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Kwak SH, Hernandez-Cancela RB, DiCorpo DA, Condon DE, Merino J, Wu P, Brody JA, Yao J, Guo X, Ahmadizar F, Meyer M, Sincan M, Mercader JM, Lee S, Haessler J, Vy HMT, Lin Z, Armstrong ND, Gu S, Tsao NL, Lange LA, Wang N, Wiggins KL, Trompet S, Liu S, Loos RJF, Judy R, Schroeder PH, Hasbani NR, Bos MM, Morrison AC, Jackson RD, Reiner AP, Manson JE, Chaudhary NS, Carmichael LK, Chen YDI, Taylor KD, Ghanbari M, van Meurs J, Pitsillides AN, Psaty BM, Noordam R, Do R, Park KS, Jukema JW, Kavousi M, Correa A, Rich SS, Damrauer SM, Hajek C, Cho NH, Irvin MR, Pankow JS, Nadkarni GN, Sladek R, Goodarzi MO, Florez JC, Chasman DI, Heckbert SR, Kooperberg C, Dupuis J, Malhotra R, de Vries PS, Liu CT, Rotter JI, Meigs JB. Time-to-Event Genome-Wide Association Study for Incident Cardiovascular Disease in People With Type 2 Diabetes. Diabetes Care 2024:dc232274. [PMID: 38652672 DOI: 10.2337/dc23-2274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/14/2024] [Indexed: 04/25/2024]
Abstract
OBJECTIVE To identify genetic risk factors for incident cardiovascular disease (CVD) among people with type 2 diabetes (T2D). RESEARCH DESIGN AND METHODS We conducted a multiancestry time-to-event genome-wide association study for incident CVD among people with T2D. We also tested 204 known coronary artery disease (CAD) variants for association with incident CVD. RESULTS Among 49,230 participants with T2D, 8,956 had incident CVD events (event rate 18.2%). We identified three novel genetic loci for incident CVD: rs147138607 (near CACNA1E/ZNF648, hazard ratio [HR] 1.23, P = 3.6 × 10-9), rs11444867 (near HS3ST1, HR 1.89, P = 9.9 × 10-9), and rs335407 (near TFB1M/NOX3, HR 1.25, P = 1.5 × 10-8). Among 204 known CAD loci, 5 were associated with incident CVD in T2D (multiple comparison-adjusted P < 0.00024, 0.05/204). A standardized polygenic score of these 204 variants was associated with incident CVD with HR 1.14 (P = 1.0 × 10-16). CONCLUSIONS The data point to novel and known genomic regions associated with incident CVD among individuals with T2D.
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Affiliation(s)
- Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | | | - Daniel A DiCorpo
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | | | - Jordi Merino
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Jie Yao
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA
| | - Fariba Ahmadizar
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Data Science and Biostatistics, Julius Global Health, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mariah Meyer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Murat Sincan
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Josep M Mercader
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Sujin Lee
- Division of Vascular Surgery and Endovascular Therapy, Massachusetts General Hospital, Boston, MA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Ha My T Vy
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zhaotong Lin
- Department of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Nicole D Armstrong
- Department of Epidemiology, The University of Alabama at Birmingham, Birmingham, AL
| | - Shaopeng Gu
- Department of Internal Medicine, Sanford Health, Sioux Falls, SD
| | - Noah L Tsao
- Corporal Michael J. Crescenz VA Medical Center and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ningyuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Stella Trompet
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Simin Liu
- Department of Epidemiology, Brown University, Providence, RI
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Renae Judy
- Corporal Michael J. Crescenz VA Medical Center and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
| | - Philip H Schroeder
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Natalie R Hasbani
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Maxime M Bos
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, Ohio State University, Columbus, OH
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - JoAnn E Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ninad S Chaudhary
- Department of Epidemiology, The University of Alabama at Birmingham, Birmingham, AL
| | | | - Yii-Der Ida Chen
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA
| | - Kent D Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Joyce van Meurs
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | | | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Ron Do
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kyong Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Netherlands Heart Institute, Utrecht, the Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Scott M Damrauer
- Corporal Michael J. Crescenz VA Medical Center and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, Perelman School of Medicine, Philadelphia, PA
| | - Catherine Hajek
- Department of Internal Medicine, Sanford Health, Sioux Falls, SD
| | - Nam H Cho
- Department of Preventive Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Marguerite R Irvin
- Department of Epidemiology, The University of Alabama at Birmingham, Birmingham, AL
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN
| | - Girish N Nadkarni
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Robert Sladek
- Department of Medicine and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Jose C Florez
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Daniel I Chasman
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Jerome I Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA
| | - James B Meigs
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Department of General Internal Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, MA
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2
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Ghosh A, Leung YH, Yu J, Sladek R, Chénier I, Oppong AK, Peyot ML, Madiraju SRM, Al-Khairi I, Thanaraj TA, Abubaker J, Al-Mulla F, Prentki M, Abu-Farha M. Silencing ANGPTL8 reduces mouse preadipocyte differentiation and insulin signaling. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159461. [PMID: 38272177 DOI: 10.1016/j.bbalip.2024.159461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
ANGPTL8, expressed mainly in the liver and adipose tissue, regulates the activity of lipoprotein lipase (LPL) present in the extracellular space and triglyceride (TG) metabolism through its interaction with ANGPTL3 and ANGPTL4. Whether intracellular ANGPTL8 can also exert effects in tissues where it is expressed is uncertain. ANGPTL8 expression was low in preadipocytes and much increased during differentiation. To better understand the role of intracellular ANGPTL8 in adipocytes and assess whether it may play a role in adipocyte differentiation, we knocked down its expression in normal mouse subcutaneous preadipocytes. ANGPTL8 knockdown reduced adipocyte differentiation, cellular TG accumulation and also isoproterenol-stimulated lipolysis at day 7 of differentiation. RNA-Seq analysis of ANGPTL8 siRNA or control siRNA transfected SC preadipocytes on days 0, 2, 4 and 7 of differentiation showed that ANGPTL8 knockdown impeded the early (day 2) expression of adipogenic and insulin signaling genes, PPARγ, as well as genes related to extracellular matrix and NF-κB signaling. Insulin mediated Akt phosphorylation was reduced at an early stage during adipocyte differentiation. This study based on normal primary cells shows that ANGPTL8 has intracellular actions in addition to effects in the extracellular space, like modulating LPL activity. Preadipocyte ANGPTL8 expression modulates their differentiation possibly via changes in insulin signaling gene expression.
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Affiliation(s)
- Anindya Ghosh
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Yat Hei Leung
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Jeffrey Yu
- Department of Medicine, McGill University, Montréal, QC, Canada
| | - Robert Sladek
- Department of Medicine, McGill University, Montréal, QC, Canada
| | - Isabelle Chénier
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Abel K Oppong
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Marie-Line Peyot
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - S R Murthy Madiraju
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | | | | | | | | | - Marc Prentki
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.
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3
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Yu V, Yong F, Marta A, Khadayate S, Osakwe A, Bhattacharya S, Varghese SS, Chabosseau P, Tabibi SM, Chen K, Georgiadou E, Parveen N, Suleiman M, Stamoulis Z, Marselli L, De Luca C, Tesi M, Ostinelli G, Delgadillo-Silva L, Wu X, Hatanaka Y, Montoya A, Elliott J, Patel B, Demchenko N, Whilding C, Hajkova P, Shliaha P, Kramer H, Ali Y, Marchetti P, Sladek R, Dhawan S, Withers DJ, Rutter GA, Millership SJ. Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneity. Diabetologia 2024:10.1007/s00125-024-06123-6. [PMID: 38512414 DOI: 10.1007/s00125-024-06123-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 03/23/2024]
Abstract
AIMS/HYPOTHESIS Beta cells within the pancreatic islet represent a heterogenous population wherein individual sub-groups of cells make distinct contributions to the overall control of insulin secretion. These include a subpopulation of highly connected 'hub' cells, important for the propagation of intercellular Ca2+ waves. Functional subpopulations have also been demonstrated in human beta cells, with an altered subtype distribution apparent in type 2 diabetes. At present, the molecular mechanisms through which beta cell hierarchy is established are poorly understood. Changes at the level of the epigenome provide one such possibility, which we explore here by focusing on the imprinted gene Nnat (encoding neuronatin [NNAT]), which is required for normal insulin synthesis and secretion. METHODS Single-cell RNA-seq datasets were examined using Seurat 4.0 and ClusterProfiler running under R. Transgenic mice expressing enhanced GFP under the control of the Nnat enhancer/promoter regions were generated for FACS of beta cells and downstream analysis of CpG methylation by bisulphite sequencing and RNA-seq, respectively. Animals deleted for the de novo methyltransferase DNA methyltransferase 3 alpha (DNMT3A) from the pancreatic progenitor stage were used to explore control of promoter methylation. Proteomics was performed using affinity purification mass spectrometry and Ca2+ dynamics explored by rapid confocal imaging of Cal-520 AM and Cal-590 AM. Insulin secretion was measured using homogeneous time-resolved fluorescence imaging. RESULTS Nnat mRNA was differentially expressed in a discrete beta cell population in a developmental stage- and DNA methylation (DNMT3A)-dependent manner. Thus, pseudo-time analysis of embryonic datasets demonstrated the early establishment of Nnat-positive and -negative subpopulations during embryogenesis. NNAT expression is also restricted to a subset of beta cells across the human islet that is maintained throughout adult life. NNAT+ beta cells also displayed a discrete transcriptome at adult stages, representing a subpopulation specialised for insulin production, and were diminished in db/db mice. 'Hub' cells were less abundant in the NNAT+ population, consistent with epigenetic control of this functional specialisation. CONCLUSIONS/INTERPRETATION These findings demonstrate that differential DNA methylation at Nnat represents a novel means through which beta cell heterogeneity is established during development. We therefore hypothesise that changes in methylation at this locus may contribute to a loss of beta cell hierarchy and connectivity, potentially contributing to defective insulin secretion in some forms of diabetes. DATA AVAILABILITY The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD048465.
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Affiliation(s)
- Vanessa Yu
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Fiona Yong
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore
| | - Angellica Marta
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | | | - Adrien Osakwe
- Quantitative Life Sciences Program, McGill University, Montréal, QC, Canada
| | - Supriyo Bhattacharya
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sneha S Varghese
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Pauline Chabosseau
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Sayed M Tabibi
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Keran Chen
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Eleni Georgiadou
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Nazia Parveen
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Zoe Stamoulis
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Medical Sciences Division, University of Oxford, Oxford, UK
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Carmela De Luca
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Marta Tesi
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Giada Ostinelli
- CHUM Research Center and Faculty of Medicine, University of Montréal, Montréal, QC, Canada
| | - Luis Delgadillo-Silva
- CHUM Research Center and Faculty of Medicine, University of Montréal, Montréal, QC, Canada
| | - Xiwei Wu
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Yuki Hatanaka
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | | | | | | | - Nikita Demchenko
- MRC Laboratory of Medical Sciences, London, UK
- Imaging Resource Facility, Research Operations, St George's, University of London, London, UK
| | | | - Petra Hajkova
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | | | | | - Yusuf Ali
- Nutrition, Metabolism and Health Programme & Centre for Microbiome Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Republic of Singapore
- Singapore Eye Research Institute (SERI), Singapore General Hospital, Singapore, Republic of Singapore
- Clinical Research Unit, Khoo Teck Puat Hospital, National Healthcare Group, Singapore, Republic of Singapore
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Robert Sladek
- Quantitative Life Sciences Program, McGill University, Montréal, QC, Canada
- Departments of Medicine and Human Genetics, McGill University, Montréal, QC, Canada
| | - Sangeeta Dhawan
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Dominic J Withers
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Guy A Rutter
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore.
- CHUM Research Center and Faculty of Medicine, University of Montréal, Montréal, QC, Canada.
| | - Steven J Millership
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
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4
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Yu V, Yong F, Marta A, Khadayate S, Osakwe A, Bhattacharya S, Varghese SS, Chabosseau P, Tabibi SM, Chen K, Georgiadou E, Parveen N, Suleiman M, Stamoulis Z, Marselli L, De Luca C, Tesi M, Ostinelli G, Delgadillo-Silva L, Wu X, Hatanaka Y, Montoya A, Elliott J, Patel B, Demchenko N, Whilding C, Hajkova P, Shliaha P, Kramer H, Ali Y, Marchetti P, Sladek R, Dhawan S, Withers DJ, Rutter GA, Millership SJ. Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneity. bioRxiv 2023:2023.02.04.527050. [PMID: 38076935 PMCID: PMC10705251 DOI: 10.1101/2023.02.04.527050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Aims/hypothesis Beta cells within the pancreatic islet represent a heterogenous population wherein individual sub-groups of cells make distinct contributions to the overall control of insulin secretion. These include a subpopulation of highly-connected 'hub' cells, important for the propagation of intercellular Ca2+ waves. Functional subpopulations have also been demonstrated in human beta cells, with an altered subtype distribution apparent in type 2 diabetes. At present, the molecular mechanisms through which beta cell hierarchy is established are poorly understood. Changes at the level of the epigenome provide one such possibility which we explore here by focussing on the imprinted gene neuronatin (Nnat), which is required for normal insulin synthesis and secretion. Methods Single cell RNA-seq datasets were examined using Seurat 4.0 and ClusterProfiler running under R. Transgenic mice expressing eGFP under the control of the Nnat enhancer/promoter regions were generated for fluorescence-activated cell (FAC) sorting of beta cells and downstream analysis of CpG methylation by bisulphite and RNA sequencing, respectively. Animals deleted for the de novo methyltransferase, DNMT3A from the pancreatic progenitor stage were used to explore control of promoter methylation. Proteomics was performed using affinity purification mass spectrometry and Ca2+ dynamics explored by rapid confocal imaging of Cal-520 and Cal-590. Insulin secretion was measured using Homogeneous Time Resolved Fluorescence Imaging. Results Nnat mRNA was differentially expressed in a discrete beta cell population in a developmental stage- and DNA methylation (DNMT3A)-dependent manner. Thus, pseudo-time analysis of embryonic data sets demonstrated the early establishment of Nnat-positive and negative subpopulations during embryogenesis. NNAT expression is also restricted to a subset of beta cells across the human islet that is maintained throughout adult life. NNAT+ beta cells also displayed a discrete transcriptome at adult stages, representing a sub-population specialised for insulin production, reminiscent of recently-described "βHI" cells and were diminished in db/db mice. 'Hub' cells were less abundant in the NNAT+ population, consistent with epigenetic control of this functional specialization. Conclusions/interpretation These findings demonstrate that differential DNA methylation at Nnat represents a novel means through which beta cell heterogeneity is established during development. We therefore hypothesise that changes in methylation at this locus may thus contribute to a loss of beta cell hierarchy and connectivity, potentially contributing to defective insulin secretion in some forms of diabetes.
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Affiliation(s)
- Vanessa Yu
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Fiona Yong
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, 637553, Singapore
| | - Angellica Marta
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Sanjay Khadayate
- MRC Laboratory of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Adrien Osakwe
- Departments of Medicine, Human Genetics and Quantitative Life Sciences, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Supriyo Bhattacharya
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, 1500 E Duarte Road, Duarte, CA 91010, USA
| | - Sneha S. Varghese
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, 1500 E Duarte Road, Duarte, CA 91010, USA
| | - Pauline Chabosseau
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Sayed M. Tabibi
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Keran Chen
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Eleni Georgiadou
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Nazia Parveen
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, 1500 E Duarte Road, Duarte, CA 91010, USA
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Zoe Stamoulis
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Carmela De Luca
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Marta Tesi
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Giada Ostinelli
- CHUM Research Center and Faculty of Medicine, University of Montréal, 900 Rue St Denis, Montréal, H2X OA9, QC, Canada
| | - Luis Delgadillo-Silva
- CHUM Research Center and Faculty of Medicine, University of Montréal, 900 Rue St Denis, Montréal, H2X OA9, QC, Canada
| | - Xiwei Wu
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, 1500 E Duarte Road, Duarte, CA 91010, USA
| | - Yuki Hatanaka
- MRC Laboratory of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Alex Montoya
- MRC Laboratory of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - James Elliott
- MRC Laboratory of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Bhavik Patel
- MRC Laboratory of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Nikita Demchenko
- MRC Laboratory of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Chad Whilding
- MRC Laboratory of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Petra Hajkova
- MRC Laboratory of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Pavel Shliaha
- MRC Laboratory of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Holger Kramer
- MRC Laboratory of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Yusuf Ali
- Nutrition, Metabolism and Health Programme & Centre for Microbiome Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, 308232
- Singapore Eye Research Institute (SERI), Singapore General Hospital, Singapore, 168751
- Clinical Research Unit, Khoo Teck Puat Hospital, National Healthcare Group, Singapore, 768828
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa 56126, Italy
| | - Robert Sladek
- Departments of Medicine, Human Genetics and Quantitative Life Sciences, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Sangeeta Dhawan
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, 1500 E Duarte Road, Duarte, CA 91010, USA
| | - Dominic J. Withers
- MRC Laboratory of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Guy A. Rutter
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, 637553, Singapore
- CHUM Research Center and Faculty of Medicine, University of Montréal, 900 Rue St Denis, Montréal, H2X OA9, QC, Canada
| | - Steven J. Millership
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
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5
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Kiss RS, Chicoine J, Khalil Y, Sladek R, Chen H, Pisaturo A, Martin C, Dale JD, Brudenell TA, Kamath A, Kyei-Boahen J, Hafiane A, Daliah G, Alecki C, Hopes TS, Heier M, Aligianis IA, Lebrun JJ, Aspden J, Paci E, Kerksiek A, Lütjohann D, Clayton P, Wills JC, von Kriegsheim A, Nilsson T, Sheridan E, Handley MT. Comparative proximity biotinylation implicates the small GTPase RAB18 in sterol mobilization and biosynthesis. J Biol Chem 2023; 299:105295. [PMID: 37774976 PMCID: PMC10641524 DOI: 10.1016/j.jbc.2023.105295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023] Open
Abstract
Loss of functional RAB18 causes the autosomal recessive condition Warburg Micro syndrome. To better understand this disease, we used proximity biotinylation to generate an inventory of potential RAB18 effectors. A restricted set of 28 RAB18 interactions were dependent on the binary RAB3GAP1-RAB3GAP2 RAB18-guanine nucleotide exchange factor complex. Twelve of these 28 interactions are supported by prior reports, and we have directly validated novel interactions with SEC22A, TMCO4, and INPP5B. Consistent with a role for RAB18 in regulating membrane contact sites, interactors included groups of microtubule/membrane-remodeling proteins, membrane-tethering and docking proteins, and lipid-modifying/transporting proteins. Two of the putative interactors, EBP and OSBPL2/ORP2, have sterol substrates. EBP is a Δ8-Δ7 sterol isomerase, and ORP2 is a lipid transport protein. This prompted us to investigate a role for RAB18 in cholesterol biosynthesis. We found that the cholesterol precursor and EBP-product lathosterol accumulates in both RAB18-null HeLa cells and RAB3GAP1-null fibroblasts derived from an affected individual. Furthermore, de novo cholesterol biosynthesis is impaired in cells in which RAB18 is absent or dysregulated or in which ORP2 expression is disrupted. Our data demonstrate that guanine nucleotide exchange factor-dependent Rab interactions are highly amenable to interrogation by proximity biotinylation and may suggest that Micro syndrome is a cholesterol biosynthesis disorder.
