analysis identified DNA methylation of the HIF3A (hypoxia-inducible factor 3A) as strongest correlate of BMI. Here we tested the hypothesis that HIF3A mRNA expression and CpG-sites methylation in adipose tissue (AT) and genetic variants in HIF3A are related to parameters of AT distribution and function. In paired samples of subcutaneous AT (SAT) and visceral AT (VAT) from 603 individuals, we measured HIF3A mRNA expression and analyzed its correlation with obesity and related traits. In subgroups of individuals, we investigated the effects on HIF3A genetic variants on its AT expression (N = 603) and methylation of CpG-sites (N = 87). HIF3A expression was significantly higher in SAT compared to VAT and correlated with obesity and parameters of AT dysfunction (including CRP and leucocytes count). HIF3A methylation at cg22891070 was significantly higher in VAT compared to SAT and correlated with BMI, abdominal SAT and VAT area. Rs8102595 showed a nominal significant association with AT HIF3A methylation levels as well as with obesity and fat distribution. HIF3A expression and methylation in AT are fat depot specific, related to obesity and AT dysfunction. Our data support the hypothesis that HIF pathways may play an important role in the development of AT dysfunction in obesity.
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Affiliation(s)
- Susanne Pfeiffer
- Department of Medicine, Dermatology und Neurology, Department of Endocrinology und Nephrology, University of Leipzig, Leipzig, Germany
| | - Jacqueline Krüger
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Anna Maierhofer
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Yvonne Böttcher
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Nora Klöting
- Department of Medicine, Dermatology und Neurology, Department of Endocrinology und Nephrology, University of Leipzig, Leipzig, Germany
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Nady El Hajj
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Dorit Schleinitz
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Michael R. Schön
- Clinic of Visceral Surgery, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | - Arne Dietrich
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Surgery, University of Leipzig, Leipzig, Germany
| | - Mathias Fasshauer
- Department of Medicine, Dermatology und Neurology, Department of Endocrinology und Nephrology, University of Leipzig, Leipzig, Germany
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | | | | | - Michael Stumvoll
- Department of Medicine, Dermatology und Neurology, Department of Endocrinology und Nephrology, University of Leipzig, Leipzig, Germany
| | - Thomas Haaf
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Matthias Blüher
- Department of Medicine, Dermatology und Neurology, Department of Endocrinology und Nephrology, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
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A Genome-Wide mQTL Analysis in Human Adipose Tissue Identifies Genetic Variants Associated with DNA Methylation, Gene Expression and Metabolic Traits. PLoS One 2016; 11:e0157776. [PMID: 27322064 PMCID: PMC4913906 DOI: 10.1371/journal.pone.0157776] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 06/03/2016] [Indexed: 01/17/2023] Open
Abstract
Little is known about the extent to which interactions between genetics and epigenetics may affect the risk of complex metabolic diseases and/or their intermediary phenotypes. We performed a genome-wide DNA methylation quantitative trait locus (mQTL) analysis in human adipose tissue of 119 men, where 592,794 single nucleotide polymorphisms (SNPs) were related to DNA methylation of 477,891 CpG sites, covering 99% of RefSeq genes. SNPs in significant mQTLs were further related to gene expression in adipose tissue and obesity related traits. We found 101,911 SNP-CpG pairs (mQTLs) in cis and 5,342 SNP-CpG pairs in trans showing significant associations between genotype and DNA methylation in adipose tissue after correction for multiple testing, where cis is defined as distance less than 500 kb between a SNP and CpG site. These mQTLs include reported obesity, lipid and type 2 diabetes loci, e.g. ADCY3/POMC, APOA5, CETP, FADS2, GCKR, SORT1 and LEPR. Significant mQTLs were overrepresented in intergenic regions meanwhile underrepresented in promoter regions and CpG islands. We further identified 635 SNPs in significant cis-mQTLs associated with expression of 86 genes in adipose tissue including CHRNA5, G6PC2, GPX7, RPL27A, THNSL2 and ZFP57. SNPs in significant mQTLs were also associated with body mass index (BMI), lipid traits and glucose and insulin levels in our study cohort and public available consortia data. Importantly, the Causal Inference Test (CIT) demonstrates how genetic variants mediate their effects on metabolic traits (e.g. BMI, cholesterol, high-density lipoprotein (HDL), hemoglobin A1c (HbA1c) and homeostatic model assessment of insulin resistance (HOMA-IR)) via altered DNA methylation in human adipose tissue. This study identifies genome-wide interactions between genetic and epigenetic variation in both cis and trans positions influencing gene expression in adipose tissue and in vivo (dys)metabolic traits associated with the development of obesity and diabetes.