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Affiliation(s)
- Robert S Kiss
- Cardiovascular Health Across the Lifespan (CHAL) Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
| | - Jarred Chicoine
- Metabolic Disorders and Complications (MEDIC) Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Youssef Khalil
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Robert Sladek
- Metabolic Disorders and Complications (MEDIC) Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - He Chen
- Cardiovascular Health Across the Lifespan (CHAL) Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Alessandro Pisaturo
- Cardiovascular Health Across the Lifespan (CHAL) Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Cyril Martin
- Cardiovascular Health Across the Lifespan (CHAL) Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Jessica D Dale
- Leeds Institute of Medical Research, St James's University Hospital, Leeds, United Kingdom
| | - Tegan A Brudenell
- Leeds Institute of Medical Research, St James's University Hospital, Leeds, United Kingdom
| | - Archith Kamath
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom; Division of Medical Sciences, University of Oxford, Oxford, United Kingdom
| | - Jeffrey Kyei-Boahen
- Department of Medicine, McGill University Health Centre, CHAL Research Program, Montreal, Canada
| | - Anouar Hafiane
- Department of Medicine, McGill University Health Centre, CHAL Research Program, Montreal, Canada
| | - Girija Daliah
- Department of Medicine, McGill University Health Centre, Cancer Research Program, Montreal, Canada
| | - Célia Alecki
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Tayah S Hopes
- Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Martin Heier
- Department of Clinical Neuroscience for Children, Oslo University Hospital, Oslo, Norway
| | - Irene A Aligianis
- Medical and Developmental Genetics, Medical Research Council Human Genetics Unit, Edinburgh, United Kingdom
| | - Jean-Jacques Lebrun
- Department of Medicine, McGill University Health Centre, Cancer Research Program, Montreal, Canada
| | - Julie Aspden
- Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Anja Kerksiek
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Dieter Lütjohann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Peter Clayton
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Jimi C Wills
- Cancer Research United Kingdom Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom; Firefinch Software Ltd, Edinburgh, United Kingdom
| | - Alex von Kriegsheim
- Cancer Research United Kingdom Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Tommy Nilsson
- Cancer Research Program (CRP), Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Eamonn Sheridan
- Leeds Institute of Medical Research, St James's University Hospital, Leeds, United Kingdom
| | - Mark T Handley
- Leeds Institute of Medical Research, St James's University Hospital, Leeds, United Kingdom; Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
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6
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Kwak SH, Hernandez-Cancela RB, DiCorpo DA, Condon DE, Merino J, Wu P, Brody JA, Yao J, Guo X, Ahmadizar F, Meyer M, Sincan M, Mercader JM, Lee S, Haessler J, Vy HMT, Lin Z, Armstrong ND, Gu S, Tsao NL, Lange LA, Wang N, Wiggins KL, Trompet S, Liu S, Loos RJ, Judy R, Schroeder PH, Hasbani NR, Bos MM, Morrison AC, Jackson RD, Reiner AP, Manson JE, Chaudhary NS, Carmichael LK, Chen YDI, Taylor KD, Ghanbari M, van Meurs J, Pitsillides AN, Psaty BM, Noordam R, Do R, Park KS, Jukema JW, Kavousi M, Correa A, Rich SS, Damrauer SM, Hajek C, Cho NH, Irvin MR, Pankow JS, Nadkarni GN, Sladek R, Goodarzi MO, Florez JC, Chasman DI, Heckbert SR, Kooperberg C, Dupuis J, Malhotra R, de Vries PS, Liu CT, Rotter JI, Meigs JB. Time-to-Event Genome-Wide Association Study for Incident Cardiovascular Disease in People with Type 2 Diabetes Mellitus. medRxiv 2023:2023.07.25.23293180. [PMID: 37546893 PMCID: PMC10402212 DOI: 10.1101/2023.07.25.23293180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
BACKGROUND Type 2 diabetes mellitus (T2D) confers a two- to three-fold increased risk of cardiovascular disease (CVD). However, the mechanisms underlying increased CVD risk among people with T2D are only partially understood. We hypothesized that a genetic association study among people with T2D at risk for developing incident cardiovascular complications could provide insights into molecular genetic aspects underlying CVD. METHODS From 16 studies of the Cohorts for Heart & Aging Research in Genomic Epidemiology (CHARGE) Consortium, we conducted a multi-ancestry time-to-event genome-wide association study (GWAS) for incident CVD among people with T2D using Cox proportional hazards models. Incident CVD was defined based on a composite of coronary artery disease (CAD), stroke, and cardiovascular death that occurred at least one year after the diagnosis of T2D. Cohort-level estimated effect sizes were combined using inverse variance weighted fixed effects meta-analysis. We also tested 204 known CAD variants for association with incident CVD among patients with T2D. RESULTS A total of 49,230 participants with T2D were included in the analyses (31,118 European ancestries and 18,112 non-European ancestries) which consisted of 8,956 incident CVD cases over a range of mean follow-up duration between 3.2 and 33.7 years (event rate 18.2%). We identified three novel, distinct genetic loci for incident CVD among individuals with T2D that reached the threshold for genome-wide significance (P<5.0×10-8): rs147138607 (intergenic variant between CACNA1E and ZNF648) with a hazard ratio (HR) 1.23, 95% confidence interval (CI) 1.15 - 1.32, P=3.6×10-9, rs11444867 (intergenic variant near HS3ST1) with HR 1.89, 95% CI 1.52 - 2.35, P=9.9×10-9, and rs335407 (intergenic variant between TFB1M and NOX3) HR 1.25, 95% CI 1.16 - 1.35, P=1.5×10-8. Among 204 known CAD loci, 32 were associated with incident CVD in people with T2D with P<0.05, and 5 were significant after Bonferroni correction (P<0.00024, 0.05/204). A polygenic score of these 204 variants was significantly associated with incident CVD with HR 1.14 (95% CI 1.12 - 1.16) per 1 standard deviation increase (P=1.0×10-16). CONCLUSIONS The data point to novel and known genomic regions associated with incident CVD among individuals with T2D.
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Affiliation(s)
- Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | | | - Daniel A DiCorpo
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | | | - Jordi Merino
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Jie Yao
- Department of Pediatrics, Institute for Translational Genomics and Population Science, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Science, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Fariba Ahmadizar
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Data Science and Biostatistics, Julius Global Health, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mariah Meyer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Murat Sincan
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Josep M. Mercader
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Sujin Lee
- Division of Vascular Surgery and Endovascular Therapy, Massachusetts General Hospital, Boston, MA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Ha My T. Vy
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zhaotong Lin
- Department of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Nicole D. Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL
| | - Shaopeng Gu
- Department of Internal Medicine, Sanford Health, Sioux Falls, SD
| | - Noah L. Tsao
- Corporal Michael Crescenz VA Medical Center, and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
| | - Leslie A. Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ningyuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Simin Liu
- Department of Epidemiology, Brown University, Providence, RI
| | - Ruth J.F. Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Renae Judy
- Corporal Michael Crescenz VA Medical Center, and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
| | - Philip H. Schroeder
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Natalie R. Hasbani
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Maxime M. Bos
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Rebecca D. Jackson
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, Ohio State University, Columbus, OH
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - JoAnn E. Manson
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Ninad S. Chaudhary
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL
| | | | - Yii-Der Ida Chen
- Department of Pediatrics, Institute for Translational Genomics and Population Science, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Kent D. Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Science, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Joyce van Meurs
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Ron Do
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kyong Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- The Netherlands Heart Institute, Utrecht, the Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Scott M. Damrauer
- Corporal Michael Crescenz VA Medical Center, and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, Perelman School of Medicine, Philadelphia, PA
| | - Catherine Hajek
- Department of Internal Medicine, Sanford Health, Sioux Falls, SD
| | - Nam H. Cho
- Department of Preventive Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL
| | - James S. Pankow
- Department of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Girish N. Nadkarni
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Robert Sladek
- Department of Medicine and Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center
| | - Jose C. Florez
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Daniel I. Chasman
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division of the Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Jerome I. Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Science, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - James B. Meigs
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Department of General Internal Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, MA
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7
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Chabosseau P, Yong F, Delgadillo-Silva LF, Lee EY, Melhem R, Li S, Gandhi N, Wastin J, Noriega LL, Leclerc I, Ali Y, Hughes JW, Sladek R, Martinez-Sanchez A, Rutter GA. Molecular phenotyping of single pancreatic islet leader beta cells by "Flash-Seq". Life Sci 2023; 316:121436. [PMID: 36706832 DOI: 10.1016/j.lfs.2023.121436] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
AIMS Spatially-organized increases in cytosolic Ca2+ within pancreatic beta cells in the pancreatic islet underlie the stimulation of insulin secretion by high glucose. Recent data have revealed the existence of subpopulations of beta cells including "leaders" which initiate Ca2+ waves. Whether leader cells possess unique molecular features, or localisation, is unknown. MAIN METHODS High speed confocal Ca2+ imaging was used to identify leader cells and connectivity analysis, running under MATLAB and Python, to identify highly connected "hub" cells. To explore transcriptomic differences between beta cell sub-groups, individual leaders or followers were labelled by photo-activation of the cryptic fluorescent protein PA-mCherry and subjected to single cell RNA sequencing ("Flash-Seq"). KEY FINDINGS Distinct Ca2+ wave types were identified in individual islets, with leader cells present in 73 % (28 of 38 islets imaged). Scale-free, power law-adherent behaviour was also observed in 29 % of islets, though "hub" cells in these islets did not overlap with leaders. Transcripts differentially expressed (295; padj < 0.05) between leader and follower cells included genes involved in cilium biogenesis and transcriptional regulation. Providing some support for these findings, ADCY6 immunoreactivity tended to be higher in leader than follower cells, whereas cilia number and length tended to be lower in the former. Finally, leader cells were located significantly closer to delta, but not alpha, cells in Euclidian space than were follower cells. SIGNIFICANCE The existence of both a discrete transcriptome and unique localisation implies a role for these features in defining the specialized function of leaders. These data also raise the possibility that localised signalling between delta and leader cells contributes to the initiation and propagation of islet Ca2+ waves.
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Affiliation(s)
- Pauline Chabosseau
- Centre de Recherche du CHUM, Faculté de Médicine, Université de Montréal, Montréal, QC, Canada
| | - Fiona Yong
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom; Lee Kong Chian Imperial Medical School, Nanyang Technological University, Singapore
| | - Luis F Delgadillo-Silva
- Centre de Recherche du CHUM, Faculté de Médicine, Université de Montréal, Montréal, QC, Canada
| | - Eun Young Lee
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States; Division of Endocrinology and Metabolism, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Rana Melhem
- Centre de Recherche du CHUM, Faculté de Médicine, Université de Montréal, Montréal, QC, Canada
| | - Shiying Li
- Centre de Recherche du CHUM, Faculté de Médicine, Université de Montréal, Montréal, QC, Canada
| | - Nidhi Gandhi
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Jules Wastin
- Centre de Recherche du CHUM, Faculté de Médicine, Université de Montréal, Montréal, QC, Canada
| | - Livia Lopez Noriega
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Isabelle Leclerc
- Centre de Recherche du CHUM, Faculté de Médicine, Université de Montréal, Montréal, QC, Canada
| | - Yusuf Ali
- Lee Kong Chian Imperial Medical School, Nanyang Technological University, Singapore
| | - Jing W Hughes
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Robert Sladek
- Departments of Medicine and Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Aida Martinez-Sanchez
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Guy A Rutter
- Centre de Recherche du CHUM, Faculté de Médicine, Université de Montréal, Montréal, QC, Canada; Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom; Lee Kong Chian Imperial Medical School, Nanyang Technological University, Singapore.
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8
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Sladek R. Predicting the response to GLP-1 receptor agonists: an unexpected role for β-arrestin-1. Lancet Diabetes Endocrinol 2023; 11:3-4. [PMID: 36528348 DOI: 10.1016/s2213-8587(22)00357-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Robert Sladek
- Department of Medicine and Department of Human Genetics, McGill University, Montréal, QC H3A 0G1, Canada.
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9
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Vivoli A, Ghislain J, Filali-Mouhim A, Angeles ZE, Castell AL, Sladek R, Poitout V. Single-Cell RNA Sequencing Reveals a Role for Reactive Oxygen Species and Peroxiredoxins in Fatty Acid-Induced Rat β-Cell Proliferation. Diabetes 2023; 72:45-58. [PMID: 36191509 PMCID: PMC9797324 DOI: 10.2337/db22-0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/24/2022] [Indexed: 01/19/2023]
Abstract
The functional mass of insulin-secreting pancreatic β-cells expands to maintain glucose homeostasis in the face of nutrient excess, in part via replication of existing β-cells. Type 2 diabetes appears when these compensatory mechanisms fail. Nutrients including glucose and fatty acids are important contributors to the β-cell compensatory response, but their underlying mechanisms of action remain poorly understood. We investigated the transcriptional mechanisms of β-cell proliferation in response to fatty acids. Isolated rat islets were exposed to 16.7 mmol/L glucose with or without 0.5 mmol/L oleate (C18:1) or palmitate (C16:0) for 48 h. The islet transcriptome was assessed by single-cell RNA sequencing. β-Cell proliferation was measured by flow cytometry. Unsupervised clustering of pooled β-cells identified different subclusters, including proliferating β-cells. β-Cell proliferation increased in response to oleate but not palmitate. Both fatty acids enhanced the expression of genes involved in energy metabolism and mitochondrial activity. Comparison of proliferating versus nonproliferating β-cells and pseudotime ordering suggested the involvement of reactive oxygen species (ROS) and peroxiredoxin signaling. Accordingly, N-acetyl cysteine and the peroxiredoxin inhibitor conoidin A both blocked oleate-induced β-cell proliferation. Our study reveals a key role for ROS signaling through peroxiredoxin activation in oleate-induced β-cell proliferation.
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Affiliation(s)
- Alexis Vivoli
- Montreal Diabetes Research Center, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
| | - Julien Ghislain
- Montreal Diabetes Research Center, Montréal, Québec, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
| | - Ali Filali-Mouhim
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
| | - Zuraya Elisa Angeles
- Montreal Diabetes Research Center, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
| | - Anne-Laure Castell
- Montreal Diabetes Research Center, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
| | - Robert Sladek
- Montreal Diabetes Research Center, Montréal, Québec, Canada
- Department of Human Genetics, McGill University and McGill Genome Centre, Montréal, Québec, Canada
| | - Vincent Poitout
- Montreal Diabetes Research Center, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Québec, Canada
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Vivoli A, Ghislain J, Filali-Mouhim A, Angeles Z, Castell AL, Sladek R, Poitout V. Single-cell RNA Sequencing Reveals a Role for Reactive Oxygen Species and Peroxiredoxins in Fatty Acid-induced Rat ß-cell Proliferation. Can J Diabetes 2022. [DOI: 10.1016/j.jcjd.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Al-Mass A, Poursharifi P, Peyot ML, Lussier R, Chenier I, Leung YH, Ghosh A, Oppong A, Possik E, Mugabo Y, Ahmad R, Sladek R, Murthy Madiraju S, Al-Mulla F, Prentki M. Hepatic glycerol shunt and glycerol-3-phosphate phosphatase control liver metabolism and glucodetoxification under hyperglycemia. Mol Metab 2022; 66:101609. [PMID: 36198384 PMCID: PMC9579801 DOI: 10.1016/j.molmet.2022.101609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE Glycerol-3-phosphate (Gro3P) phosphatase (G3PP) hydrolyzes Gro3P to glycerol that exits the cell, thereby operating a "glycerol shunt", a metabolic pathway that we identified recently in mammalian cells. We have investigated the role of G3PP and the glycerol shunt in the regulation of glucose metabolism and lipogenesis in mouse liver. METHODS We generated hepatocyte-specific G3PP-KO mice (LKO), by injecting AAV8-TBG-iCre to male G3PPfl/fl mice. Controls received AAV8-TBG-eGFP. Both groups were fed chow diet for 10 weeks. Hyperglycemia (16-20 mM) was induced by glucose infusion for 55 h. Hepatocytes were isolated from normoglycemic mice for ex vivo studies and targeted metabolomics were measured in mice liver after glucose infusion. RESULTS LKO mice showed no change in body weight, food intake, fed and fasted glycemia but had increased fed plasma triglycerides. Hepatic glucose production from glycerol was increased in fasted LKO mice. LKO mouse hepatocytes displayed reduced glycerol production, elevated triglyceride and lactate production at high glucose concentration. Hyperglycemia in LKO mice led to increased liver weight and accumulation of triglycerides, glycogen and cholesterol together with elevated levels of Gro3P, dihydroxyacetone phosphate, acetyl-CoA and some Krebs cycle intermediates in liver. Hyperglycemic LKO mouse liver showed elevated expression of proinflammatory cytokines and M1-macrophage markers accompanied by increased plasma triglycerides, LDL/VLDL, urea and uric acid and myocardial triglycerides. CONCLUSIONS The glycerol shunt orchestrated by G3PP acts as a glucose excess detoxification pathway in hepatocytes by preventing metabolic disturbances that contribute to enhanced liver fat, glycogen storage, inflammation and lipid build-up in the heart. We propose G3PP as a novel therapeutic target for hepatic disorders linked to nutrient excess.
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Affiliation(s)
- Anfal Al-Mass
- Department of Medicine, McGill University, Montréal, QC, Canada,Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Pegah Poursharifi
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Marie-Line Peyot
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Roxane Lussier
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Isabelle Chenier
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Yat Hei Leung
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Anindya Ghosh
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Abel Oppong
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Elite Possik
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Yves Mugabo
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Rasheed Ahmad
- Departments of Immunology, Microbiology, Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Robert Sladek
- Department of Medicine, McGill University, Montréal, QC, Canada
| | - S.R. Murthy Madiraju
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada,Corresponding author. CRCHUM, Room R08-418, Tour Viger, 900 rue Saint Denis, Montreal, QC H2X 0A9, Canada.
| | - Fahd Al-Mulla
- Departments of Immunology, Microbiology, Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Marc Prentki
- Departments of Nutrition, Biochemistry and Molecular Medicine, University of Montreal, and Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada,Corresponding author. Biochemistry and Molecular Medicine, Université de Montréal CRCHUM, Room R08-412, Tour Viger, 900 rue Saint Denis Montreal, QC H2X 0A9, Canada.
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Abstract
Participants in the human gene editing debate often consider examples from science fiction but have rarely engaged directly with the science fiction community as stakeholders. To understand how science fiction authors develop and spread their views on gene editing, we created an online questionnaire that was answered by 78 authors, including 71 who had previously written about genetic engineering. When asked which ethical issues science fiction should explore, respondents most frequently mentioned affordability, new social divisions, consent and unforeseen safety risks. They rarely advocated exploring psychological effects or religious objections. When asked which works of fiction had influenced their perceptions of gene editing, the most frequent responses were the film Gattaca, the Star Trek franchise and the novels The Island of Doctor Moreau and Brave New World Unlike other stakeholders, they rarely cited Frankenstein as an influence. This article examines several differences between bioethicists, the general public and science fiction authors, and discusses how this community's involvement might benefit proponents and opponents of gene editing. It also provides an overview of works mentioned by our respondents that might serve as useful references in the debate.
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Affiliation(s)
- Derek So
- Human Genetics, Centre of Genomics and Policy, McGill University, Montreal, Quebec, Canada
| | - Kelsey Crocker
- Human Genetics, Centre of Genomics and Policy, McGill University, Montreal, Quebec, Canada
| | - Robert Sladek
- Medicine and Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Yann Joly
- Human Genetics, Centre of Genomics and Policy, McGill University, Montreal, Quebec, Canada
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13
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DiCorpo D, Gaynor SM, Russell EM, Westerman KE, Raffield LM, Majarian TD, Wu P, Sarnowski C, Highland HM, Jackson A, Hasbani NR, de Vries PS, Brody JA, Hidalgo B, Guo X, Perry JA, O'Connell JR, Lent S, Montasser ME, Cade BE, Jain D, Wang H, D'Oliveira Albanus R, Varshney A, Yanek LR, Lange L, Palmer ND, Almeida M, Peralta JM, Aslibekyan S, Baldridge AS, Bertoni AG, Bielak LF, Chen CS, Chen YDI, Choi WJ, Goodarzi MO, Floyd JS, Irvin MR, Kalyani RR, Kelly TN, Lee S, Liu CT, Loesch D, Manson JE, Minster RL, Naseri T, Pankow JS, Rasmussen-Torvik LJ, Reiner AP, Reupena MS, Selvin E, Smith JA, Weeks DE, Xu H, Yao J, Zhao W, Parker S, Alonso A, Arnett DK, Blangero J, Boerwinkle E, Correa A, Cupples LA, Curran JE, Duggirala R, He J, Heckbert SR, Kardia SLR, Kim RW, Kooperberg C, Liu S, Mathias RA, McGarvey ST, Mitchell BD, Morrison AC, Peyser PA, Psaty BM, Redline S, Shuldiner AR, Taylor KD, Vasan RS, Viaud-Martinez KA, Florez JC, Wilson JG, Sladek R, Rich SS, Rotter JI, Lin X, Dupuis J, Meigs JB, Wessel J, Manning AK. Whole genome sequence association analysis of fasting glucose and fasting insulin levels in diverse cohorts from the NHLBI TOPMed program. Commun Biol 2022; 5:756. [PMID: 35902682 PMCID: PMC9334637 DOI: 10.1038/s42003-022-03702-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 07/12/2022] [Indexed: 01/04/2023] Open
Abstract
The genetic determinants of fasting glucose (FG) and fasting insulin (FI) have been studied mostly through genome arrays, resulting in over 100 associated variants. We extended this work with high-coverage whole genome sequencing analyses from fifteen cohorts in NHLBI's Trans-Omics for Precision Medicine (TOPMed) program. Over 23,000 non-diabetic individuals from five race-ethnicities/populations (African, Asian, European, Hispanic and Samoan) were included. Eight variants were significantly associated with FG or FI across previously identified regions MTNR1B, G6PC2, GCK, GCKR and FOXA2. We additionally characterize suggestive associations with FG or FI near previously identified SLC30A8, TCF7L2, and ADCY5 regions as well as APOB, PTPRT, and ROBO1. Functional annotation resources including the Diabetes Epigenome Atlas were compiled for each signal (chromatin states, annotation principal components, and others) to elucidate variant-to-function hypotheses. We provide a catalog of nucleotide-resolution genomic variation spanning intergenic and intronic regions creating a foundation for future sequencing-based investigations of glycemic traits.
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Affiliation(s)
- Daniel DiCorpo
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Sheila M Gaynor
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Emily M Russell
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Kenneth E Westerman
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, 02114, USA
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Timothy D Majarian
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Chloé Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Anne Jackson
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Natalie R Hasbani
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA
- Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Bertha Hidalgo
- Ryals School of Public Health, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - James A Perry
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jeffrey R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Samantha Lent
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Ricardo D'Oliveira Albanus
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Arushi Varshney
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Leslie Lange
- Department of Medicine, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Marcio Almeida
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
| | - Juan M Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
| | | | - Abigail S Baldridge
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Alain G Bertoni
- Department of Epidemiology & Prevention, Wake Forest School of Medicine, Winston-, Salem, NC, 27157, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Chung-Shiuan Chen
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | | | - Mark O Goodarzi
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Marguerite R Irvin
- Ryals School of Public Health, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Rita R Kalyani
- GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | | | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Douglas Loesch
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - JoAnn E Manson
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Ryan L Minster
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
| | | | - Elizabeth Selvin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21287, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Daniel E Weeks
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Huichun Xu
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Stephen Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, 40506, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, 39211, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- National Heart Lung and Blood Institute and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ryan W Kim
- Psomagen, Inc, Rockville, MD, 20850, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Simin Liu
- Center for Global Cardiometabolic Health (CGCH), Boston, MA, 02215, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Stephen T McGarvey
- International Health Institute and Department of Epidemiology, Brown University School of Public Health, Providence, RI, 02912, USA
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Geriatrics Research and Education Clinical Center, Baltimore VA Medical Center, Baltimore, MD, 21201, USA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA
- Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
- Department of Health Services, University of Washington, Seattle, WA, 98101, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Alan R Shuldiner
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21231, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
- Evans Department of Medicine, Section of Preventive Medicine and Epidemiology, Boston University School of Medicine, Boston, MA, 02118, USA
- Evans Department of Medicine, Whitaker Cardiovascular Institute and Cardiology Section, Boston University School of Medicine, Boston, MA, 02118, USA
| | | | - Jose C Florez
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - James G Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Robert Sladek
- Department of Human Genetics, McGill University, Montreal, Montreal, Quebec, H3A 0G1, Canada
- Department of Medicine, McGill University, Montreal, Montreal, Quebec, H3A 0G1, Canada
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - James B Meigs
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Jennifer Wessel
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, IN, 46202, USA.
- Department of Medicine, School of Medicine, Indiana University, IN, 46202, USA.
- Diabetes Translational Research Center, Indiana University, IN, 46202, USA.
| | - Alisa K Manning
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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14
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Almass A, Poursharifi P, Peyot M, Lussier R, Levens E, Guida J, Mugabo Y, Possik E, Erb H, Joly E, Madiraju S, Sladek R, Prentki M. Glycerol‐3‐phosphate phosphatase/ Pgp in Pancreatic ß‐cells Functions as a Glucose Excess Security Valve Preventing Oversecretion of Insulin Secretion and Glucotoxicity. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.01592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Heidi Erb
- Montreal Diabetes Research CenterMontrealQC
| | - Erik Joly
- Montreal Diabetes Research CenterMontrealQC
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15
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Hebbar P, Abubaker JA, Abu-Farha M, Alsmadi O, Elkum N, Alkayal F, John SE, Channanath A, Iqbal R, Pitkaniemi J, Tuomilehto J, Sladek R, Al-Mulla F, Thanaraj TA. Genome-wide landscape establishes novel association signals for metabolic traits in the Arab population. Hum Genet 2020; 140:505-528. [PMID: 32902719 PMCID: PMC7889551 DOI: 10.1007/s00439-020-02222-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023]
Abstract
While the Arabian population has a high prevalence of metabolic disorders, it has not been included in global studies that identify genetic risk loci for metabolic traits. Determining the transferability of such largely Euro-centric established risk loci is essential to transfer the research tools/resources, and drug targets generated by global studies to a broad range of ethnic populations. Further, consideration of populations such as Arabs, that are characterized by consanguinity and a high level of inbreeding, can lead to identification of novel risk loci. We imputed published GWAS data from two Kuwaiti Arab cohorts (n = 1434 and 1298) to the 1000 Genomes Project haplotypes and performed meta-analysis for associations with 13 metabolic traits. We compared the observed association signals with those established for metabolic traits. Our study highlighted 70 variants from 9 different genes, some of which have established links to metabolic disorders. By relaxing the genome-wide significance threshold, we identified ‘novel’ risk variants from 11 genes for metabolic traits. Many novel risk variant association signals were observed at or borderline to genome-wide significance. Furthermore, 349 previously established variants from 187 genes were validated in our study. Pleiotropic effect of risk variants on multiple metabolic traits were observed. Fine-mapping illuminated rs7838666/CSMD1 rs1864163/CETP and rs112861901/[INTS10,LPL] as candidate causal variants influencing fasting plasma glucose and high-density lipoprotein levels. Computational functional analysis identified a variety of gene regulatory signals around several variants. This study enlarges the population ancestry diversity of available GWAS and elucidates new variants in an ethnic group burdened with metabolic disorders.
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Affiliation(s)
- Prashantha Hebbar
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait.,Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | | | | | - Naser Elkum
- Sidra Medical and Research Center, Doha, Qatar
| | - Fadi Alkayal
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait
| | - Sumi Elsa John
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait
| | | | - Rasheeba Iqbal
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait
| | - Janne Pitkaniemi
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jaakko Tuomilehto
- Department of Public Health, University of Helsinki, Helsinki, Finland.,Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Robert Sladek
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Fahd Al-Mulla
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait.
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16
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Manning AK, Goustin AS, Kleinbrink EL, Thepsuwan P, Cai J, Ju D, Leong A, Udler MS, Brown JB, Goodarzi MO, Rotter JI, Sladek R, Meigs JB, Lipovich L. A Long Non-coding RNA, LOC157273, Is an Effector Transcript at the Chromosome 8p23.1- PPP1R3B Metabolic Traits and Type 2 Diabetes Risk Locus. Front Genet 2020; 11:615. [PMID: 32754192 PMCID: PMC7367044 DOI: 10.3389/fgene.2020.00615] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/20/2020] [Indexed: 01/08/2023] Open
Abstract
Aims Causal transcripts at genomic loci associated with type 2 diabetes (T2D) are mostly unknown. The chr8p23.1 variant rs4841132, associated with an insulin-resistant diabetes risk phenotype, lies in the second exon of a long non-coding RNA (lncRNA) gene, LOC157273, located 175 kilobases from PPP1R3B, which encodes a key protein regulating insulin-mediated hepatic glycogen storage in humans. We hypothesized that LOC157273 regulates expression of PPP1R3B in human hepatocytes. Methods We tested our hypothesis using Stellaris fluorescent in situ hybridization to assess subcellular localization of LOC157273; small interfering RNA (siRNA) knockdown of LOC157273, followed by RT-PCR to quantify LOC157273 and PPP1R3B expression; RNA-seq to quantify the whole-transcriptome gene expression response to LOC157273 knockdown; and an insulin-stimulated assay to measure hepatocyte glycogen deposition before and after knockdown. Results We found that siRNA knockdown decreased LOC157273 transcript levels by approximately 80%, increased PPP1R3B mRNA levels by 1.7-fold, and increased glycogen deposition by >50% in primary human hepatocytes. An A/G heterozygous carrier (vs. three G/G carriers) had reduced LOC157273 abundance due to reduced transcription of the A allele and increased PPP1R3B expression and glycogen deposition. Conclusion We show that the lncRNA LOC157273 is a negative regulator of PPP1R3B expression and glycogen deposition in human hepatocytes and a causal transcript at an insulin-resistant T2D risk locus.
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Affiliation(s)
- Alisa K Manning
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States.,Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Anton Scott Goustin
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Erica L Kleinbrink
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Pattaraporn Thepsuwan
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Juan Cai
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Donghong Ju
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States.,Karmanos Cancer Institute at Wayne State University, Detroit, MI, United States
| | - Aaron Leong
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States.,Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Miriam S Udler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States.,Diabetes Unit, Massachusetts General Hospital, Boston, MA, United States
| | - James Bentley Brown
- Department of Statistics, University of California, Berkeley, Berkeley, CA, United States.,Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom.,Computational Biosciences Group, Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Robert Sladek
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Department of Medicine, McGill University, Montréal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, QC, Canada
| | - James B Meigs
- Department of Medicine, Harvard Medical School, Boston, MA, United States.,Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Leonard Lipovich
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States.,Department of Neurology, School of Medicine, Wayne State University, Detroit, MI, United States
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17
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Dias C, Elzein S, Sladek R, Goodyer CG. Sex-specific effects of a microsatellite polymorphism on human growth hormone receptor gene expression. Mol Cell Endocrinol 2019; 492:110442. [PMID: 31063794 DOI: 10.1016/j.mce.2019.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 01/05/2023]
Abstract
Growth hormone (GH) binds to its specific receptor (GHR) at the surface of target cells activating multiple signaling pathways implicated in growth and metabolism. Dysregulation of GHRs leads to pathophysiological states that most commonly affect stature. We previously showed the association of a polymorphic (n = 15-37) GT microsatellite in the human GHR gene promoter with short stature in a sex-specific manner. In the present study we evaluated the functional relevance of this polymorphism in regulating GHR expression. Using luciferase reporter assays, we found that the GT repeat had a significant cis regulatory effect in response to HIF1α and a potential repressor role following C/EBPβ stimulation. Using a digital PCR application to measure allelic imbalance (AI), we showed a high prevalence of AI (∼76%) at the GHR locus in lymphoblastoid cell lines (LCLs), with a significantly higher degree of imbalance in LCLs derived from males. Examination of expression of GHR as well as other members of the GH-IGF1 axis in the LCLs revealed significant associations of GHR, IGF1 and BCL2 expression with GT genotype in a sex-specific manner. Our results suggest that this GT microsatellite exerts both cis and trans effects in a sex-specific context, revealing a new mechanism by which GHR gene expression is regulated.
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Affiliation(s)
- Christel Dias
- Division of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada
| | - Samar Elzein
- Division of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada
| | - Robert Sladek
- Division of Experimental Medicine and Department of Human Genetics, McGill University, Montreal, Quebec, H4A 3J1, Canada
| | - Cynthia Gates Goodyer
- Division of Experimental Medicine and Department of Pediatrics, McGill University, Montreal, Quebec, H4A 3J1, Canada.
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18
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Mancini M, Caignard G, Charbonneau B, Dumaine A, Wu N, Leiva-Torres GA, Gerondakis S, Pearson A, Qureshi ST, Sladek R, Vidal SM. Rel-Dependent Immune and Central Nervous System Mechanisms Control Viral Replication and Inflammation during Mouse Herpes Simplex Encephalitis. J I 2019; 202:1479-1493. [DOI: 10.4049/jimmunol.1800063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 12/21/2018] [Indexed: 01/01/2023]
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19
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Dali R, Verginelli F, Pramatarova A, Sladek R, Stifani S. Characterization of a FOXG1:TLE1 transcriptional network in glioblastoma-initiating cells. Mol Oncol 2018; 12:775-787. [PMID: 29316219 PMCID: PMC5983107 DOI: 10.1002/1878-0261.12168] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/12/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022] Open
Abstract
Glioblastoma (GBM) is the most common and deadly malignant brain cancer of glial cell origin, with a median patient survival of less than 20 months. Transcription factors FOXG1 and TLE1 promote GBM propagation by supporting maintenance of brain tumour-initiating cells (BTICs) with stem-like properties. Here, we characterize FOXG1 and TLE1 target genes in GBM patient-derived BTICs using ChIP-Seq and RNA-Seq approaches. These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival, chemotaxis and angiogenesis. Negative regulators of NOTCH signalling, including CHAC1, are among the transcriptional repression targets of FOXG1:TLE1 complexes, suggesting a crosstalk between FOXG1:TLE1 and NOTCH-mediated pathways in GBM. These results provide previously unavailable insight into the transcriptional programs underlying the tumour-promoting functions of FOXG1:TLE1 in GBM.