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114
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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: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [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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Lemche E, Chaban OS, Lemche AV. Neuroendocrinological and Epigenetic Mechanisms Subserving Autonomic Imbalance and HPA Dysfunction in the Metabolic Syndrome. Front Neurosci 2016; 10:142. [PMID: 27147943 PMCID: PMC4830841 DOI: 10.3389/fnins.2016.00142] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/21/2016] [Indexed: 12/18/2022] Open
Abstract
Impact of environmental stress upon pathophysiology of the metabolic syndrome (MetS) has been substantiated by epidemiological, psychophysiological, and endocrinological studies. This review discusses recent advances in the understanding of causative roles of nutritional factors, sympathomedullo-adrenal (SMA) and hypothalamic-pituitary adrenocortical (HPA) axes, and adipose tissue chronic low-grade inflammation processes in MetS. Disturbances in the neuroendocrine systems for leptin, melanocortin, and neuropeptide Y (NPY)/agouti-related protein systems have been found resulting directly in MetS-like conditions. The review identifies candidate risk genes from factors shown critical for the functioning of each of these neuroendocrine signaling cascades. In its meta-analytic part, recent studies in epigenetic modification (histone methylation, acetylation, phosphorylation, ubiquitination) and posttranscriptional gene regulation by microRNAs are evaluated. Several studies suggest modification mechanisms of early life stress (ELS) and diet-induced obesity (DIO) programming in the hypothalamic regions with populations of POMC-expressing neurons. Epigenetic modifications were found in cortisol (here HSD11B1 expression), melanocortin, leptin, NPY, and adiponectin genes. With respect to adiposity genes, epigenetic modifications were documented for fat mass gene cluster APOA1/C3/A4/A5, and the lipolysis gene LIPE. With regard to inflammatory, immune and subcellular metabolism, PPARG, NKBF1, TNFA, TCF7C2, and those genes expressing cytochrome P450 family enzymes involved in steroidogenesis and in hepatic lipoproteins were documented for epigenetic modifications.
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Affiliation(s)
- Erwin Lemche
- Section of Cognitive Neuropsychiatry, Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London London, UK
| | - Oleg S Chaban
- Section of Psychosomatic Medicine, Bogomolets National Medical University Kiev, Ukraine
| | - Alexandra V Lemche
- Department of Medical Science, Institute of Clinical Research Berlin, Germany
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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] [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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Blood-based biomarkers of age-associated epigenetic changes in human islets associate with insulin secretion and diabetes. Nat Commun 2016; 7:11089. [PMID: 27029739 PMCID: PMC4821875 DOI: 10.1038/ncomms11089] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/19/2016] [Indexed: 12/18/2022] Open
Abstract
Aging associates with impaired pancreatic islet function and increased type 2 diabetes (T2D) risk. Here we examine whether age-related epigenetic changes affect human islet function and if blood-based epigenetic biomarkers reflect these changes and associate with future T2D. We analyse DNA methylation genome-wide in islets from 87 non-diabetic donors, aged 26-74 years. Aging associates with increased DNA methylation of 241 sites. These sites cover loci previously associated with T2D, for example, KLF14. Blood-based epigenetic biomarkers reflect age-related methylation changes in 83 genes identified in human islets (for example, KLF14, FHL2, ZNF518B and FAM123C) and some associate with insulin secretion and T2D. DNA methylation correlates with islet expression of multiple genes, including FHL2, ZNF518B, GNPNAT1 and HLTF. Silencing these genes in β-cells alter insulin secretion. Together, we demonstrate that blood-based epigenetic biomarkers reflect age-related DNA methylation changes in human islets, and associate with insulin secretion in vivo and T2D.
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118
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Sierra MI, Fernández AF, Fraga MF. Epigenetics of Aging. Curr Genomics 2016; 16:435-40. [PMID: 27019618 PMCID: PMC4765531 DOI: 10.2174/1389202916666150817203459] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 06/20/2015] [Accepted: 06/26/2015] [Indexed: 01/10/2023] Open
Abstract
The best-known phenomenon exemplifying epigenetic drift (the alteration of epigenetic patterns during aging) is the gradual decrease of global DNA methylation. Aging cells, different tissue types, as well as a variety of human diseases possess their own distinct DNA methylation profiles, although the functional impact of these is not always clear. DNA methylation appears to be a dynamic tool of transcriptional regulation, with an extra layer of complexity due to the recent discovery of the conversion of 5-methylcytosine into 5-hydroxymethylcytosine. This age-related DNA demethylation is associated with changes in histone modification patterns and, furthermore, we now know that ncRNAs have evolved in eukaryotes as epigenetic regulators of gene expression. In this review, we will discuss current knowledge on how all these epigenetic phenomena are implicated in human aging, and their links with external, internal and stochastic factors which can affect human age-related diseases onset.