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Affiliation(s)
- Rola Dali
- Department of Neurology and NeurosurgeryMontreal Neurological InstituteMcGill UniversityMontrealCanada
- McGill Center for BioinformaticsMcGill UniversityMontrealCanada
| | - Federica Verginelli
- Department of Neurology and NeurosurgeryMontreal Neurological InstituteMcGill UniversityMontrealCanada
- Present address:
Laboratory of Cancer Stem Cell ResearchCandiolo Cancer InstituteFPO‐IRCCSCandioloItaly
| | - Albena Pramatarova
- Departments of Human Genetics and MedicineMcGill UniversityMontrealCanada
| | - Robert Sladek
- Departments of Human Genetics and MedicineMcGill UniversityMontrealCanada
| | - Stefano Stifani
- Department of Neurology and NeurosurgeryMontreal Neurological InstituteMcGill UniversityMontrealCanada
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20
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Wheeler E, Leong A, Liu CT, Hivert MF, Strawbridge RJ, Podmore C, Li M, Yao J, Sim X, Hong J, Chu AY, Zhang W, Wang X, Chen P, Maruthur NM, Porneala BC, Sharp SJ, Jia Y, Kabagambe EK, Chang LC, Chen WM, Elks CE, Evans DS, Fan Q, Giulianini F, Go MJ, Hottenga JJ, Hu Y, Jackson AU, Kanoni S, Kim YJ, Kleber ME, Ladenvall C, Lecoeur C, Lim SH, Lu Y, Mahajan A, Marzi C, Nalls MA, Navarro P, Nolte IM, Rose LM, Rybin DV, Sanna S, Shi Y, Stram DO, Takeuchi F, Tan SP, van der Most PJ, Van Vliet-Ostaptchouk JV, Wong A, Yengo L, Zhao W, Goel A, Martinez Larrad MT, Radke D, Salo P, Tanaka T, van Iperen EPA, Abecasis G, Afaq S, Alizadeh BZ, Bertoni AG, Bonnefond A, Böttcher Y, Bottinger EP, Campbell H, Carlson OD, Chen CH, Cho YS, Garvey WT, Gieger C, Goodarzi MO, Grallert H, Hamsten A, Hartman CA, Herder C, Hsiung CA, Huang J, Igase M, Isono M, Katsuya T, Khor CC, Kiess W, Kohara K, Kovacs P, Lee J, Lee WJ, Lehne B, Li H, Liu J, Lobbens S, Luan J, Lyssenko V, Meitinger T, Miki T, Miljkovic I, Moon S, Mulas A, Müller G, Müller-Nurasyid M, Nagaraja R, Nauck M, Pankow JS, Polasek O, Prokopenko I, Ramos PS, Rasmussen-Torvik L, Rathmann W, Rich SS, Robertson NR, Roden M, Roussel R, Rudan I, Scott RA, Scott WR, Sennblad B, Siscovick DS, Strauch K, Sun L, Swertz M, Tajuddin SM, Taylor KD, Teo YY, Tham YC, Tönjes A, Wareham NJ, Willemsen G, Wilsgaard T, Hingorani AD, Egan J, Ferrucci L, Hovingh GK, Jula A, Kivimaki M, Kumari M, Njølstad I, Palmer CNA, Serrano Ríos M, Stumvoll M, Watkins H, Aung T, Blüher M, Boehnke M, Boomsma DI, Bornstein SR, Chambers JC, Chasman DI, Chen YDI, Chen YT, Cheng CY, Cucca F, de Geus EJC, Deloukas P, Evans MK, Fornage M, Friedlander Y, Froguel P, Groop L, Gross MD, Harris TB, Hayward C, Heng CK, Ingelsson E, Kato N, Kim BJ, Koh WP, Kooner JS, Körner A, Kuh D, Kuusisto J, Laakso M, Lin X, Liu Y, Loos RJF, Magnusson PKE, März W, McCarthy MI, Oldehinkel AJ, Ong KK, Pedersen NL, Pereira MA, Peters A, Ridker PM, Sabanayagam C, Sale M, Saleheen D, Saltevo J, Schwarz PEH, Sheu WHH, Snieder H, Spector TD, Tabara Y, Tuomilehto J, van Dam RM, Wilson JG, Wilson JF, Wolffenbuttel BHR, Wong TY, Wu JY, Yuan JM, Zonderman AB, Soranzo N, Guo X, Roberts DJ, Florez JC, Sladek R, Dupuis J, Morris AP, Tai ES, Selvin E, Rotter JI, Langenberg C, Barroso I, Meigs JB. Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis. PLoS Med 2017; 14:e1002383. [PMID: 28898252 PMCID: PMC5595282 DOI: 10.1371/journal.pmed.1002383] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/03/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Glycated hemoglobin (HbA1c) is used to diagnose type 2 diabetes (T2D) and assess glycemic control in patients with diabetes. Previous genome-wide association studies (GWAS) have identified 18 HbA1c-associated genetic variants. These variants proved to be classifiable by their likely biological action as erythrocytic (also associated with erythrocyte traits) or glycemic (associated with other glucose-related traits). In this study, we tested the hypotheses that, in a very large scale GWAS, we would identify more genetic variants associated with HbA1c and that HbA1c variants implicated in erythrocytic biology would affect the diagnostic accuracy of HbA1c. We therefore expanded the number of HbA1c-associated loci and tested the effect of genetic risk-scores comprised of erythrocytic or glycemic variants on incident diabetes prediction and on prevalent diabetes screening performance. Throughout this multiancestry study, we kept a focus on interancestry differences in HbA1c genetics performance that might influence race-ancestry differences in health outcomes. METHODS & FINDINGS Using genome-wide association meta-analyses in up to 159,940 individuals from 82 cohorts of European, African, East Asian, and South Asian ancestry, we identified 60 common genetic variants associated with HbA1c. We classified variants as implicated in glycemic, erythrocytic, or unclassified biology and tested whether additive genetic scores of erythrocytic variants (GS-E) or glycemic variants (GS-G) were associated with higher T2D incidence in multiethnic longitudinal cohorts (N = 33,241). Nineteen glycemic and 22 erythrocytic variants were associated with HbA1c at genome-wide significance. GS-G was associated with higher T2D risk (incidence OR = 1.05, 95% CI 1.04-1.06, per HbA1c-raising allele, p = 3 × 10-29); whereas GS-E was not (OR = 1.00, 95% CI 0.99-1.01, p = 0.60). In Europeans and Asians, erythrocytic variants in aggregate had only modest effects on the diagnostic accuracy of HbA1c. Yet, in African Americans, the X-linked G6PD G202A variant (T-allele frequency 11%) was associated with an absolute decrease in HbA1c of 0.81%-units (95% CI 0.66-0.96) per allele in hemizygous men, and 0.68%-units (95% CI 0.38-0.97) in homozygous women. The G6PD variant may cause approximately 2% (N = 0.65 million, 95% CI 0.55-0.74) of African American adults with T2D to remain undiagnosed when screened with HbA1c. Limitations include the smaller sample sizes for non-European ancestries and the inability to classify approximately one-third of the variants. Further studies in large multiethnic cohorts with HbA1c, glycemic, and erythrocytic traits are required to better determine the biological action of the unclassified variants. CONCLUSIONS As G6PD deficiency can be clinically silent until illness strikes, we recommend investigation of the possible benefits of screening for the G6PD genotype along with using HbA1c to diagnose T2D in populations of African ancestry or groups where G6PD deficiency is common. Screening with direct glucose measurements, or genetically-informed HbA1c diagnostic thresholds in people with G6PD deficiency, may be required to avoid missed or delayed diagnoses.
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Affiliation(s)
- Eleanor Wheeler
- Department of Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Aaron Leong
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, United States of America
- Massachusetts General Hospital, Boston, MA, United States of America
| | - Rona J. Strawbridge
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Centre for Molecular Medicine, Karolinska Universitetsjukhuset, Solna, Sweden
| | - Clara Podmore
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Department of Internal Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Man Li
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- Division of Nephrology, University of Utah, Salt Lake City, UT, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, UT, United States of America
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Jaeyoung Hong
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
| | - Audrey Y. Chu
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, United States of America
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, Middlesex, United Kingdom
| | - Xu Wang
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Peng Chen
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, United States of America
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, Jilin, China
- College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Nisa M. Maruthur
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- Division of General Internal Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- Welch Center for Prevention, Epidemiology and Clinical Research, The Johns Hopkins University, Baltimore, MD, United States of America
| | - Bianca C. Porneala
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, United States of America
| | - Stephen J. Sharp
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Yucheng Jia
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Edmond K. Kabagambe
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Li-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei-Min Chen
- University of Virginia Center for Public Health Genomics, Charlottesville, VA, United States of America
| | - Cathy E. Elks
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, United States of America
| | - Qiao Fan
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Min Jin Go
- Division of Structural and Functional Genomics, Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
| | - Jouke-Jan Hottenga
- Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Yao Hu
- The Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Anne U. Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Young Jin Kim
- Division of Structural and Functional Genomics, Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
| | - Marcus E. Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Claes Ladenvall
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Lund University Diabetes Centre, Lund University, Lund, Sweden
| | - Cecile Lecoeur
- University of Lille, CNRS, Institut Pasteur of Lille, UMR 8199—EGID, Lille, France
| | - Sing-Hui Lim
- Singapore Eye Research Institute, The Academia Level 6, Discovery Tower, Singapore, Singapore
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Carola Marzi
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Partner Munich, Munich, Germany
| | - Mike A. Nalls
- Data Tecnica International, Glen Echo, MD, United States of America
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, United States of America
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland
| | - Ilja M. Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Lynda M. Rose
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Denis V. Rybin
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
- Data Coordinating Center, Boston University School of Public Health, Boston, MA, United States of America
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy
| | - Yuan Shi
- Singapore Eye Research Institute, The Academia Level 6, Discovery Tower, Singapore, Singapore
| | - Daniel O. Stram
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shu Pei Tan
- Singapore Eye Research Institute, The Academia Level 6, Discovery Tower, Singapore, Singapore
| | - Peter J. van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jana V. Van Vliet-Ostaptchouk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Andrew Wong
- MRC Unit for Lifelong Health & Ageing, London, United Kingdom
| | - Loic Yengo
- University of Lille, CNRS, Institut Pasteur of Lille, UMR 8199—EGID, Lille, France
| | - Wanting Zhao
- Singapore Eye Research Institute, The Academia Level 6, Discovery Tower, Singapore, Singapore
| | - Anuj Goel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Maria Teresa Martinez Larrad
- Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Dörte Radke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Perttu Salo
- National Institute for Health and Welfare (THL), Helsinki, Finland
- University of Helsinki, Institute for Molecular Medicine, Finland (FIMM) and Diabetes and Obesity Research Program, Helsinki, Finland
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, United States of America
| | - Erik P. A. van Iperen
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, Utrecht, Netherlands
| | - Goncalo Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Saima Afaq
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Behrooz Z. Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alain G. Bertoni
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Amelie Bonnefond
- University of Lille, CNRS, Institut Pasteur of Lille, UMR 8199—EGID, Lille, France
| | - Yvonne Böttcher
- Integrated Research and Treatment (IFB) Center Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - Olga D. Carlson
- Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, MD, United States of America
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- School of Chinese Medicine, China Medical University, Taichung City, Taiwan
| | - Yoon Shin Cho
- Division of Structural and Functional Genomics, Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
- Department of Biomedical Science, Hallym University, Chuncheon, Gangwon-do, South Korea
| | - W. Timothy Garvey
- Department of Nutrition Sciences, University of Alabama at Birmingham and the Birmingham Veterans Affairs Medical Center, Birmingham, AL, United States of America
| | - Christian Gieger
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Harald Grallert
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Partner Munich, Munich, Germany
| | - Anders Hamsten
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Centre for Molecular Medicine, Karolinska Universitetsjukhuset, Solna, Sweden
| | - Catharina A. Hartman
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Institute for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Chao Agnes Hsiung
- Division of Endocrinology, Diabetes, Metabolism, Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus, OH, United States of America
| | - Jie Huang
- Boston VA Research Institute, Inc., Boston, MA, United States of America
| | - Michiya Igase
- Department of Geriatric Medicine, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Masato Isono
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Geriatric Medicine and Nephrology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Wieland Kiess
- Center of Pediatric Research, University Hospital for Children & Adolescents, Dept. of Women's & Child Health, University of Leipzig, Leipzig, Germany
- LIFE Child, LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Katsuhiko Kohara
- Faculty of Collaborative Regional Innovation, Ehime University, Ehime, Japan
| | - Peter Kovacs
- Integrated Research and Treatment (IFB) Center Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Juyoung Lee
- Division of Structural and Functional Genomics, Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Huaixing Li
- The Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Stephane Lobbens
- University of Lille, CNRS, Institut Pasteur of Lille, UMR 8199—EGID, Lille, France
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | | | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Tetsuro Miki
- Department of Geriatric Medicine, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Iva Miljkovic
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Sanghoon Moon
- Division of Structural and Functional Genomics, Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
| | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy
| | - Gabriele Müller
- Center for Evidence-based Healthcare, University Hospital and Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Ramaiah Nagaraja
- Laboratory of Genetics, National Institute on Aging, Baltimore, MD, United States of America
| | - Matthias Nauck
- Institute for Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - James S. Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, United States of America
| | - Ozren Polasek
- University of Split, Split, Croatia
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, United Kingdom
| | - Paula S. Ramos
- Department of Medicine, Medical University of South Carolina, Charleston, SC, United States of America
| | - Laura Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - Wolfgang Rathmann
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Neil R. Robertson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Institute for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
- Department of Endocrinology and Diabetology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Ronan Roussel
- INSERM, UMR_S 1138, Centre de Recherche des Cordelier, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, UFR de Médecine, Paris, France
- Assistance Publique Hôpitaux de Paris, Bichat Hospital, DHU FIRE, Department of Diabetology, Endocrinology and Nutrition, Paris, France
| | - Igor Rudan
- University of Edinburgh, Edinburgh, United Kingdom
| | - Robert A. Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - William R. Scott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, Middlesex, United Kingdom
| | - Bengt Sennblad
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Centre for Molecular Medicine, Karolinska Universitetsjukhuset, Solna, Sweden
- Science for life laboratory, Karolinska Institutet, Solna, Sweden
| | - David S. Siscovick
- The New York Academy of Medicine, New York, NY, United States of America
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Liang Sun
- The Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Morris Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Salman M. Tajuddin
- Health Disparities Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Yih Chung Tham
- Singapore Eye Research Institute, The Academia Level 6, Discovery Tower, Singapore, Singapore
| | - Anke Tönjes
- Department of Medicine; University of Leipzig, Leipzig, Germany
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Gonneke Willemsen
- Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Tom Wilsgaard
- Dept of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Aroon D. Hingorani
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | | | | | | | - Josephine Egan
- Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, MD, United States of America
| | - Luigi Ferrucci
- Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, MD, United States of America
| | - G. Kees Hovingh
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, Netherlands
| | - Antti Jula
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, London, United Kingdom
| | - Meena Kumari
- Department of Epidemiology and Public Health, University College London, London, United Kingdom
- Institute for Social and Economic Research, University of Essex, Colchester, United Kingdom
| | - Inger Njølstad
- Dept of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Colin N. A. Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Medical Research Institute, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Manuel Serrano Ríos
- Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | | | - Hugh Watkins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tin Aung
- Singapore Eye Research Institute, The Academia Level 6, Discovery Tower, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore National Eye Centre, Singapore, Singapore
| | - Matthias Blüher
- Department of Medicine; University of Leipzig, Leipzig, Germany
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Dorret I. Boomsma
- Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Stefan R. Bornstein
- Dept of Medicine III, University of Dresden, Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - John C. Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, Middlesex, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Yduan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, The Academia Level 6, Discovery Tower, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore National Eye Centre, Singapore, Singapore
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, Italy
| | - Eco J. C. de Geus
- Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Michele K. Evans
- Health Disparities Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, Division of Epidemiology, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Yechiel Friedlander
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Philippe Froguel
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, United Kingdom
- CNRS 8199-Lille University, France
| | - Leif Groop
- Lund University Diabetes Centre, Lund University, Lund, Sweden
- Finnish Institute for Molecular Medicine (FIMM), Helsinki, Finland
| | - Myron D. Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States of America
| | - Tamara B. Harris
- National Institute on Aging, Bethesda, MD, United States of America
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore, Singapore
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Bong-Jo Kim
- Division of Structural and Functional Genomics, Center for Genome Science, Korean National Institute of Health, Osong, Chungchungbuk-do, South Korea
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School Singapore, Singapore
| | - Jaspal S. Kooner
- Department of Cardiology, Ealing Hospital NHS Trust, Southall, Middlesex, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Antje Körner
- Center of Pediatric Research, University Hospital for Children & Adolescents, Dept. of Women's & Child Health, University of Leipzig, Leipzig, Germany
- LIFE Child, LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Diana Kuh
- MRC Unit for Lifelong Health & Ageing, London, United Kingdom
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Xu Lin
- The Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest University, Winston-Salem, NC, United States of America
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- The Mindich Child Health Development Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Insitutet, Stockholm, Sweden
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
- Synlab Academy, Synlab Services GmbH, Mannheim, Germany
| | - Mark I. McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, United Kingdom
| | - Albertine J. Oldehinkel
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ken K. Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Insitutet, Stockholm, Sweden
| | - Mark A. Pereira
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, United States of America
| | - Annette Peters
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Cardiovascular Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, The Academia Level 6, Discovery Tower, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Michele Sale
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Danish Saleheen
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, United States of America
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Juha Saltevo
- Department of Medicine, Central Hospital, Central Finland, Jyväskylä, Finland
| | - Peter EH. Schwarz
- Dept of Medicine III, University of Dresden, Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - Wayne H. H. Sheu
- Division of Endocrine and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jaakko Tuomilehto
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
- Dasman Diabetes Institute, Dasman, Kuwait
- Centre for Vascular Prevention, Danube-University Krems, Krems, Austria
- Saudi Diabetes Research Group, King Abdulaziz University, Fahd Medical Research Center, Jeddah, Saudi Arabia
| | - Rob M. van Dam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, United States of America
| | - James F. Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - Bruce H. R. Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Tien Yin Wong
- Singapore Eye Research Institute, The Academia Level 6, Discovery Tower, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore National Eye Centre, Singapore, Singapore
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- School of Chinese Medicine, China Medical University, Taichung City, Taiwan
| | - Jian-Min Yuan
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States of America
- Division of Cancer Control and Population Sciences,University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States of America
| | - Alan B. Zonderman
- Laboratory of Epidemiology & Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, United Kingdom
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - David J. Roberts
- Biomedical Research Centre Oxford Haematology Theme and Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, United Kingdom
- NHS Blood and Transplant, Headington, Oxford, United Kingdom
| | - Jose C. Florez
- Harvard Medical School, Boston, MA, United States of America
- Diabetes Unit and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, United States of America
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Robert Sladek
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, United States of America
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Elizabeth Selvin
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
- Division of General Internal Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- Welch Center for Prevention, Epidemiology and Clinical Research, The Johns Hopkins University, Baltimore, MD, United States of America
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Inês Barroso
- Department of Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - James B. Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, United States of America
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Duncan L, Yilmaz Z, Gaspar H, Walters R, Goldstein J, Anttila V, Bulik-Sullivan B, Ripke S, Thornton L, Hinney A, Daly M, Sullivan PF, Zeggini E, Breen G, Bulik CM, Duncan L, Yilmaz Z, Gaspar H, Walters R, Goldstein J, Anttila V, Bulik-Sullivan B, Ripke S, Adan R, Alfredsson L, Ando T, Andreassen O, Aschauer H, Baker J, Barrett J, Bencko V, Bergen A, Berrettini W, Birgegård A, Boni C, Perica VB, Brandt H, Burghardt R, Carlberg L, Cassina M, Cesta C, Cichon S, Clementi M, Cohen-Woods S, Coleman J, Cone R, Courtet P, Crawford S, Crow S, Crowley J, Danner U, Davis O, de Zwaan M, Dedoussis G, Degortes D, DeSocio J, Dick D, Dikeos D, Dina C, Ding B, Dmitrzak-Weglarz M, Docampo E, Egberts K, Ehrlich S, Escaramís G, Esko T, Espeseth T, Estivill X, Favaro A, Fernández-Aranda F, Fichter M, Finan C, Fischer K, Floyd J, Föcker M, Foretova L, Forzan M, Fox C, Franklin C, Gaborieau V, Gallinger S, Gambaro G, Giegling I, Gonidakis F, Gorwood P, Gratacos M, Guillaume S, Guo Y, Hakonarson H, Halmi K, Harrison R, Hatzikotoulas K, Hauser J, Hebebrand J, Helder S, Hendriks J, Herms S, Herpertz-Dahlmann B, Herzog W, Hilliard C, Huckins L, Hudson J, Huemer J, Imgart H, Inoko H, Jall S, Jamain S, Janout V, Jiménez-Murcia S, Johnson C, Jordan J, Julià A, Juréus A, Kalsi G, Kaplan A, Kaprio J, Karhunen L, Karwautz A, Kas M, Kaye W, Kennedy M, Kennedy J, Keski-Rahkonen A, Kiezebrink K, Kim YR, Klareskog L, Klump K, Knudsen GP, Koeleman B, Koubek D, La Via M, Landén M, Le Hellard S, Leboyer M, Levitan R, Li D, Lichtenstein P, Lilenfeld L, Lissowska J, Lundervold A, Magistretti P, Maj M, Mannik K, Marsal S, Kaminska D, Martin N, Mattingsdal M, McDevitt S, McGuffin P, Merl E, Metspalu A, Meulenbelt I, Micali N, Mitchell J, Mitchell K, Monteleone P, Monteleone AM, Montgomery G, Mortensen P, Munn-Chernoff M, Müller T, Nacmias B, Navratilova M, Nilsson I, Norring C, Ntalla I, Ophoff R, O’Toole J, Palotie A, Pantel J, Papezova H, Parker R, Pinto D, Rabionet R, Raevuori A, Rajewski A, Ramoz N, Rayner NW, Reichborn-Kjennerud T, Ricca V, Ripatti S, Ritschel F, Roberts M, Rotondo A, Rujescu D, Rybakowski F, Santonastaso P, Scherag A, Scherer S, Schmidt U, Schork N, Schosser A, Scott L, Seitz J, Slachtova L, Sladek R, Slagboom PE, ’t Landt MSO, Slopien A, Smith T, Soranzo N, Sorbi S, Southam L, Steen V, Strengman E, Strober M, Szatkiewicz J, Szeszenia-Dabrowska N, Tachmazidou I, Tenconi E, Tortorella A, Tozzi F, Treasure J, Tschöp M, Tsitsika A, Tziouvas K, van Elburg A, van Furth E, Wade T, Wagner G, Walton E, Watson H, Wichmann HE, Widen E, Woodside DB, Yanovski J, Yao S, Zerwas S, Zipfel S, Thornton L, Hinney A, Daly M, Sullivan PF, Zeggini E, Breen G, Bulik CM. Significant Locus and Metabolic Genetic Correlations Revealed in Genome-Wide Association Study of Anorexia Nervosa. Am J Psychiatry 2017; 174:850-858. [PMID: 28494655 PMCID: PMC5581217 DOI: 10.1176/appi.ajp.2017.16121402] [Citation(s) in RCA: 297] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The authors conducted a genome-wide association study of anorexia nervosa and calculated genetic correlations with a series of psychiatric, educational, and metabolic phenotypes. METHOD Following uniform quality control and imputation procedures using the 1000 Genomes Project (phase 3) in 12 case-control cohorts comprising 3,495 anorexia nervosa cases and 10,982 controls, the authors performed standard association analysis followed by a meta-analysis across cohorts. Linkage disequilibrium score regression was used to calculate genome-wide common variant heritability (single-nucleotide polymorphism [SNP]-based heritability [h2SNP]), partitioned heritability, and genetic correlations (rg) between anorexia nervosa and 159 other phenotypes. RESULTS Results were obtained for 10,641,224 SNPs and insertion-deletion variants with minor allele frequencies >1% and imputation quality scores >0.6. The h2SNP of anorexia nervosa was 0.20 (SE=0.02), suggesting that a substantial fraction of the twin-based heritability arises from common genetic variation. The authors identified one genome-wide significant locus on chromosome 12 (rs4622308) in a region harboring a previously reported type 1 diabetes and autoimmune disorder locus. Significant positive genetic correlations were observed between anorexia nervosa and schizophrenia, neuroticism, educational attainment, and high-density lipoprotein cholesterol, and significant negative genetic correlations were observed between anorexia nervosa and body mass index, insulin, glucose, and lipid phenotypes. CONCLUSIONS Anorexia nervosa is a complex heritable phenotype for which this study has uncovered the first genome-wide significant locus. Anorexia nervosa also has large and significant genetic correlations with both psychiatric phenotypes and metabolic traits. The study results encourage a reconceptualization of this frequently lethal disorder as one with both psychiatric and metabolic etiology.
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Affiliation(s)
- Laramie Duncan
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Zeynep Yilmaz
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Helena Gaspar
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Raymond Walters
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Jackie Goldstein
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Verneri Anttila
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Brendan Bulik-Sullivan
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Stephan Ripke
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Laura Thornton
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Anke Hinney
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Mark Daly
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Patrick F. Sullivan
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Eleftheria Zeggini
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Gerome Breen
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
| | - Cynthia M. Bulik
- From the UNC Center of Excellence for Eating Disorders, Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, N.C.; the Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm; the Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston; the Social, Genetic, and Developmental Psychiatry Research Centre and Biomedical Research Centre for Mental Health at King's College London and South London
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22
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Almeida M, Blondell L, Peralta JM, Kent JW, Jun G, Teslovich TM, Fuchsberger C, Wood AR, Manning AK, Frayling TM, Cingolani PE, Sladek R, Dyer TD, Abecasis G, Duggirala R, Blangero J. Independent test assessment using the extreme value distribution theory. BMC Proc 2016; 10:245-249. [PMID: 27980644 PMCID: PMC5133519 DOI: 10.1186/s12919-016-0038-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The new generation of whole genome sequencing platforms offers great possibilities and challenges for dissecting the genetic basis of complex traits. With a very high number of sequence variants, a naïve multiple hypothesis threshold correction hinders the identification of reliable associations by the overreduction of statistical power. In this report, we examine 2 alternative approaches to improve the statistical power of a whole genome association study to detect reliable genetic associations. The approaches were tested using the Genetic Analysis Workshop 19 (GAW19) whole genome sequencing data. The first tested method estimates the real number of effective independent tests actually being performed in whole genome association project by the use of an extreme value distribution and a set of phenotype simulations. Given the familiar nature of the GAW19 data and the finite number of pedigree founders in the sample, the number of correlations between genotypes is greater than in a set of unrelated samples. Using our procedure, we estimate that the effective number represents only 15 % of the total number of independent tests performed. However, even using this corrected significance threshold, no genome-wide significant association could be detected for systolic and diastolic blood pressure traits. The second approach implements a biological relevance-driven hypothesis tested by exploiting prior computational predictions on the effect of nonsynonymous genetic variants detected in a whole genome sequencing association study. This guided testing approach was able to identify 2 promising single-nucleotide polymorphisms (SNPs), 1 for each trait, targeting biologically relevant genes that could help shed light on the genesis of the human hypertension. The first gene, PFH14, associated with systolic blood pressure, interacts directly with genes involved in calcium-channel formation and the second gene, MAP4, encodes a microtubule-associated protein and had already been detected by previous genome-wide association study experiments conducted in an Asian population. Our results highlight the necessity of the development of alternative approached to improve the efficiency on the detection of reasonable candidate associations in whole genome sequencing studies.
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Affiliation(s)
- Marcio Almeida
- South Texas Diabetes and Obesity Institute, University of Texas at Brownsville, 2700 East Jackson Street, Brownsville, TX 78520 USA
| | - Lucy Blondell
- South Texas Diabetes and Obesity Institute, University of Texas at Brownsville, 2700 East Jackson Street, Brownsville, TX 78520 USA
| | - Juan M Peralta
- South Texas Diabetes and Obesity Institute, University of Texas at Brownsville, 2700 East Jackson Street, Brownsville, TX 78520 USA
| | - Jack W Kent
- Department of Genetics, Texas Biomedical Research Institute, P.O. Box 760549, San Antonio, TX 78245-0549 USA
| | - Goo Jun
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 7000 Fannin Street, Houston, TX 77030 USA
| | - Tanya M Teslovich
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, SPH II, 1420 Washington Heights, Ann Arbor, MI 48109-2029 USA
| | - Christian Fuchsberger
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, SPH II, 1420 Washington Heights, Ann Arbor, MI 48109-2029 USA
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Mail Room, The Old Library, Prince of Wales Road, Exeter, Devon UK
| | | | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Mail Room, The Old Library, Prince of Wales Road, Exeter, Devon UK
| | - Pablo E Cingolani
- School of Computer Science & Genome Quebec Innovation Centre, McIntyre Medical Building, 903 3655 Promenade Sir William Osler McGill University, Quebec, Canada
| | - Robert Sladek
- School of Computer Science & Genome Quebec Innovation Centre, McIntyre Medical Building, 903 3655 Promenade Sir William Osler McGill University, Quebec, Canada
| | - Thomas D Dyer
- South Texas Diabetes and Obesity Institute, University of Texas at Brownsville, 2700 East Jackson Street, Brownsville, TX 78520 USA
| | - Goncalo Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, SPH II, 1420 Washington Heights, Ann Arbor, MI 48109-2029 USA
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute, University of Texas at Brownsville, 2700 East Jackson Street, Brownsville, TX 78520 USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas at Brownsville, 2700 East Jackson Street, Brownsville, TX 78520 USA
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23
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Bouttier M, Laperriere D, Memari B, Mangiapane J, Fiore A, Mitchell E, Verway M, Behr MA, Sladek R, Barreiro LB, Mader S, White JH. Alu repeats as transcriptional regulatory platforms in macrophage responses to M. tuberculosis infection. Nucleic Acids Res 2016; 44:10571-10587. [PMID: 27604870 PMCID: PMC5159539 DOI: 10.1093/nar/gkw782] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 12/19/2022] Open
Abstract
To understand the epigenetic regulation of transcriptional response of macrophages during early-stage M. tuberculosis (Mtb) infection, we performed ChIPseq analysis of H3K4 monomethylation (H3K4me1), a marker of poised or active enhancers. De novo H3K4me1 peaks in infected cells were associated with genes implicated in host defenses and apoptosis. Our analysis revealed that 40% of de novo regions contained human/primate-specific Alu transposable elements, enriched in the AluJ and S subtypes. These contained several transcription factor binding sites, including those for members of the MEF2 and ATF families, and LXR and RAR nuclear receptors, all of which have been implicated in macrophage differentiation, survival, and responses to stress and infection. Combining bioinformatics, molecular genetics, and biochemical approaches, we linked genes adjacent to H3K4me1-associated Alu repeats to macrophage metabolic responses against Mtb infection. In particular, we show that LXRα signaling, which reduced Mtb viability 18-fold by altering cholesterol metabolism and enhancing macrophage apoptosis, can be initiated at response elements present in Alu repeats. These studies decipher the mechanism of early macrophage transcriptional responses to Mtb, highlighting the role of Alu element transposition in shaping human transcription programs during innate immunity.
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Affiliation(s)
- Manuella Bouttier
- Department of Physiology, Montréal, Québec, Canada .,McGill University, Montréal, Québec, Canada
| | - David Laperriere
- Département de Biochimie, Montréal, Québec, Canada.,Institut de Recherche en Immunologie et Cancérologie (IRIC), Montréal, Québec, Canada.,Université de Montréal, Montréal, Québec, Canada
| | - Babak Memari
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Joseph Mangiapane
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Amanda Fiore
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Eric Mitchell
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Mark Verway
- Department of Physiology, Montréal, Québec, Canada.,McGill University, Montréal, Québec, Canada
| | - Marcel A Behr
- McGill University, Montréal, Québec, Canada.,Division of Infectious Diseases and Medical Microbiology, Montréal, Québec, Canada.,McGill International TB Centre, Montréal, Québec, Canada
| | - Robert Sladek
- McGill University, Montréal, Québec, Canada.,School of Computer Science, Montréal, Québec, Canada.,Genome Quebec Innovation Centre, Montréal, Québec, Canada
| | - Luis B Barreiro
- Université de Montréal, Montréal, Québec, Canada.,Department of Pediatrics, Montréal, Québec, Canada
| | - Sylvie Mader
- Département de Biochimie, Montréal, Québec, Canada.,Institut de Recherche en Immunologie et Cancérologie (IRIC), Montréal, Québec, Canada.,Université de Montréal, Montréal, Québec, Canada
| | - John H White
- Department of Physiology, Montréal, Québec, Canada .,McGill University, Montréal, Québec, Canada.,Department of Medecine, Montréal, Québec, Canada
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24
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Pepin É, Al-Mass A, Attané C, Zhang K, Lamontagne J, Lussier R, Madiraju SRM, Joly E, Ruderman NB, Sladek R, Prentki M, Peyot ML. Pancreatic β-Cell Dysfunction in Diet-Induced Obese Mice: Roles of AMP-Kinase, Protein Kinase Cε, Mitochondrial and Cholesterol Metabolism, and Alterations in Gene Expression. PLoS One 2016; 11:e0153017. [PMID: 27043434 PMCID: PMC4820227 DOI: 10.1371/journal.pone.0153017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/22/2016] [Indexed: 12/27/2022] Open
Abstract
Diet induced obese (DIO) mice can be stratified according to their weight gain in response to high fat diet as low responders (LDR) and high responders (HDR). This allows the study of β-cell failure and the transitions to prediabetes (LDR) and early diabetes (HDR). C57BL/6N mice were fed for 8 weeks with a normal chow diet (ND) or a high fat diet and stratified as LDR and HDR. Freshly isolated islets from ND, LDR and HDR mice were studied ex-vivo for mitochondrial metabolism, AMPK activity and signalling, the expression and activity of key enzymes of energy metabolism, cholesterol synthesis, and mRNA profiling. Severely compromised glucose-induced insulin secretion in HDR islets, as compared to ND and LDR islets, was associated with suppressed AMP-kinase activity. HDR islets also showed reduced acetyl-CoA carboxylase activity and enhanced activity of 3-hydroxy-3-methylglutaryl-CoA reductase, which led respectively to elevated fatty acid oxidation and increased cholesterol biosynthesis. HDR islets also displayed mitochondrial membrane hyperpolarization and reduced ATP turnover in the presence of elevated glucose. Expression of protein kinase Cε, which reduces both lipolysis and production of signals for insulin secretion, was elevated in DIO islets. Genes whose expression increased or decreased by more than 1.2-fold were minor between LDR and ND islets (17 differentially expressed), but were prominent between HDR and ND islets (1508 differentially expressed). In HDR islets, particularly affected genes were related to cell cycle and proliferation, AMPK signaling, mitochondrial metabolism and cholesterol metabolism. In conclusion, chronically reduced AMPK activity, mitochondrial dysfunction, elevated cholesterol biosynthesis in islets, and substantial alterations in gene expression accompany β-cell failure in HDR islets. The β-cell compensation process in the prediabetic state (LDR) is largely independent of transcriptional adaptive changes, whereas the transition to early diabetes (HDR) is associated with major alterations in gene expression.
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Affiliation(s)
- Émilie Pepin
- Montreal Diabetes Research Center and Centre de Recherche du CHUM, Montréal, Québec, Canada
| | - Anfal Al-Mass
- Montreal Diabetes Research Center and Centre de Recherche du CHUM, Montréal, Québec, Canada
- Departments of Medicine and Human Genetics, McGill University, Montreal, Québec, Canada
| | - Camille Attané
- Montreal Diabetes Research Center and Centre de Recherche du CHUM, Montréal, Québec, Canada
| | - Kezhuo Zhang
- Departments of Medicine and Human Genetics, McGill University, Montreal, Québec, Canada
| | - Julien Lamontagne
- Montreal Diabetes Research Center and Centre de Recherche du CHUM, Montréal, Québec, Canada
| | - Roxane Lussier
- Montreal Diabetes Research Center and Centre de Recherche du CHUM, Montréal, Québec, Canada
| | - S. R. Murthy Madiraju
- Montreal Diabetes Research Center and Centre de Recherche du CHUM, Montréal, Québec, Canada
| | - Erik Joly
- Montreal Diabetes Research Center and Centre de Recherche du CHUM, Montréal, Québec, Canada
| | - Neil B. Ruderman
- Departments of Medicine and Physiology and Biophysics, Boston University School of Medicine and Diabetes Unit, Boston Medical Center, Boston, MA, United States of America
| | - Robert Sladek
- Departments of Medicine and Human Genetics, McGill University, Montreal, Québec, Canada
| | - Marc Prentki
- Montreal Diabetes Research Center and Centre de Recherche du CHUM, Montréal, Québec, Canada
- Departments of Nutrition, Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montréal, Montreal, Québec, Canada
- * E-mail: (MP); (MLP)
| | - Marie-Line Peyot
- Montreal Diabetes Research Center and Centre de Recherche du CHUM, Montréal, Québec, Canada
- * E-mail: (MP); (MLP)
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25
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Mahshid S, Ahamed MJ, Berard D, Amin S, Sladek R, Leslie SR, Reisner W. Development of a platform for single cell genomics using convex lens-induced confinement. Lab Chip 2015; 15:3013-20. [PMID: 26062011 DOI: 10.1039/c5lc00492f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We demonstrate a lab-on-a-chip that combines micro/nano-fabricated features with a Convex Lens-Induced Confinement (CLIC) device for the in situ analysis of single cells. A complete cycle of single cell analysis was achieved that includes: cell trapping, cell isolation, lysis, protein digestion, genomic DNA extraction and on-chip genomic DNA linearization. The ability to dynamically alter the flow-cell dimensions using the CLIC method was coupled with a flow-control mechanism for achieving efficient cell trapping, buffer exchange, and loading of long DNA molecules into nanofluidic arrays. Finite element simulation of fluid flow gives rise to optimized design parameters for overcoming the high hydraulic resistance present in the micro/nano-confinement region. By tuning design parameters such as the pressure gradient and CLIC confinement, an efficient on-chip single cell analysis protocol can be obtained. We demonstrate that we can extract Mbp long genomic DNA molecules from a single human lybphoblastoid cell and stretch these molecules in the nanochannels for optical interrogation.
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Affiliation(s)
- Sara Mahshid
- Department of Physics, McGill University, 3600 rue University, Montreal, Canada.
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26
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Ahmad OS, Morris JA, Mujammami M, Forgetta V, Leong A, Li R, Turgeon M, Greenwood CMT, Thanassoulis G, Meigs JB, Sladek R, Richards JB. A Mendelian randomization study of the effect of type-2 diabetes on coronary heart disease. Nat Commun 2015; 6:7060. [PMID: 26017687 PMCID: PMC4458864 DOI: 10.1038/ncomms8060] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/27/2015] [Indexed: 12/25/2022] Open
Abstract
In observational studies, type-2 diabetes (T2D) is associated with an increased risk of coronary heart disease (CHD), yet interventional trials have shown no clear effect of glucose-lowering on CHD. Confounding may have therefore influenced these observational estimates. Here we use Mendelian randomization to obtain unconfounded estimates of the influence of T2D and fasting glucose (FG) on CHD risk. Using multiple genetic variants associated with T2D and FG, we find that risk of T2D increases CHD risk (odds ratio (OR)=1.11 (1.05–1.17), per unit increase in odds of T2D, P=8.8 × 10−5; using data from 34,840/114,981 T2D cases/controls and 63,746/130,681 CHD cases/controls). FG in non-diabetic individuals tends to increase CHD risk (OR=1.15 (1.00–1.32), per mmol·per l, P=0.05; 133,010 non-diabetic individuals and 63,746/130,681 CHD cases/controls). These findings provide evidence supporting a causal relationship between T2D and CHD and suggest that long-term trials may be required to discern the effects of T2D therapies on CHD risk. In order to effectively design interventions, it is useful to understand the complex interplay between multiple syndromes. Here, Ahmad et al. use genome-wide association study data and Mendelian randomisation to examine the influence of Type 2 diabetes and fasting glucose levels on coronary heart disease.