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Affiliation(s)
- Marta I Sierra
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo and Nanomaterials and Nanotechnology Research Center (CINN-CSIC)-Universidad de Oviedo (UO) -Principado de Asturias, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo and Nanomaterials and Nanotechnology Research Center (CINN-CSIC)-Universidad de Oviedo (UO) -Principado de Asturias, Spain
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo and Nanomaterials and Nanotechnology Research Center (CINN-CSIC)-Universidad de Oviedo (UO) -Principado de Asturias, Spain
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119
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Epigenetic and Transcriptional Alterations in Human Adipose Tissue of Polycystic Ovary Syndrome. Sci Rep 2016; 6:22883. [PMID: 26975253 PMCID: PMC4791632 DOI: 10.1038/srep22883] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/23/2016] [Indexed: 01/08/2023] Open
Abstract
Genetic and epigenetic factors may predispose women to polycystic ovary syndrome (PCOS), a common heritable disorder of unclear etiology. Here we investigated differences in genome-wide gene expression and DNA methylation in adipose tissue from 64 women with PCOS and 30 controls. In total, 1720 unique genes were differentially expressed (Q < 0.05). Six out of twenty selected genes with largest expression difference (CYP1B1, GPT), genes linked to PCOS (RAB5B) or type 2 diabetes (PPARG, SVEP1), and methylation (DMAP1) were replicated in a separate case-control study. In total, 63,213 sites (P < 0.05) and 440 sites (Q < 0.15) were differently methylated. Thirty differentially expressed genes had corresponding changes in 33 different DNA methylation sites. Moreover, a total number of 1913 pairs of differentially expressed “gene-CpG” probes were significantly correlated after correction for multiple testing and corresponded with 349 unique genes. In conclusion, we identified a large number of genes and pathways that are affected in adipose tissue from women with PCOS. We also identified specific DNA methylation pathways that may affect mRNA expression. Together, these novel findings show that women with PCOS have multiple transcriptional and epigenetic changes in adipose tissue that are relevant for development of the disease.
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120
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Zhang JY, Kothapalli KS, Brenna JT. Desaturase and elongase-limiting endogenous long-chain polyunsaturated fatty acid biosynthesis. Curr Opin Clin Nutr Metab Care 2016; 19:103-10. [PMID: 26828581 PMCID: PMC4768719 DOI: 10.1097/mco.0000000000000254] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW Endogenous synthesis of the long-chain polyunsaturated fatty acids (LCPUFAs) is mediated by the fatty acid desaturase (FADS) gene cluster (11q12-13.1) and elongation of very long-chain fatty acids 2 (ELOVL2) (6p24.2) and ELOVL5 (6p12.1). Although older biochemical work identified the product of one gene, FADS2, rate limiting for LCPUFA synthesis, recent studies suggest that polymorphisms in any of these genes can limit accumulation of product LCPUFA. RECENT FINDINGS Genome-wide association study (GWAS) of Greenland Inuit shows strong adaptation signals within FADS gene cluster, attributed to high omega-3 fatty acid intake, while GWAS found ELOVL2 associated with sleep duration, age and DNA methylation. ELOVL5 coding mutations cause spinocerebellar ataxia 38, and epigenetic marks were associated with depression and suicide risk. Two sterol response element binding sites were found on ELOVL5, a SREBP-1c target gene. Minor allele carriers of a 3 single nucleotide polymorphism (SNP) haplotype in ELOVL2 have decreased 22 : 6n-3 levels. Unequivocal molecular evidence shows mammalian FADS2 catalyzes direct Δ4-desaturation to yield 22 : 6n-3 and 22 : 5n-6. An SNP near FADS1 influences the levels of 5-lipoxygenase products and epigenetic alteration. SUMMARY Genetic polymorphisms within FADS and ELOVL can limit LCPUFA product accumulation at any step of the biosynthetic pathway.
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Affiliation(s)
| | | | - J. Thomas Brenna
- Corresponding author: J. Thomas Brenna, voice (607) 255-9182, fax (607) 255-1033,
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121
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Huang YT, Chu S, Loucks EB, Lin CL, Eaton CB, Buka SL, Kelsey KT. Epigenome-wide profiling of DNA methylation in paired samples of adipose tissue and blood. Epigenetics 2016; 11:227-36. [PMID: 26891033 DOI: 10.1080/15592294.2016.1146853] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Many epigenetic association studies have attempted to identify DNA methylation markers in blood that are able to mirror those in target tissues. Although some have suggested potential utility of surrogate epigenetic markers in blood, few studies have collected data to directly compare DNA methylation across tissues from the same individuals. Here, epigenomic data were collected from adipose tissue and blood in 143 subjects using Illumina HumanMethylation450 BeadChip array. The top axis of epigenome-wide variation differentiates adipose tissue from blood, which is confirmed internally using cross-validation and externally with independent data from the two tissues. We identified 1,285 discordant genes and 1,961 concordant genes between blood and adipose tissue. RNA expression data of the two classes of genes show consistent patterns with those observed in DNA methylation. The discordant genes are enriched in biological functions related to immune response, leukocyte activation or differentiation, and blood coagulation. We distinguish the CpG-specific correlation from the within-subject correlation and emphasize that the magnitude of within-subject correlation does not guarantee the utility of surrogate epigenetic markers. The study reinforces the critical role of DNA methylation in regulating gene expression and cellular phenotypes across tissues, and highlights the caveats of using methylation markers in blood to mirror the corresponding profile in the target tissue.
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Affiliation(s)
- Yen-Tsung Huang
- a Departments of Epidemiology and Biostatistics , Brown University , Providence , RI , USA
| | - Su Chu
- b Department of Epidemiology , Brown University , Providence , RI , USA
| | - Eric B Loucks
- c Department of Epidemiology , Brown University , Providence , RI , USA
| | - Chien-Ling Lin
- d Department of Molecular Biology , Cell Biology and Biochemistry, Brown University , Providence , RI , USA
| | - Charles B Eaton
- e Departments of Family Medicine and Epidemiology , Brown University , Providence , RI , USA
| | - Stephen L Buka
- f Department of Epidemiology , Brown University , Providence , RI , USA
| | - Karl T Kelsey
- g Departments of Epidemiology and Pathobiology , Brown University , Providence , RI , USA
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Pennington KL, DeAngelis MM. Epigenetic Mechanisms of the Aging Human Retina. J Exp Neurosci 2016; 9:51-79. [PMID: 26966390 PMCID: PMC4777243 DOI: 10.4137/jen.s25513] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/07/2016] [Accepted: 01/13/2016] [Indexed: 12/20/2022] Open
Abstract
Degenerative retinal diseases, such as glaucoma, age-related macular degeneration, and diabetic retinopathy, have complex etiologies with environmental, genetic, and epigenetic contributions to disease pathology. Much effort has gone into elucidating both the genetic and the environmental risk factors for these retinal diseases. However, little is known about how these genetic and environmental risk factors bring about molecular changes that lead to pathology. Epigenetic mechanisms have received extensive attention of late for their promise of bridging the gap between environmental exposures and disease development via their influence on gene expression. Recent studies have identified epigenetic changes that associate with the incidence and/or progression of each of these retinal diseases. Therefore, these epigenetic modifications may be involved in the underlying pathological mechanisms leading to blindness. Further genome-wide epigenetic studies that incorporate well-characterized tissue samples, consider challenges similar to those relevant to gene expression studies, and combine the genome-wide epigenetic data with genome-wide genetic and expression data to identify additional potentially causative agents of disease are needed. Such studies will allow researchers to create much-needed therapeutics to prevent and/or intervene in disease progression. Improved therapeutics will greatly enhance the quality of life and reduce the burden of disease management for millions of patients living with these potentially blinding conditions.
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Affiliation(s)
- Katie L Pennington
- Postdoctoral Fellow, Department of Ophthalmology & Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | - Margaret M DeAngelis
- Associate Professor, Department of Ophthalmology & Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
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123
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Epigenetic associations of type 2 diabetes and BMI in an Arab population. Clin Epigenetics 2016; 8:13. [PMID: 26823690 PMCID: PMC4730771 DOI: 10.1186/s13148-016-0177-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 01/18/2016] [Indexed: 01/07/2023] Open
Abstract
Background The prevalence of type 2 diabetes (T2D) and obesity has dramatically increased within a few generations, reaching epidemic levels. In addition to genetic risk factors, epigenetic mechanisms triggered by changing environment are investigated for their role in the pathogenesis of these complex diseases. Epigenome-wide association studies (EWASs) have revealed significant associations of T2D, obesity, and BMI with DNA methylation. However, populations from the Middle East, where T2D and obesity rates are highest worldwide, have not been investigated so far. Methods We performed the first EWAS in an Arab population with T2D and BMI and attempted to replicate 47 EWAS associations previously reported in Caucasians. We used the Illumina Infinium HumanMethylation450 BeadChip to quantify DNA methylation in whole blood DNA from 123 subjects of 15 multigenerational families from Qatar. To investigate the effect of differing genetic background and environment on the epigenetic associations, we further assessed the effect of replicated loci in 810 twins from UK. Results Our EWAS suggested a novel association between T2D and cg06721411 (DQX1; p value = 1.18 × 10−9). We replicated in the Qatari population seven CpG associations with BMI (SOCS3, p value = 3.99 × 10−6; SREBF1, p value = 4.33 × 10−5; SBNO2, p value = 5.87 × 10−5; CPT1A, p value = 7.99 × 10−5; PRR5L, p value = 1.85 × 10−4; cg03078551, intergenic region on chromosome 17; p value = 1.00 × 10−3; LY6G6E, p value = 1.10 × 10−3) and one with T2D (TXNIP, p value = 2.46 × 10−5). All the associations were further confirmed in the UK cohort for both BMI and T2D. Meta-analysis increased the significance of the observed associations and revealed strong heterogeneity of the effect sizes (apart from CPT1A), although associations at these loci showed concordant direction in the two populations. Conclusions Our study replicated eight known CpG associations with T2D or BMI in an Arab population. Heterogeneity of the effects at all loci except CPT1A between the Qatari and UK studies suggests that the underlying mechanisms might depend on genetic background and environmental pressure. Our EWAS results provide a basis for comparison with other ethnicities. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0177-6) contains supplementary material, which is available to authorized users.