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Affiliation(s)
- Omar S Ahmad
- 1] Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec H3A 0G4, Canada [2] Department of Medicine, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - John A Morris
- 1] Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec H3A 0G4, Canada [2] Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
| | - Muhammad Mujammami
- 1] Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec H3A 0G4, Canada [2] Department of Medicine, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Vincenzo Forgetta
- 1] Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec H3A 0G4, Canada [2] Department of Medicine, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Aaron Leong
- Division of General Internal Medicine, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rui Li
- 1] Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec H3A 0G4, Canada [2] Department of Medicine, McGill University, Montreal, Quebec H3A 0G4, Canada [3] Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
| | - Maxime Turgeon
- Department of Oncology, Epidemiology, Biostatistics and Occupational Health, and Human Genetics, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Celia M T Greenwood
- Department of Oncology, Epidemiology, Biostatistics and Occupational Health, and Human Genetics, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - George Thanassoulis
- 1] Department of Medicine, McGill University, Montreal, Quebec H3A 0G4, Canada [2] Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Robert Sladek
- 1] Department of Medicine, McGill University, Montreal, Quebec H3A 0G4, Canada [2] Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
| | - J Brent Richards
- 1] Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec H3A 0G4, Canada [2] Department of Medicine, McGill University, Montreal, Quebec H3A 0G4, Canada [3] Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada [4] Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
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27
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Cornes BK, Brody JA, Nikpoor N, Morrison AC, Chu H, Ahn BS, Wang S, Dauriz M, Barzilay JI, Dupuis J, Florez JC, Coresh J, Gibbs RA, Kao WHL, Liu CT, McKnight B, Muzny D, Pankow JS, Reid JG, White CC, Johnson AD, Wong TY, Psaty BM, Boerwinkle E, Rotter JI, Siscovick DS, Sladek R, Meigs JB. Association of levels of fasting glucose and insulin with rare variants at the chromosome 11p11.2-MADD locus: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study. ACTA ACUST UNITED AC 2015; 7:374-382. [PMID: 24951664 DOI: 10.1161/circgenetics.113.000169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND Common variation at the 11p11.2 locus, encompassing MADD, ACP2, NR1H3, MYBPC3, and SPI1, has been associated in genome-wide association studies with fasting glucose and insulin (FI). In the Cohorts for Heart and Aging Research in Genomic Epidemiology Targeted Sequencing Study, we sequenced 5 gene regions at 11p11.2 to identify rare, potentially functional variants influencing fasting glucose or FI levels. METHODS AND RESULTS Sequencing (mean depth, 38×) across 16.1 kb in 3566 individuals without diabetes mellitus identified 653 variants, 79.9% of which were rare (minor allele frequency <1%) and novel. We analyzed rare variants in 5 gene regions with FI or fasting glucose using the sequence kernel association test. At NR1H3, 53 rare variants were jointly associated with FI (P=2.73×10(-3)); of these, 7 were predicted to have regulatory function and showed association with FI (P=1.28×10(-3)). Conditioning on 2 previously associated variants at MADD (rs7944584, rs10838687) did not attenuate this association, suggesting that there are >2 independent signals at 11p11.2. One predicted regulatory variant, chr11:47227430 (hg18; minor allele frequency=0.00068), contributed 20.6% to the overall sequence kernel association test score at NR1H3, lies in intron 2 of NR1H3, and is a predicted binding site for forkhead box A1 (FOXA1), a transcription factor associated with insulin regulation. In human HepG2 hepatoma cells, the rare chr11:47227430 A allele disrupted FOXA1 binding and reduced FOXA1-dependent transcriptional activity. CONCLUSIONS Sequencing at 11p11.2-NR1H3 identified rare variation associated with FI. One variant, chr11:47227430, seems to be functional, with the rare A allele reducing transcription factor FOXA1 binding and FOXA1-dependent transcriptional activity.
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Affiliation(s)
- Belinda K Cornes
- General Medicine Division, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Naghmeh Nikpoor
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Alanna C Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Huan Chu
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Byung Soo Ahn
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Shuai Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Marco Dauriz
- General Medicine Division, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Verona Medical School and Hospital Trust of Verona, Verona, Italy
| | - Joshua I Barzilay
- Division of Endocrinology, Kaiser Permanente of Georgia and Emory University School of Medicine
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.,National Heart, Lung, and Blood Institute's The Framingham Heart Study, Cardiovascular Epidemiology and Human Genomics Center, Framingham, MA, USA
| | - Jose C Florez
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Center for Human Genetic Research, Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Josef Coresh
- Department of Medicine, The Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.,Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, University of Texas Health Science Center, Houston, TX
| | - W H Linda Kao
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Barbara McKnight
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA.,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, University of Texas Health Science Center, Houston, TX
| | - James S Pankow
- Division of Epidemiology and Community Health (J.S.P.), University of Minnesota, MN, USA
| | - Jeffrey G Reid
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Charles C White
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Andrew D Johnson
- National Heart, Lung, and Blood Institute's The Framingham Heart Study, Cardiovascular Epidemiology and Human Genomics Center, Framingham, MA, USA
| | - Tien Y Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Duke-NUS Graduate Medical School, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA; Group Health Research Institute, Group Health Cooperative, Seattle, WA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, University of Texas Health Science Center, Houston, TX
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Reasearch Institute and Department of Pediatrics, Harbor-UCLA Medical Center Torrance, California, USA
| | - David S Siscovick
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA.,Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Robert Sladek
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - James B Meigs
- General Medicine Division, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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28
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Gauthier MS, Pérusse JR, Lavoie MÈ, Sladek R, Madiraju SRM, Ruderman NB, Coulombe B, Prentki M, Rabasa-Lhoret R. Increased subcutaneous adipose tissue expression of genes involved in glycerolipid-fatty acid cycling in obese insulin-resistant versus -sensitive individuals. J Clin Endocrinol Metab 2014; 99:E2518-28. [PMID: 25210878 PMCID: PMC5393488 DOI: 10.1210/jc.2014-1662] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT A subpopulation of obese individuals remains insulin sensitive (ISO). They represent a unique human model to investigate factors underlying insulin resistance (IR) without the confounding effect of major differences in weight/adiposity. Altered fatty-acid (FA) metabolism in sc adipose tissue (SAT) contributes to obesity-associated IR. OBJECTIVE To test the hypothesis that ISO and body mass index-matched insulin-resistant obese (IRO) patients demonstrate differential SAT expression profiles of genes involved in glycerolipid-FA metabolism and that weight loss-induced improvement of IR ameliorates these changes. DESIGN AND SETTING A cross-sectional and longitudinal study. PATIENTS AND INTERVENTION Thirty-eight nondiabetic obese women were stratified into ISO (n = 25) or IRO (n = 13) groups based on hyperinsulinemic-euglycemic clamp results. Subjects were studied before and after a 6-month hypocaloric diet intervention. MAIN OUTCOME MEASURES mRNA (quantitative RT-PCR) and protein (mass spectrometry and immunoblots) levels were measured in SAT biopsies. RESULTS Despite having age, body mass index, and fat mass similar to ISO individuals, IRO patients had lower insulin sensitivity and glucose tolerance (P < .05). Baseline SAT mRNA and protein levels of genes involved in both the synthesis and lipolysis of glycerolipid-FAs were higher in IRO individuals (P < .05), even when groups were matched for visceral adipose tissue content. The dietary intervention resulted in approximately 6% weight loss in both the IRO and ISO groups (P < .05) but only ameliorated insulin sensitivity in IRO individuals (P < .05). Likewise, the intervention reduced the expression of most glycerolipid-FA metabolism genes (P < .05), with expression levels in IRO individuals being restored to ISO levels. CONCLUSIONS Increased SAT expression of genes involved in both the synthesis and hydrolysis of glycerolipid-FAs is closely associated with IR in obese women. The results suggest that enhanced glycerolipid-FA cycling in SAT contributes to obesity-associated IR.
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Affiliation(s)
- Marie-Soleil Gauthier
- Institut de recherches cliniques de Montréal (M.-S.G., J.R.P., M.-E.L., B.C., R.R.-L.), Montréal, QC H2W 1R7, Canada; Montreal Diabetes Research Center at the Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM) (M.-S.G., M.-E.L., R.S., S.R.M.M., M.P., R.R.-L.), Montréal, QC H2X 0A9, Canada; McGill University and Centre d'Innovation Génome Québec (R.S.), Montréal, QC H3A 0G1, Canada; Molecular Nutrition Unit at the CRCHUM (S.R.M.M., M.P.), Montréal, QC H2X 0A9, Canada; Diabetes and Metabolism Research Unit (N.B.R.), and Department of Medicine and Section of Endocrinology (N.B.R.), Boston University School of Medicine, Boston, Massachusetts 02118; Departments of Biochemistry (B.C., M.P.) and Nutrition (M.-E.L., M.P., R.R.-L.), Faculty of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
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29
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Boraska V, Franklin CS, Floyd JAB, Thornton LM, Huckins LM, Southam L, Rayner NW, Tachmazidou I, Klump KL, Treasure J, Lewis CM, Schmidt U, Tozzi F, Kiezebrink K, Hebebrand J, Gorwood P, Adan RAH, Kas MJH, Favaro A, Santonastaso P, Fernández-Aranda F, Gratacos M, Rybakowski F, Dmitrzak-Weglarz M, Kaprio J, Keski-Rahkonen A, Raevuori A, Van Furth EF, Slof-Op 't Landt MCT, Hudson JI, Reichborn-Kjennerud T, Knudsen GPS, Monteleone P, Kaplan AS, Karwautz A, Hakonarson H, Berrettini WH, Guo Y, Li D, Schork NJ, Komaki G, Ando T, Inoko H, Esko T, Fischer K, Männik K, Metspalu A, Baker JH, Cone RD, Dackor J, DeSocio JE, Hilliard CE, O'Toole JK, Pantel J, Szatkiewicz JP, Taico C, Zerwas S, Trace SE, Davis OSP, Helder S, Bühren K, Burghardt R, de Zwaan M, Egberts K, Ehrlich S, Herpertz-Dahlmann B, Herzog W, Imgart H, Scherag A, Scherag S, Zipfel S, Boni C, Ramoz N, Versini A, Brandys MK, Danner UN, de Kovel C, Hendriks J, Koeleman BPC, Ophoff RA, Strengman E, van Elburg AA, Bruson A, Clementi M, Degortes D, Forzan M, Tenconi E, Docampo E, Escaramís G, Jiménez-Murcia S, Lissowska J, Rajewski A, Szeszenia-Dabrowska N, Slopien A, Hauser J, Karhunen L, Meulenbelt I, Slagboom PE, Tortorella A, Maj M, Dedoussis G, Dikeos D, Gonidakis F, Tziouvas K, Tsitsika A, Papezova H, Slachtova L, Martaskova D, Kennedy JL, Levitan RD, Yilmaz Z, Huemer J, Koubek D, Merl E, Wagner G, Lichtenstein P, Breen G, Cohen-Woods S, Farmer A, McGuffin P, Cichon S, Giegling I, Herms S, Rujescu D, Schreiber S, Wichmann HE, Dina C, Sladek R, Gambaro G, Soranzo N, Julia A, Marsal S, Rabionet R, Gaborieau V, Dick DM, Palotie A, Ripatti S, Widén E, Andreassen OA, Espeseth T, Lundervold A, Reinvang I, Steen VM, Le Hellard S, Mattingsdal M, Ntalla I, Bencko V, Foretova L, Janout V, Navratilova M, Gallinger S, Pinto D, Scherer SW, Aschauer H, Carlberg L, Schosser A, Alfredsson L, Ding B, Klareskog L, Padyukov L, Courtet P, Guillaume S, Jaussent I, Finan C, Kalsi G, Roberts M, Logan DW, Peltonen L, Ritchie GRS, Barrett JC, Estivill X, Hinney A, Sullivan PF, Collier DA, Zeggini E, Bulik CM. A genome-wide association study of anorexia nervosa. Mol Psychiatry 2014; 19:1085-94. [PMID: 24514567 PMCID: PMC4325090 DOI: 10.1038/mp.2013.187] [Citation(s) in RCA: 241] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 11/21/2013] [Accepted: 11/25/2013] [Indexed: 02/06/2023]
Abstract
Anorexia nervosa (AN) is a complex and heritable eating disorder characterized by dangerously low body weight. Neither candidate gene studies nor an initial genome-wide association study (GWAS) have yielded significant and replicated results. We performed a GWAS in 2907 cases with AN from 14 countries (15 sites) and 14 860 ancestrally matched controls as part of the Genetic Consortium for AN (GCAN) and the Wellcome Trust Case Control Consortium 3 (WTCCC3). Individual association analyses were conducted in each stratum and meta-analyzed across all 15 discovery data sets. Seventy-six (72 independent) single nucleotide polymorphisms were taken forward for in silico (two data sets) or de novo (13 data sets) replication genotyping in 2677 independent AN cases and 8629 European ancestry controls along with 458 AN cases and 421 controls from Japan. The final global meta-analysis across discovery and replication data sets comprised 5551 AN cases and 21 080 controls. AN subtype analyses (1606 AN restricting; 1445 AN binge-purge) were performed. No findings reached genome-wide significance. Two intronic variants were suggestively associated: rs9839776 (P=3.01 × 10(-7)) in SOX2OT and rs17030795 (P=5.84 × 10(-6)) in PPP3CA. Two additional signals were specific to Europeans: rs1523921 (P=5.76 × 10(-)(6)) between CUL3 and FAM124B and rs1886797 (P=8.05 × 10(-)(6)) near SPATA13. Comparing discovery with replication results, 76% of the effects were in the same direction, an observation highly unlikely to be due to chance (P=4 × 10(-6)), strongly suggesting that true findings exist but our sample, the largest yet reported, was underpowered for their detection. The accrual of large genotyped AN case-control samples should be an immediate priority for the field.