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Potential Diagnostic and Prognostic Biomarkers of Epigenetic Drift within the Cardiovascular Compartment. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2465763. [PMID: 26942189 PMCID: PMC4749768 DOI: 10.1155/2016/2465763] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 11/02/2015] [Accepted: 11/24/2015] [Indexed: 12/15/2022]
Abstract
Biomarkers encompass a wide range of different measurable indicators, representing a tangible link to physiological changes occurring within the body. Accessibility, sensitivity, and specificity are significant factors in biomarker suitability. New biomarkers continue to be discovered, and questions over appropriate selection and assessment of their usefulness remain. If traditional markers of inflammation are not sufficiently robust in their specificity, then perhaps alternative means of detection may provide more information. Epigenetic drift (epigenetic modifications as they occur as a direct function with age), and its ancillary elements, including platelets, secreted microvesicles (MVs), and microRNA (miRNA), may hold enormous predictive potential. The majority of epigenetic drift observed in blood is independent of variations in blood cell composition, addressing concerns affecting traditional blood-based biomarker efficacy. MVs are found in plasma and other biological fluids in healthy individuals. Altered MV/miRNA profiles may also be found in individuals with various diseases. Platelets are also highly reflective of physiological and lifestyle changes, making them extremely sensitive biomarkers of human health. Platelets release increased levels of MVs in response to various stimuli and under a plethora of disease states, which demonstrate a functional effect on other cell types.
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Schleinitz D. Genetic Determination of Serum Levels of Diabetes-Associated Adipokines. Rev Diabet Stud 2016; 12:277-98. [PMID: 26859657 PMCID: PMC5275755 DOI: 10.1900/rds.2015.12.277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 10/06/2015] [Indexed: 12/16/2022] Open
Abstract
Adipose tissue secretes an abundance of proteins. Some of these proteins are known as adipokines and adipose-derived hormones which have been linked with metabolic disorders, including type 2 diabetes, and even with cancer. Variance in serum adipokine concentration is often closely associated with an increase (obesity) or decrease (lipodystrophy) in fat tissue mass, and it is affected by age, gender, and localization of the adipose tissue. However, there may be genetic variants which, in consequence, influence the serum concentration of a certain adipokine, and thereby promote metabolic disturbances or, with regard to the "protective" allele, exert beneficial effects. This review focuses on the genetic determination of serum levels of the following adipokines: adiponectin, chemerin, leptin, progranulin, resistin, retinol binding protein 4, vaspin, adipsin, apelin, and omentin. The article reports on the latest findings from genome-wide association studies (GWAS) and candidate gene studies, showing variants located in/nearby the adipokine genes and other (non-receptor) genes. An extra chapter highlights adipokine-receptor variants. Epigenetic studies on adipokines are also addressed.
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Affiliation(s)
- Dorit Schleinitz
- Integrated Research and Treatment Center AdiposityDiseases, University of Leipzig, Liebigstr. 21, 04103 Leipzig, Germany
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Bray MS, Loos RJF, McCaffery JM, Ling C, Franks PW, Weinstock GM, Snyder MP, Vassy JL, Agurs-Collins T. NIH working group report-using genomic information to guide weight management: From universal to precision treatment. Obesity (Silver Spring) 2016; 24:14-22. [PMID: 26692578 PMCID: PMC4689320 DOI: 10.1002/oby.21381] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/16/2015] [Accepted: 10/17/2015] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Precision medicine utilizes genomic and other data to optimize and personalize treatment. Although more than 2,500 genetic tests are currently available, largely for extreme and/or rare phenotypes, the question remains whether this approach can be used for the treatment of common, complex conditions like obesity, inflammation, and insulin resistance, which underlie a host of metabolic diseases. METHODS This review, developed from a Trans-NIH Conference titled "Genes, Behaviors, and Response to Weight Loss Interventions," provides an overview of the state of genetic and genomic research in the area of weight change and identifies key areas for future research. RESULTS Although many loci have been identified that are associated with cross-sectional measures of obesity/body size, relatively little is known regarding the genes/loci that influence dynamic measures of weight change over time. Although successful short-term weight loss has been achieved using many different strategies, sustainable weight loss has proven elusive for many, and there are important gaps in our understanding of energy balance regulation. CONCLUSIONS Elucidating the molecular basis of variability in weight change has the potential to improve treatment outcomes and inform innovative approaches that can simultaneously take into account information from genomic and other sources in devising individualized treatment plans.
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Affiliation(s)
- Molly S Bray
- Department of Nutritional Sciences, The University of Texas at AustinAustin, Texas, USA
| | - Ruth JF Loos
- Department of Preventive Medicine, The Charles Bronfman Institute for Personalized Medicine, The Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount SinaiNew York City, New York, USA
| | - Jeanne M McCaffery
- Department of Psychiatry and Human Behavior, Weight Control and Diabetes Research Center, The Alpert Medical School of Brown University/The Miriam HospitalProvidence, Rhode Island, USA
| | - Charlotte Ling
- Department of Clinical Sciences, Skåne University HospitalMalmö, Sweden
| | - Paul W Franks
- Department of Clinical Sciences, Skåne University HospitalMalmö, Sweden
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of MedicineStanford, California, USA
| | - Jason L Vassy
- Division of General Medicine, Brigham and Women's Hospital and Harvard Medical SchoolBoston, Massachusetts, USA
| | - Tanya Agurs-Collins
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of HealthBethesda, Maryland, USA.
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Florath I, Butterbach K, Heiss J, Bewerunge-Hudler M, Zhang Y, Schöttker B, Brenner H. Type 2 diabetes and leucocyte DNA methylation: an epigenome-wide association study in over 1,500 older adults. Diabetologia 2016; 59:130-138. [PMID: 26433941 DOI: 10.1007/s00125-015-3773-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/08/2015] [Indexed: 12/20/2022]
Abstract
AIMS/HYPOTHESIS Development of type 2 diabetes depends on environmental and genetic factors. We investigated the epigenome-wide association of prevalent diabetes with DNA methylation (DNAm) in peripheral blood. METHODS DNAm was measured in whole blood with the Illumina Infinium HumanMethylation450 BeadChip in two subsamples of participants from the ESTHER cohort study. Cohort 1 included 988 participants, who were consecutively recruited between July and October 2000 and cohort 2 included 527 randomly selected participants. The association of DNAm with prevalent type 2 diabetes at recruitment was estimated using median regression analysis adjusting for sex, age, BMI, smoking behaviour, cell composition and batch at 361,922 CpG sites. RESULTS Type 2 diabetes was prevalent in 16% of the participants, and diabetes was poorly controlled in 45% of the diabetic patients. In cohort 1 (discovery) DNAm at 39 CpGs was significantly associated with prevalent diabetes after correction for multiple testing. In cohort 2 (replication) at one of these CpGs, DNAm was still significantly associated. Decreasing methylation levels at cg19693031 with increasing fasting glucose and HbA1c concentrations were observed using restricted cubic spline analysis. In diabetic patients with poorly controlled diabetes, the decrease in estimated DNAm levels was approximately 5% in comparison with participants free of diagnosed diabetes. CONCLUSIONS/INTERPRETATION Cg19693031, which is located within the 3'-untranslated region of TXNIP, might play a role in the pathophysiology of type 2 diabetes. This result appears biologically plausible given that thioredoxin-interacting protein is overexpressed in diabetic animals and humans and 3'-untranslated regions are known to play a regulatory role in gene expression.
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Affiliation(s)
- Ines Florath
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Jonathan Heiss
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | | | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research (C070), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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128
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Giuliani C, Cilli E, Bacalini MG, Pirazzini C, Sazzini M, Gruppioni G, Franceschi C, Garagnani P, Luiselli D. Inferring chronological age from DNA methylation patterns of human teeth. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:585-95. [PMID: 26667772 DOI: 10.1002/ajpa.22921] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Current methods to determine chronological age from modern and ancient remains rely on both morphological and molecular approaches. However, low accuracy and the lack of standardized protocols make the development of alternative methods for the estimation of individual's age even more urgent for several research fields, such as biological anthropology, biodemography, forensics, evolutionary genetics, and ancient DNA studies. Therefore, the aim of this study is to identify genomic regions whose DNA methylation level correlates with age in modern teeth. METHODS We used MALDI-TOF mass spectrometry to analyze DNA methylation levels of specific CpGs located in the ELOVL2, FHL2, and PENK genes. We considered methylation data from cementum, dentin and pulp of 21 modern teeth (from 17 to 77 years old) to construct a mathematical model able to exploit DNA methylation values to predict age of the individuals. RESULTS The median difference between the real age and that estimated using DNA methylation values is 1.20 years (SD = 1.9) if DNA is recovered from both cementum and pulp of the same modern teeth, 2.25 years (SD = 2.5) if DNA is recovered from dental pulp, 2.45 years (SD = 3.3) if DNA is extracted from cementum and 7.07 years (SD = 7.0) when DNA is recovered from dentin only. DISCUSSION We propose for the first time the evaluation of DNA methylation at ELOVL2, FHL2, and PENK genes as a powerful tool to predict age in modern teeth for anthropological applications. Future studies are needed to apply this method also to historical and relatively ancient human teeth.