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Affiliation(s)
- V Boraska
- 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK [2] University of Split School of Medicine, Split, Croatia
| | - C S Franklin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - J A B Floyd
- 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK [2] William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
| | - L M Thornton
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - L M Huckins
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - L Southam
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - N W Rayner
- 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK [2] Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, Oxford, UK [3] Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Oxford, UK
| | - I Tachmazidou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - K L Klump
- Department of Psychology, Michigan State University, East Lansing, MI, USA
| | - J Treasure
- Section of Eating Disorders, Institute of Psychiatry, King's College London, London, UK
| | - C M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - U Schmidt
- Section of Eating Disorders, Institute of Psychiatry, King's College London, London, UK
| | - F Tozzi
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - K Kiezebrink
- Health Services Research Unit, University of Aberdeen, Aberdeen, UK
| | - J Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Universitätsklinikum Essen, University of Duisburg-Essen, Essen, Germany
| | - P Gorwood
- 1] INSERM U894, Centre of Psychiatry and Neuroscience, Paris, France [2] Sainte-Anne Hospital (CMME), University of Paris-Descartes, Paris, France
| | - R A H Adan
- 1] Brain Center Rudolf Magnus, Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands [2] Altrecht Eating Disorders Rintveld, Zeist, The Netherlands
| | - M J H Kas
- Brain Center Rudolf Magnus, Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A Favaro
- Department of Neurosciences, University of Padova, Padova, Italy
| | - P Santonastaso
- Department of Neurosciences, University of Padova, Padova, Italy
| | - F Fernández-Aranda
- 1] Department of Psychiatry and CIBERON, University Hospital of Bellvitge-IDIBELL, Barcelona, Spain [2] Department of Clinical Sciences, School of Medicine, University of Barcelona, Barcelona, Spain
| | - M Gratacos
- 1] Genomics and Disease Group, Centre for Genomic Regulation (CRG), Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain [3] Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain [4] Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - F Rybakowski
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - M Dmitrzak-Weglarz
- Department of Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | - J Kaprio
- 1] Hjelt Institute, University of Helsinki, Helsinki, Finland [2] Institute of Molecular Medicine, University of Helsinki, Helsinki, Finland [3] Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, Helsinki, Finland
| | | | - A Raevuori
- 1] Hjelt Institute, University of Helsinki, Helsinki, Finland [2] Department of Adolescent Psychiatry, Helsinki University Central Hospital, Helsinki, Finland
| | - E F Van Furth
- 1] Center for Eating Disorders Ursula, Leidschendam, The Netherlands [2] Department of Psychiatry, Leiden University Medical Centre, Leiden, The Netherlands
| | - M C T Slof-Op 't Landt
- 1] Center for Eating Disorders Ursula, Leidschendam, The Netherlands [2] Molecular Epidemiology Section, Department of Medical Statistics, Leiden University Medical Centre, Leiden, The Netherlands
| | - J I Hudson
- Department of Psychiatry, McLean Hospital/Harvard Medical School, Belmont, MA, USA
| | - T Reichborn-Kjennerud
- 1] Department of Genetics, Environment and Mental Health, Norwegian Institute of Public Health, Oslo, Norway [2] Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - G P S Knudsen
- Department of Genetics, Environment and Mental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - P Monteleone
- 1] Department of Psychiatry, University of Naples SUN, Naples, Italy [2] Chair of Psychiatry, University of Salerno, Salerno, Italy
| | - A S Kaplan
- 1] Centre for Addiction and Mental Health, Toronto, ON, Canada [2] Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - A Karwautz
- Eating Disorders Unit, Department of Child and Adolescent Psychiatry, Medical University of Vienna, Vienna, Austria
| | - H Hakonarson
- 1] The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA [2] The Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - W H Berrettini
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Y Guo
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - D Li
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - N J Schork
- Department of Molecular and Experimental Medicine and The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA, USA
| | - G Komaki
- 1] Department of Psychosomatic Research, National Institute of Mental Health, NCNP, Tokyo, Japan [2] School of Health Sciences at Fukuoka, International University of Health and Welfare, Fukuoka, Japan
| | - T Ando
- Department of Psychosomatic Research, National Institute of Mental Health, NCNP, Tokyo, Japan
| | - H Inoko
- Department of Molecular Life Sciences, Tokai University School of Medicine, Kanagawa, Japan
| | - T Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - K Fischer
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - K Männik
- 1] Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia [2] Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - A Metspalu
- 1] Estonian Genome Center, University of Tartu, Tartu, Estonia [2] Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - J H Baker
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - R D Cone
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - J Dackor
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J E DeSocio
- Seattle University College of Nursing, Seattle, WA, USA
| | - C E Hilliard
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - J Pantel
- Centre de Psychiatrie et Neurosciences - Inserm U894, Paris, France
| | - J P Szatkiewicz
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - C Taico
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - S Zerwas
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - S E Trace
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - O S P Davis
- 1] Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK [2] Department of Genetics, Evolution and Environment, University College London, UCL Genetics Institute, London, UK
| | - S Helder
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - K Bühren
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Clinics RWTH Aachen, Aachen, Germany
| | - R Burghardt
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Charité, Berlin, Germany
| | - M de Zwaan
- 1] Department of Psychosomatic Medicine and Psychotherapy, Hannover Medical School, Hannover, Germany [2] Department of Psychosomatic Medicine and Psychotherapy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - K Egberts
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Würzburg, Würzburg, Germany
| | - S Ehrlich
- 1] Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany [2] Athinoula A. Martinos Center for Biomedical Imaging, Psychiatric Neuroimaging Research Program, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA, USA
| | - B Herpertz-Dahlmann
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Clinics RWTH Aachen, Aachen, Germany
| | - W Herzog
- Departments of Psychosocial and Internal Medicine, Heidelberg University, Heidelberg, Germany
| | - H Imgart
- Parklandklinik, Bad Wildungen, Germany
| | - A Scherag
- Institute for Medical Informatics, Biometry and Epidemiology, Universitätsklinikum Essen, University of Duisburg-Essen, Essen, Germany
| | - S Scherag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Universitätsklinikum Essen, University of Duisburg-Essen, Essen, Germany
| | - S Zipfel
- Department of Internal Medicine VI, Psychosomatic Medicine and Psychotherapy, University Medical Hospital Tübingen, Tübingen, Germany
| | - C Boni
- INSERM U894, Centre of Psychiatry and Neuroscience, Paris, France
| | - N Ramoz
- INSERM U894, Centre of Psychiatry and Neuroscience, Paris, France
| | - A Versini
- INSERM U894, Centre of Psychiatry and Neuroscience, Paris, France
| | - M K Brandys
- 1] Brain Center Rudolf Magnus, Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands [2] Altrecht Eating Disorders Rintveld, Zeist, The Netherlands
| | - U N Danner
- Altrecht Eating Disorders Rintveld, Zeist, The Netherlands
| | - C de Kovel
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - J Hendriks
- Brain Center Rudolf Magnus, Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - B P C Koeleman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - R A Ophoff
- 1] Center for Neurobehavioral Genetics, University of California, Los Angeles, Los Angeles, CA, USA [2] Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - E Strengman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A A van Elburg
- 1] Altrecht Eating Disorders Rintveld, Zeist, The Netherlands [2] Department of Child and Adolescent Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A Bruson
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, Padova, Italy
| | - M Clementi
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, Padova, Italy
| | - D Degortes
- Department of Neurosciences, University of Padova, Padova, Italy
| | - M Forzan
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, Padova, Italy
| | - E Tenconi
- Department of Neurosciences, University of Padova, Padova, Italy
| | - E Docampo
- 1] Genomics and Disease Group, Centre for Genomic Regulation (CRG), Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain [3] Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain [4] Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - G Escaramís
- 1] Genomics and Disease Group, Centre for Genomic Regulation (CRG), Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain [3] Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain [4] Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - S Jiménez-Murcia
- 1] Department of Psychiatry and CIBERON, University Hospital of Bellvitge-IDIBELL, Barcelona, Spain [2] Department of Clinical Sciences, School of Medicine, University of Barcelona, Barcelona, Spain
| | - J Lissowska
- M. Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - A Rajewski
- Department of Epidemiology, Institute of Occupational Medicine, Department of Epidemiology, Lodz, Poland
| | - N Szeszenia-Dabrowska
- Department of Epidemiology, Institute of Occupational Medicine, Department of Epidemiology, Lodz, Poland
| | - A Slopien
- Department of Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | - J Hauser
- Department of Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | - L Karhunen
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - I Meulenbelt
- Molecular Epidemiology Section, Department of Medical Statistics, Leiden University Medical Centre, Leiden, The Netherlands
| | - P E Slagboom
- 1] Molecular Epidemiology Section, Department of Medical Statistics, Leiden University Medical Centre, Leiden, The Netherlands [2] Netherlands Consortium for Healthy Ageing, Leiden University Medical Center, Leiden, The Netherlands
| | - A Tortorella
- Department of Psychiatry, University of Naples SUN, Naples, Italy
| | - M Maj
- Department of Psychiatry, University of Naples SUN, Naples, Italy
| | - G Dedoussis
- Department of Nutrition and Dietetics, Harokopio University, Athens, Greece
| | - D Dikeos
- 1st Department of Psychiatry, Athens University Medical School, Athens, Greece
| | - F Gonidakis
- Eating Disorders Unit, 1st Department of Psychiatry, Athens University Medical School, Athens, Greece
| | - K Tziouvas
- Department of Nutrition and Dietetics, Harokopio University, Athens, Greece
| | - A Tsitsika
- Adolescent Health Unit (A.H.U.), 2nd Department of Pediatrics - Medical School, University of Athens 'P. & A. Kyriakou' Children's Hospital, Athens, Greece
| | - H Papezova
- Department of Psychiatry, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - L Slachtova
- Department of Pediatrics, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - D Martaskova
- Department of Psychiatry, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - J L Kennedy
- 1] Centre for Addiction and Mental Health, Toronto, ON, Canada [2] Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - R D Levitan
- 1] Centre for Addiction and Mental Health, Toronto, ON, Canada [2] Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Z Yilmaz
- 1] Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA [2] Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - J Huemer
- Eating Disorders Unit, Department of Child and Adolescent Psychiatry, Medical University of Vienna, Vienna, Austria
| | - D Koubek
- Eating Disorders Unit, Department of Child and Adolescent Psychiatry, Medical University of Vienna, Vienna, Austria
| | - E Merl
- Eating Disorders Unit, Department of Child and Adolescent Psychiatry, Medical University of Vienna, Vienna, Austria
| | - G Wagner
- Eating Disorders Unit, Department of Child and Adolescent Psychiatry, Medical University of Vienna, Vienna, Austria
| | - P Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - G Breen
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - S Cohen-Woods
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - A Farmer
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - P McGuffin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - S Cichon
- 1] Department of Genomics, Life & Brain Center, Institute of Human Genetics, University of Bonn, Bonn, Germany [2] Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany [3] Division of Medical Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - I Giegling
- Klinikum der Medizinischen Fakultät, Martin-Luther-Universität Halle-Wittenberg, Halle/Saale, Germany
| | - S Herms
- 1] Department of Genomics, Life & Brain Center, Institute of Human Genetics, University of Bonn, Bonn, Germany [2] Division of Medical Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - D Rujescu
- Klinikum der Medizinischen Fakultät, Martin-Luther-Universität Halle-Wittenberg, Halle/Saale, Germany
| | - S Schreiber
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - H-E Wichmann
- 1] Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany [2] Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University, Munich, Germany
| | - C Dina
- CNRS 8090-Institute of Biology, Pasteur Institute, Lille, France
| | - R Sladek
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - G Gambaro
- Division of Nephrology, Department of Internal Medicine and Medical Specialties, Columbus-Gemelly Hospitals, Catholic University, Rome, Italy
| | - N Soranzo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - A Julia
- Unitat de Recerca de Reumatologia (URR), Institut de Recerca Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - S Marsal
- Unitat de Recerca de Reumatologia (URR), Institut de Recerca Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - R Rabionet
- 1] Genomics and Disease Group, Centre for Genomic Regulation (CRG), Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain [3] Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain [4] Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - V Gaborieau
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - D M Dick
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - A Palotie
- 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK [2] The Finnish Institute of Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland [3] The Program for Human and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - S Ripatti
- 1] The Finnish Institute of Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland [2] Finnish Institute of Occupational Health, Helsinki, Finland
| | - E Widén
- 1] The Finnish Institute of Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland [2] Finnish Institute of Occupational Health, Helsinki, Finland
| | - O A Andreassen
- NORMENT, K.G. Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - T Espeseth
- 1] NORMENT, K.G. Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway [2] Department of Psychology, University of Oslo, Oslo, Norway
| | - A Lundervold
- 1] Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway [2] Kavli Research Centre for Aging and Dementia, Haraldsplass Deaconess Hospital, Bergen, Norway [3] K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - I Reinvang
- Department of Psychology, University of Oslo, Oslo, Norway
| | - V M Steen
- 1] Department of Clinical Science, K.G. Jebsen Centre for Psychosis Research, Norwegian Centre For Mental Disorders Research (NORMENT), University of Bergen, Bergen, Norway [2] Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - S Le Hellard
- 1] Department of Clinical Science, K.G. Jebsen Centre for Psychosis Research, Norwegian Centre For Mental Disorders Research (NORMENT), University of Bergen, Bergen, Norway [2] Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - M Mattingsdal
- NORMENT, K.G. Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - I Ntalla
- Department of Nutrition and Dietetics, Harokopio University, Athens, Greece
| | - V Bencko
- Institute of Hygiene and Epidemiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - L Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - V Janout
- Palacky University, Olomouc, Czech Republic
| | - M Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - S Gallinger
- 1] University Health Network, Toronto General Hospital, Toronto, ON, Canada [2] Mount Sinai Hospital, Samuel Lunenfeld Research Institute, Toronto, ON, Canada
| | - D Pinto
- Departments of Psychiatry, and Genetics and Genomic Sciences, Seaver Autism Center, and the Mindich Child Health and Development Institute, Mount Sinai School of Medicine, New York, NY, USA
| | - S W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - H Aschauer
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - L Carlberg
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - A Schosser
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - L Alfredsson
- The Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - B Ding
- The Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - L Klareskog
- Rheumatology Unit, Department of Medicine at the Karolinska University Hospital, Solna, Sweden
| | - L Padyukov
- Rheumatology Unit, Department of Medicine at the Karolinska University Hospital, Solna, Sweden
| | - P Courtet
- 1] Inserm, U1061, Université Montpellier 1, Montpellier, France [2] Department of Emergency Psychiatry, CHU Montpellier, Montpellier, France
| | - S Guillaume
- 1] Inserm, U1061, Université Montpellier 1, Montpellier, France [2] Department of Emergency Psychiatry, CHU Montpellier, Montpellier, France
| | - I Jaussent
- 1] Inserm, U1061, Université Montpellier 1, Montpellier, France [2] Department of Emergency Psychiatry, CHU Montpellier, Montpellier, France
| | - C Finan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - G Kalsi
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - M Roberts
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - D W Logan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - L Peltonen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - G R S Ritchie
- 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK [2] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge
| | - J C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - X Estivill
- 1] Genomics and Disease Group, Centre for Genomic Regulation (CRG), Barcelona, Spain [2] Universitat Pompeu Fabra (UPF), Barcelona, Spain [3] Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain [4] Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - A Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Universitätsklinikum Essen, University of Duisburg-Essen, Essen, Germany
| | - P F Sullivan
- 1] Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA [2] Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D A Collier
- 1] Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK [2] Eli Lilly and Company, Erl Wood Manor, Windlesham, UK
| | - E Zeggini
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - C M Bulik
- 1] Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA [2] Department of Nutrition, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Kanagaratham C, Marino R, Camateros P, Ren J, Houle D, Sladek R, Vidal SM, Radzioch D. Mapping of a chromosome 12 region associated with airway hyperresponsiveness in a recombinant congenic mouse strain and selection of potential candidate genes by expression and sequence variation analyses. PLoS One 2014; 9:e104234. [PMID: 25111050 PMCID: PMC4128649 DOI: 10.1371/journal.pone.0104234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/08/2014] [Indexed: 01/09/2023] Open
Abstract
In a previous study we determined that BcA86 mice, a strain belonging to a panel of AcB/BcA recombinant congenic strains, have an airway responsiveness phenotype resembling mice from the airway hyperresponsive A/J strain. The majority of the BcA86 genome is however from the hyporesponsive C57BL/6J strain. The aim of this study was to identify candidate regions and genes associated with airway hyperresponsiveness (AHR) by quantitative trait locus (QTL) analysis using the BcA86 strain. Airway responsiveness of 205 F2 mice generated from backcrossing BcA86 strain to C57BL/6J strain was measured and used for QTL analysis to identify genomic regions in linkage with AHR. Consomic mice for the QTL containing chromosomes were phenotyped to study the contribution of each chromosome to lung responsiveness. Candidate genes within the QTL were selected based on expression differences in mRNA from whole lungs, and the presence of coding non-synonymous mutations that were predicted to have a functional effect by amino acid substitution prediction tools. One QTL for AHR was identified on Chromosome 12 with its 95% confidence interval ranging from 54.6 to 82.6 Mbp and a maximum LOD score of 5.11 (p = 3.68×10−3). We confirmed that the genotype of mouse Chromosome 12 is an important determinant of lung responsiveness using a Chromosome 12 substitution strain. Mice with an A/J Chromosome 12 on a C57BL/6J background have an AHR phenotype similar to hyperresponsive strains A/J and BcA86. Within the QTL, genes with deleterious coding variants, such as Foxa1, and genes with expression differences, such as Mettl21d and Snapc1, were selected as possible candidates for the AHR phenotype. Overall, through QTL analysis of a recombinant congenic strain, microarray analysis and coding variant analysis we identified Chromosome 12 and three potential candidate genes to be in linkage with airway responsiveness.
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Affiliation(s)
- Cynthia Kanagaratham
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- * E-mail:
| | - Rafael Marino
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Pierre Camateros
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - John Ren
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Daniel Houle
- Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Robert Sladek
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Silvia M. Vidal
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Danuta Radzioch
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
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Kleinman CL, Gerges N, Papillon-Cavanagh S, Sin-Chan P, Pramatarova A, Quang DAK, Adoue V, Busche S, Caron M, Djambazian H, Bemmo A, Fontebasso AM, Spence T, Schwartzentruber J, Albrecht S, Hauser P, Garami M, Klekner A, Bognar L, Montes JL, Staffa A, Montpetit A, Berube P, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel PM, Duchaine T, Perotti C, Fleming A, Faury D, Remke M, Gallo M, Dirks P, Taylor MD, Sladek R, Pastinen T, Chan JA, Huang A, Majewski J, Jabado N. Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. Nat Genet 2014; 46:39-44. [PMID: 24316981 DOI: 10.1038/ng.2849] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 11/13/2013] [Indexed: 12/20/2022]
Abstract
Embryonal tumors with multilayered rosettes (ETMRs) are rare, deadly pediatric brain tumors characterized by high-level amplification of the microRNA cluster C19MC. We performed integrated genetic and epigenetic analyses of 12 ETMR samples and identified, in all cases, C19MC fusions to TTYH1 driving expression of the microRNAs. ETMR tumors, cell lines and xenografts showed a specific DNA methylation pattern distinct from those of other tumors and normal tissues. We detected extreme overexpression of a previously uncharacterized isoform of DNMT3B originating at an alternative promoter that is active only in the first weeks of neural tube development. Transcriptional and immunohistochemical analyses suggest that C19MC-dependent DNMT3B deregulation is mediated by RBL2, a known repressor of DNMT3B. Transfection with individual C19MC microRNAs resulted in DNMT3B upregulation and RBL2 downregulation in cultured cells. Our data suggest a potential oncogenic re-engagement of an early developmental program in ETMR via epigenetic alteration mediated by an embryonic, brain-specific DNMT3B isoform.
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Affiliation(s)
- Claudia L Kleinman
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [3]
| | - Noha Gerges
- 1] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [2]
| | | | - Patrick Sin-Chan
- Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Albena Pramatarova
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | | | - Véronique Adoue
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Stephan Busche
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Maxime Caron
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Haig Djambazian
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Amandine Bemmo
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Adam M Fontebasso
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Tara Spence
- Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Steffen Albrecht
- Department of Pathology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Peter Hauser
- Second Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Miklos Garami
- Second Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Almos Klekner
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Laszlo Bognar
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Jose-Luis Montes
- Division of Neurosurgery, Department of Surgery, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Alfredo Staffa
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Alexandre Montpetit
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Pierre Berube
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Magdalena Zakrzewska
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Krzysztof Zakrzewski
- Department of Neurosurgery, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Pawel P Liberski
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Zhifeng Dong
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Peter M Siegel
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Thomas Duchaine
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Christian Perotti
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Adam Fleming
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, McGill University and the McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Damien Faury
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, McGill University and the McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Marc Remke
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marco Gallo
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Dirks
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Robert Sladek
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tomi Pastinen
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Jennifer A Chan
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Annie Huang
- 1] Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada. [2] Program in Cell Biology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada. [3]
| | - Jacek Majewski
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [3]
| | - Nada Jabado
- 1] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [2] Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada. [3]
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Abstract
An oligonucleotide-based electrochemically controlled gold-coated microcantilever biosensor that can transduce specific biomolecular interactions is reported. The derivatized microcantilever exhibits characteristic surface stress time course patterns in response to an externally applied periodic square wave potential. Experiments demonstrate that control of the surface charge density with an electrode potential is essential to producing a sensor that exhibits large, reproducible surface stress changes. The time course of surface stress changes are proposed to be linked to an electrochemically mediated competition between the adsorption of solution-based ions and the single- or double-stranded oligonucleotides tethered to the gold surface. A similar potential-actuated change in surface stress also results from the interaction between an oligonucleotide aptamer and its cognate ligand, demonstrating the broad applicability of this methodology.
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Affiliation(s)
- Yoshihiko Nagai
- Research Institute of the McGill University Health Centre, 2155 Guy Street, Montréal, Québec H3H 2R9, Canada
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33
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Abstract
Optical mapping of DNA provides large-scale genomic information that can be used to assemble contigs from next-generation sequencing, and to detect rearrangements between single cells. A recent optical mapping technique called denaturation mapping has the advantage of using physical principles rather than the action of enzymes to probe genomic structure. Denaturation mapping uses fluorescence microscopy to image the pattern of partial melting along a DNA molecule extended in a channel of cross-section 120 nm at the heart of a nanofluidic device. We used denaturation mapping to locate single DNA molecules on the yeast genome (12.1 Mbp) by comparing images to a computationally predicted map for the entire genome sequence. By locating 84 molecules we assembled an optical map of the yeast genome with > 50% coverage.
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Affiliation(s)
- Robert L Welch
- Department of Physics, McGill University, 3600 rue University, Montreal, Canada
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Boivin GA, Pothlichet J, Skamene E, Brown EG, Loredo-Osti JC, Sladek R, Vidal SM. Mapping of clinical and expression quantitative trait loci in a sex-dependent effect of host susceptibility to mouse-adapted influenza H3N2/HK/1/68. J Immunol 2012; 188:3949-60. [PMID: 22427645 DOI: 10.4049/jimmunol.1103320] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Seasonal influenza outbreaks and recurrent influenza pandemics present major challenges to public health. By studying immunological responses to influenza in different host species, it may be possible to discover common mechanisms of susceptibility in response to various influenza strains. This could lead to novel therapeutic targets with wide clinical application. Using a mouse-adapted strain of influenza (A/HK/1/68-MA20 [H3N2]), we produced a mouse model of severe influenza that reproduces the hallmark high viral load and overexpression of cytokines associated with susceptibility to severe influenza in humans. We mapped genetic determinants of the host response using a panel of 29 closely related mouse strains (AcB/BcA panel of recombinant congenic strains) created from influenza-susceptible A/J and influenza-resistant C57BL/6J (B6) mice. Combined clinical quantitative trait loci (QTL) and lung expression QTL mapping identified candidate genes for two sex-specific QTL on chromosomes 2 and 17. The former includes the previously described Hc gene, a deficit of which is associated with the susceptibility phenotype in females. The latter includes the phospholipase gene Pla2g7 and Tnfrsf21, a member of the TNFR superfamily. Confirmation of the gene underlying the chromosome 17 QTL may reveal new strategies for influenza treatment.