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Affiliation(s)
- Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage (DBC), Laboratories of Physical Anthropology and Ancient DNA, University of Bologna, Ravenna, 48121, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy
| | - Marco Sazzini
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
| | - Giorgio Gruppioni
- Department of Cultural Heritage (DBC), Laboratories of Physical Anthropology and Ancient DNA, University of Bologna, Ravenna, 48121, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy.,IRCCS Institute of Neurological Sciences, Bologna, 40139, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy.,Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
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129
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Pietiläinen KH, Ismail K, Järvinen E, Heinonen S, Tummers M, Bollepalli S, Lyle R, Muniandy M, Moilanen E, Hakkarainen A, Lundbom J, Lundbom N, Rissanen A, Kaprio J, Ollikainen M. DNA methylation and gene expression patterns in adipose tissue differ significantly within young adult monozygotic BMI-discordant twin pairs. Int J Obes (Lond) 2015; 40:654-61. [PMID: 26499446 DOI: 10.1038/ijo.2015.221] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 08/29/2015] [Accepted: 09/21/2015] [Indexed: 11/09/2022]
Abstract
BACKGROUND Little is known about epigenetic alterations associated with subcutaneous adipose tissue (SAT) in obesity. Our aim was to study genome-wide DNA methylation and gene expression differences in SAT in monozygotic (MZ) twin pairs who are discordant for body mass index (BMI). This design completely matches lean and obese groups for genetic background, age, gender and shared environment. METHODS 14We analyzed DNA methylome and gene expression from SAT, together with body composition (magnetic resonance imaging/spectroscopy) and glucose tolerance test, lipids and C-reactive protein from 26 rare BMI-discordant (intrapair difference in BMI ⩾3 kg m(-2)) MZ twin pairs identified from 10 birth cohorts of young adult Finnish twins. RESULTS We found 17 novel obesity-associated genes that were differentially methylated across the genome between heavy and lean co-twins. Nine of them were also differentially expressed. Pathway analyses indicated that dysregulation of SAT in obesity includes a paradoxical downregulation of lipo/adipogenesis and upregulation of inflammation and extracellular matrix remodeling. Furthermore, CpG sites whose methylation correlated with metabolically harmful fat depots (intra-abdominal and liver fat) also correlated with measures of insulin resistance, dyslipidemia and low-grade inflammation, thus suggesting that epigenetic alterations in SAT are associated with the development of unhealthy obesity. CONCLUSION This is the first study in BMI-discordant MZ twin pairs reporting genome-wide DNA methylation and expression profiles in SAT. We found a number of novel genes and pathways whose methylation and expression patterns differ within the twin pairs, suggesting that the pathological adaptation of SAT to obesity is, at least in part, epigenetically regulated.
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Affiliation(s)
- K H Pietiläinen
- Obesity Research Unit, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Endocrinology, Abdominal Center, Helsinki University Central Hospital, and University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - K Ismail
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - E Järvinen
- Obesity Research Unit, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - S Heinonen
- Obesity Research Unit, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - M Tummers
- Obesity Research Unit, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - S Bollepalli
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - R Lyle
- Oslo University Hospital and University of Oslo, Department of Medical Genetics, Oslo, Norway
| | - M Muniandy
- Obesity Research Unit, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - E Moilanen
- The Immunopharmacology Research Group, University of Tampere School of Medicine and Tampere University Hospital, Tampere, Finland
| | - A Hakkarainen
- HUS Medical Imaging Center, Radiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - J Lundbom
- HUS Medical Imaging Center, Radiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University, Düsseldorf, Germany.,German Center for Diabetes Research, Partner Düsseldorf, Düsseldorf, Germany
| | - N Lundbom
- HUS Medical Imaging Center, Radiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - A Rissanen
- Obesity Research Unit, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - J Kaprio
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland.,Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,National Institute for Health and Welfare, Helsinki, Finland
| | - M Ollikainen
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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130
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Arner P, Sinha I, Thorell A, Rydén M, Dahlman-Wright K, Dahlman I. The epigenetic signature of subcutaneous fat cells is linked to altered expression of genes implicated in lipid metabolism in obese women. Clin Epigenetics 2015; 7:93. [PMID: 26351548 PMCID: PMC4562340 DOI: 10.1186/s13148-015-0126-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/27/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Obesity is associated with changes in fat cell gene expression and metabolism. What drives these changes is not well understood. We aimed to explore fat cell epigenetics, i.e., DNA methylation, as one mediator of gene regulation, in obese women. The global DNA methylome for abdominal subcutaneous fat cells was compared between 15 obese case (BMI 41.4 ± 4.4 kg/m(2), mean ± SD) and 14 never-obese control women (BMI 25.2 ± 2.5 kg/m(2)). Global array-based transcriptome analysis was analyzed for subcutaneous white adipose tissue (WAT) from 11 obese and 9 never-obese women. Limma was used for statistical analysis. RESULTS We identified 5529 differentially methylated DNA sites (DMS) for 2223 differentially expressed genes between obese cases and never-obese controls (false discovery rate <5 %). The 5529 DMS displayed a median difference in beta value of 0.09 (range 0.01 to 0.40) between groups. DMS were under-represented in CpG islands and in promoter regions, and over-represented in open sea-regions and gene bodies. The 2223 differentially expressed genes with DMS were over-represented in key fat cell pathways: 31 of 130 (25 %) genes linked to "adipogenesis" (adjusted P = 1.66 × 10(-11)), 31 of 163 (19 %) genes linked to "insulin signaling" (adjusted P = 1.91 × 10(-9)), and 18 of 67 (27 %) of genes linked to "lipolysis" (P = 6.1 × 10(-5)). In most cases, gene expression and DMS displayed reciprocal changes in obese women. Furthermore, among 99 candidate genes in genetic loci associated with body fat distribution in genome-wide association studies (GWAS); 22 genes displayed differential expression accompanied by DMS in obese versus never-obese women (P = 0.0002), supporting the notion that a significant proportion of gene loci linked to fat distribution are epigenetically regulated. CONCLUSIONS Subcutaneous WAT from obese women is characterized by congruent changes in DNA methylation and expression of genes linked to generation, distribution, and metabolic function of fat cells. These alterations may contribute to obesity-associated metabolic disturbances such as insulin resistance in women.
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Affiliation(s)
- Peter Arner
- Lipid laboratory, Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, S-141 86 Sweden
| | - Indranil Sinha
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, S-141 83 Sweden
| | - Anders Thorell
- Department of Clinical Sciences, Danderyds Hospital, Karolinska Institutet, Stockholm, Sweden ; Department of Surgery, Ersta Hospital, Stockholm, Sweden
| | - Mikael Rydén
- Lipid laboratory, Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, S-141 86 Sweden
| | - Karin Dahlman-Wright
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, S-141 83 Sweden ; SciLifeLab, Science for Life Laboratory, S-171 65 Solna, Sweden
| | - Ingrid Dahlman
- Lipid laboratory, Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, S-141 86 Sweden
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131
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van Dijk SJ, Tellam RL, Morrison JL, Muhlhausler BS, Molloy PL. Recent developments on the role of epigenetics in obesity and metabolic disease. Clin Epigenetics 2015; 7:66. [PMID: 27408648 PMCID: PMC4940755 DOI: 10.1186/s13148-015-0101-5] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/29/2015] [Indexed: 12/20/2022] Open
Abstract
The increased prevalence of obesity and related comorbidities is a major public health problem. While genetic factors undoubtedly play a role in determining individual susceptibility to weight gain and obesity, the identified genetic variants only explain part of the variation. This has led to growing interest in understanding the potential role of epigenetics as a mediator of gene-environment interactions underlying the development of obesity and its associated comorbidities. Initial evidence in support of a role of epigenetics in obesity and type 2 diabetes mellitus (T2DM) was mainly provided by animal studies, which reported epigenetic changes in key metabolically important tissues following high-fat feeding and epigenetic differences between lean and obese animals and by human studies which showed epigenetic changes in obesity and T2DM candidate genes in obese/diabetic individuals. More recently, advances in epigenetic methodologies and the reduced cost of epigenome-wide association studies (EWAS) have led to a rapid expansion of studies in human populations. These studies have also reported epigenetic differences between obese/T2DM adults and healthy controls and epigenetic changes in association with nutritional, weight loss, and exercise interventions. There is also increasing evidence from both human and animal studies that the relationship between perinatal nutritional exposures and later risk of obesity and T2DM may be mediated by epigenetic changes in the offspring. The aim of this review is to summarize the most recent developments in this rapidly moving field, with a particular focus on human EWAS and studies investigating the impact of nutritional and lifestyle factors (both pre- and postnatal) on the epigenome and their relationship to metabolic health outcomes. The difficulties in distinguishing consequence from causality in these studies and the critical role of animal models for testing causal relationships and providing insight into underlying mechanisms are also addressed. In summary, the area of epigenetics and metabolic health has seen rapid developments in a short space of time. While the outcomes to date are promising, studies are ongoing, and the next decade promises to be a time of productive research into the complex interactions between the genome, epigenome, and environment as they relate to metabolic disease.
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Affiliation(s)
- Susan J van Dijk
- CSIRO Food and Nutrition Flagship, PO Box 52, North Ryde, NSW 1670 Australia
| | - Ross L Tellam
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD 4067 Australia
| | - Janna L Morrison
- Early Origins of Adult Health Research Group, School of Pharmacy and Medical Sciences, Sansom Institute for Health Research, University of South Australia, GPO Box 2471, Adelaide, SA 5001 Australia
| | - Beverly S Muhlhausler
- FOODplus Research Centre, Waite Campus, The University of Adelaide, PMB 1, Glen Osmond, SA 5064 Australia.,Women's and Children's Health Research Institute, 72 King William Road, North Adelaide, SA 5006 Australia
| | - Peter L Molloy
- CSIRO Food and Nutrition Flagship, PO Box 52, North Ryde, NSW 1670 Australia
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