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Affiliation(s)
- Gregory A Boivin
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 1B1, Canada
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35
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Bongfen SE, Rodrigue-Gervais IG, Berghout J, Torre S, Cingolani P, Wiltshire SA, Leiva-Torres GA, Letourneau L, Sladek R, Blanchette M, Lathrop M, Behr MA, Gruenheid S, Vidal SM, Saleh M, Gros P. An N-ethyl-N-nitrosourea (ENU)-induced dominant negative mutation in the JAK3 kinase protects against cerebral malaria. PLoS One 2012; 7:e31012. [PMID: 22363534 PMCID: PMC3283600 DOI: 10.1371/journal.pone.0031012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 12/29/2011] [Indexed: 11/19/2022] Open
Abstract
Cerebral malaria (CM) is a lethal neurological complication of malaria. We implemented a genome-wide screen in mutagenized mice to identify host proteins involved in CM pathogenesis and whose inhibition may be of therapeutic value. One pedigree (P48) segregated a resistance trait whose CM-protective effect was fully penetrant, mapped to chromosome 8, and identified by genome sequencing as homozygosity for a mis-sense mutation (W81R) in the FERM domain of Janus-associated kinase 3 (Jak3). The causative effect of Jak3(W81R) was verified by complementation testing in Jak3(W81R/-) double heterozygotes that were fully protected against CM. Jak3(W81R) homozygotes showed defects in thymic development with depletion of CD8(+) T cell, B cell, and NK cell compartments, and defective T cell-dependent production of IFN-γ. Adoptive transfer of normal splenocytes abrogates CM resistance in Jak3(W81R) homozygotes, an effect attributed to the CD8(+) T cells. Jak3(W81R) behaves as a dominant negative variant, with significant CM resistance of Jak3(W81R/+) heterozygotes, compared to CM-susceptible Jak3(+/+) and Jak3(+/-) controls. CM resistance in Jak3(W81R/+) heterozygotes occurs in presence of normal T, B and NK cell numbers. These findings highlight the pathological role of CD8(+) T cells and Jak3-dependent IFN-γ-mediated Th1 responses in CM pathogenesis.
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Affiliation(s)
- Silayuv E. Bongfen
- Department of Biochemistry, McGill University, Montreal, Canada
- Complex Traits Group, McGill University, Montreal, Canada
| | - Ian-Gael Rodrigue-Gervais
- Department of Medicine, McGill University, Montreal, Canada
- Complex Traits Group, McGill University, Montreal, Canada
| | - Joanne Berghout
- Department of Biochemistry, McGill University, Montreal, Canada
- Complex Traits Group, McGill University, Montreal, Canada
| | - Sabrina Torre
- Department of Human Genetics, McGill University, Montreal, Canada
- Complex Traits Group, McGill University, Montreal, Canada
| | - Pablo Cingolani
- School of Computer Science, McGill University, Montreal, Canada
| | - Sean A. Wiltshire
- Department of Human Genetics, McGill University, Montreal, Canada
- Complex Traits Group, McGill University, Montreal, Canada
| | - Gabriel A. Leiva-Torres
- Department of Human Genetics, McGill University, Montreal, Canada
- Complex Traits Group, McGill University, Montreal, Canada
| | - Louis Letourneau
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Robert Sladek
- Department of Human Genetics, McGill University, Montreal, Canada
| | | | - Mark Lathrop
- Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Marcel A. Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
- The McGill University Health Center, Montreal, Canada
| | - Samantha Gruenheid
- Complex Traits Group, McGill University, Montreal, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Silvia M. Vidal
- Department of Human Genetics, McGill University, Montreal, Canada
- Complex Traits Group, McGill University, Montreal, Canada
| | - Maya Saleh
- Department of Medicine, McGill University, Montreal, Canada
- Complex Traits Group, McGill University, Montreal, Canada
| | - Philippe Gros
- Department of Biochemistry, McGill University, Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
- Complex Traits Group, McGill University, Montreal, Canada
- * E-mail:
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36
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Bonnefond A, Clément N, Fawcett K, Yengo L, Vaillant E, Guillaume JL, Dechaume A, Payne F, Roussel R, Czernichow S, Hercberg S, Hadjadj S, Balkau B, Marre M, Lantieri O, Langenberg C, Bouatia-Naji N, Charpentier G, Vaxillaire M, Rocheleau G, Wareham NJ, Sladek R, McCarthy MI, Dina C, Barroso I, Jockers R, Froguel P. Rare MTNR1B variants impairing melatonin receptor 1B function contribute to type 2 diabetes. Nat Genet 2012; 44:297-301. [PMID: 22286214 PMCID: PMC3773908 DOI: 10.1038/ng.1053] [Citation(s) in RCA: 265] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 12/02/2011] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies have revealed that common noncoding variants in MTNR1B (encoding melatonin receptor 1B, also known as MT(2)) increase type 2 diabetes (T2D) risk(1,2). Although the strongest association signal was highly significant (P < 1 × 10(-20)), its contribution to T2D risk was modest (odds ratio (OR) of ∼1.10-1.15)(1-3). We performed large-scale exon resequencing in 7,632 Europeans, including 2,186 individuals with T2D, and identified 40 nonsynonymous variants, including 36 very rare variants (minor allele frequency (MAF) <0.1%), associated with T2D (OR = 3.31, 95% confidence interval (CI) = 1.78-6.18; P = 1.64 × 10(-4)). A four-tiered functional investigation of all 40 mutants revealed that 14 were non-functional and rare (MAF < 1%), and 4 were very rare with complete loss of melatonin binding and signaling capabilities. Among the very rare variants, the partial- or total-loss-of-function variants but not the neutral ones contributed to T2D (OR = 5.67, CI = 2.17-14.82; P = 4.09 × 10(-4)). Genotyping the four complete loss-of-function variants in 11,854 additional individuals revealed their association with T2D risk (8,153 individuals with T2D and 10,100 controls; OR = 3.88, CI = 1.49-10.07; P = 5.37 × 10(-3)). This study establishes a firm functional link between MTNR1B and T2D risk.
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Affiliation(s)
- Amélie Bonnefond
- Centre National de la Recherche Scientifique Unité Mixte de Recherche, Lille Pasteur Institute, France
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37
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Palmer ND, McDonough CW, Hicks PJ, Roh BH, Wing MR, An SS, Hester JM, Cooke JN, Bostrom MA, Rudock ME, Talbert ME, Lewis JP, Ferrara A, Lu L, Ziegler JT, Sale MM, Divers J, Shriner D, Adeyemo A, Rotimi CN, Ng MCY, Langefeld CD, Freedman BI, Bowden DW, Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Boström KB, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney ASF, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PRV, Jørgensen T, Kao WHL, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JRB, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CNA, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI, Soranzo N, Wheeler E, Glazer NL, Bouatia-Naji N, Mägi R, Randall J, Johnson T, Elliott P, Rybin D, Henneman P, Dehghan A, Hottenga JJ, Song K, Goel A, Egan JM, Lajunen T, Doney A, Kanoni S, Cavalcanti-Proença C, Kumari M, Timpson NJ, Zabena C, Ingelsson E, An P, O'Connell J, Luan J, Elliott A, McCarroll SA, Roccasecca RM, Pattou F, Sethupathy P, Ariyurek Y, Barter P, Beilby JP, Ben-Shlomo Y, Bergmann S, Bochud M, Bonnefond A, Borch-Johnsen K, Böttcher Y, Brunner E, Bumpstead SJ, Chen YDI, Chines P, Clarke R, Coin LJM, Cooper MN, Crisponi L, Day INM, de Geus EJC, Delplanque J, Fedson AC, Fischer-Rosinsky A, Forouhi NG, Frants R, Franzosi MG, Galan P, Goodarzi MO, Graessler J, Grundy S, Gwilliam R, Hallmans G, Hammond N, Han X, Hartikainen AL, Hayward C, Heath SC, Hercberg S, Hicks AA, Hillman DR, Hingorani AD, Hui J, Hung J, Jula A, Kaakinen M, Kaprio J, Kesaniemi YA, Kivimaki M, Knight B, Koskinen S, Kovacs P, Kyvik KO, Lathrop GM, Lawlor DA, Le Bacquer O, Lecoeur C, Li Y, Mahley R, Mangino M, Manning AK, Martínez-Larrad MT, McAteer JB, McPherson R, Meisinger C, Melzer D, Meyre D, Mitchell BD, Mukherjee S, Naitza S, Neville MJ, Oostra BA, Orrù M, Pakyz R, Paolisso G, Pattaro C, Pearson D, Peden JF, Pedersen NL, Perola M, Pfeiffer AFH, Pichler I, Polasek O, Posthuma D, Potter SC, Pouta A, Province MA, Psaty BM, Rayner NW, Rice K, Ripatti S, Rivadeneira F, Rolandsson O, Sandbaek A, Sandhu M, Sanna S, Sayer AA, Scheet P, Seedorf U, Sharp SJ, Shields B, Sijbrands EJG, Silveira A, Simpson L, Singleton A, Smith NL, Sovio U, Swift A, Syddall H, Syvänen AC, Tanaka T, Tönjes A, Uitterlinden AG, van Dijk KW, Varma D, Visvikis-Siest S, Vitart V, Vogelzangs N, Waeber G, Wagner PJ, Walley A, Ward KL, Watkins H, Wild SH, Willemsen G, Witteman JCM, Yarnell JWG, Zelenika D, Zethelius B, Zhai G, Zhao JH, Zillikens MC, Borecki IB, Loos RJF, Meneton P, Magnusson PKE, Nathan DM, Williams GH, Silander K, Salomaa V, Smith GD, Bornstein SR, Schwarz P, Spranger J, Karpe F, Shuldiner AR, Cooper C, Dedoussis GV, Serrano-Ríos M, Lind L, Palmer LJ, Franks PW, Ebrahim S, Marmot M, Kao WHL, Pramstaller PP, Wright AF, Stumvoll M, Hamsten A, Buchanan TA, Valle TT, Rotter JI, Siscovick DS, Penninx BWJH, Boomsma DI, Deloukas P, Spector TD, Ferrucci L, Cao A, Scuteri A, Schlessinger D, Uda M, Ruokonen A, Jarvelin MR, Waterworth DM, Vollenweider P, Peltonen L, Mooser V, Sladek R. A genome-wide association search for type 2 diabetes genes in African Americans. PLoS One 2012; 7:e29202. [PMID: 22238593 PMCID: PMC3251563 DOI: 10.1371/journal.pone.0029202] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/22/2011] [Indexed: 12/16/2022] Open
Abstract
African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.
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Affiliation(s)
- Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America.
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Soranzo N, Sanna S, Wheeler E, Gieger C, Radke D, Dupuis J, Bouatia-Naji N, Langenberg C, Prokopenko I, Stolerman E, Sandhu MS, Heeney MM, Devaney JM, Reilly MP, Ricketts SL, Stewart AFR, Voight BF, Willenborg C, Wright B, Altshuler D, Arking D, Balkau B, Barnes D, Boerwinkle E, Böhm B, Bonnefond A, Bonnycastle LL, Boomsma DI, Bornstein SR, Böttcher Y, Bumpstead S, Burnett-Miller MS, Campbell H, Cao A, Chambers J, Clark R, Collins FS, Coresh J, de Geus EJC, Dei M, Deloukas P, Döring A, Egan JM, Elosua R, Ferrucci L, Forouhi N, Fox CS, Franklin C, Franzosi MG, Gallina S, Goel A, Graessler J, Grallert H, Greinacher A, Hadley D, Hall A, Hamsten A, Hayward C, Heath S, Herder C, Homuth G, Hottenga JJ, Hunter-Merrill R, Illig T, Jackson AU, Jula A, Kleber M, Knouff CW, Kong A, Kooner J, Köttgen A, Kovacs P, Krohn K, Kühnel B, Kuusisto J, Laakso M, Lathrop M, Lecoeur C, Li M, Li M, Loos RJF, Luan J, Lyssenko V, Mägi R, Magnusson PKE, Mälarstig A, Mangino M, Martínez-Larrad MT, März W, McArdle WL, McPherson R, Meisinger C, Meitinger T, Melander O, Mohlke KL, Mooser VE, Morken MA, Narisu N, Nathan DM, Nauck M, O'Donnell C, Oexle K, Olla N, Pankow JS, Payne F, Peden JF, Pedersen NL, Peltonen L, Perola M, Polasek O, Porcu E, Rader DJ, Rathmann W, Ripatti S, Rocheleau G, Roden M, Rudan I, Salomaa V, Saxena R, Schlessinger D, Schunkert H, Schwarz P, Seedorf U, Selvin E, Serrano-Ríos M, Shrader P, Silveira A, Siscovick D, Song K, Spector TD, Stefansson K, Steinthorsdottir V, Strachan DP, Strawbridge R, Stumvoll M, Surakka I, Swift AJ, Tanaka T, Teumer A, Thorleifsson G, Thorsteinsdottir U, Tönjes A, Usala G, Vitart V, Völzke H, Wallaschofski H, Waterworth DM, Watkins H, Wichmann HE, Wild SH, Willemsen G, Williams GH, Wilson JF, Winkelmann J, Wright AF, Zabena C, Zhao JH, Epstein SE, Erdmann J, Hakonarson HH, Kathiresan S, Khaw KT, Roberts R, Samani NJ, Fleming MD, Sladek R, Abecasis G, Boehnke M, Froguel P, Groop L, McCarthy MI, Kao WHL, Florez JC, Uda M, Wareham NJ, Barroso I, Meigs JB. Common variants at 10 genomic loci influence hemoglobin A₁(C) levels via glycemic and nonglycemic pathways. Diabetes 2010; 59:3229-39. [PMID: 20858683 PMCID: PMC2992787 DOI: 10.2337/db10-0502] [Citation(s) in RCA: 311] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Glycated hemoglobin (HbA₁(c)), used to monitor and diagnose diabetes, is influenced by average glycemia over a 2- to 3-month period. Genetic factors affecting expression, turnover, and abnormal glycation of hemoglobin could also be associated with increased levels of HbA₁(c). We aimed to identify such genetic factors and investigate the extent to which they influence diabetes classification based on HbA₁(c) levels. RESEARCH DESIGN AND METHODS We studied associations with HbA₁(c) in up to 46,368 nondiabetic adults of European descent from 23 genome-wide association studies (GWAS) and 8 cohorts with de novo genotyped single nucleotide polymorphisms (SNPs). We combined studies using inverse-variance meta-analysis and tested mediation by glycemia using conditional analyses. We estimated the global effect of HbA₁(c) loci using a multilocus risk score, and used net reclassification to estimate genetic effects on diabetes screening. RESULTS Ten loci reached genome-wide significant association with HbA(1c), including six new loci near FN3K (lead SNP/P value, rs1046896/P = 1.6 × 10⁻²⁶), HFE (rs1800562/P = 2.6 × 10⁻²⁰), TMPRSS6 (rs855791/P = 2.7 × 10⁻¹⁴), ANK1 (rs4737009/P = 6.1 × 10⁻¹²), SPTA1 (rs2779116/P = 2.8 × 10⁻⁹) and ATP11A/TUBGCP3 (rs7998202/P = 5.2 × 10⁻⁹), and four known HbA₁(c) loci: HK1 (rs16926246/P = 3.1 × 10⁻⁵⁴), MTNR1B (rs1387153/P = 4.0 × 10⁻¹¹), GCK (rs1799884/P = 1.5 × 10⁻²⁰) and G6PC2/ABCB11 (rs552976/P = 8.2 × 10⁻¹⁸). We show that associations with HbA₁(c) are partly a function of hyperglycemia associated with 3 of the 10 loci (GCK, G6PC2 and MTNR1B). The seven nonglycemic loci accounted for a 0.19 (% HbA₁(c)) difference between the extreme 10% tails of the risk score, and would reclassify ∼2% of a general white population screened for diabetes with HbA₁(c). CONCLUSIONS GWAS identified 10 genetic loci reproducibly associated with HbA₁(c). Six are novel and seven map to loci where rarer variants cause hereditary anemias and iron storage disorders. Common variants at these loci likely influence HbA₁(c) levels via erythrocyte biology, and confer a small but detectable reclassification of diabetes diagnosis by HbA₁(c).
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Affiliation(s)
- Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, U.K
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Bonnefond A, Durand E, Sand O, De Graeve F, Gallina S, Busiah K, Lobbens S, Simon A, Bellanné-Chantelot C, Létourneau L, Scharfmann R, Delplanque J, Sladek R, Polak M, Vaxillaire M, Froguel P. Molecular diagnosis of neonatal diabetes mellitus using next-generation sequencing of the whole exome. PLoS One 2010; 5:e13630. [PMID: 21049026 PMCID: PMC2964316 DOI: 10.1371/journal.pone.0013630] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 09/30/2010] [Indexed: 11/18/2022] Open
Abstract
Background Accurate molecular diagnosis of monogenic non-autoimmune neonatal diabetes mellitus (NDM) is critical for patient care, as patients carrying a mutation in KCNJ11 or ABCC8 can be treated by oral sulfonylurea drugs instead of insulin therapy. This diagnosis is currently based on Sanger sequencing of at least 42 PCR fragments from the KCNJ11, ABCC8, and INS genes. Here, we assessed the feasibility of using the next-generation whole exome sequencing (WES) for the NDM molecular diagnosis. Methodology/Principal Findings We carried out WES for a patient presenting with permanent NDM, for whom mutations in KCNJ11, ABCC8 and INS and abnormalities in chromosome 6q24 had been previously excluded. A solution hybridization selection was performed to generate WES in 76 bp paired-end reads, by using two channels of the sequencing instrument. WES quality was assessed using a high-resolution oligonucleotide whole-genome genotyping array. From our WES with high-quality reads, we identified a novel non-synonymous mutation in ABCC8 (c.1455G>C/p.Q485H), despite a previous negative sequencing of this gene. This mutation, confirmed by Sanger sequencing, was not present in 348 controls and in the patient's mother, father and young brother, all of whom are normoglycemic. Conclusions/Significance WES identified a novel de novo ABCC8 mutation in a NDM patient. Compared to the current Sanger protocol, WES is a comprehensive, cost-efficient and rapid method to identify mutations in NDM patients. We suggest WES as a near future tool of choice for further molecular diagnosis of NDM cases, negative for chr6q24, KCNJ11 and INS abnormalities.
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Affiliation(s)
| | | | - Olivier Sand
- CNRS-UMR-8199, Univ Lille Nord de France, UDSL, Lille, France
| | | | - Sophie Gallina
- CNRS-UMR-8199, Univ Lille Nord de France, UDSL, Lille, France
| | - Kanetee Busiah
- Inserm-U845, Department of Pediatric Endocrinology, Necker Enfants Malades Hospital, Université Paris Descartes, Paris, France
| | | | - Albane Simon
- Inserm-U845, Department of Pediatric Endocrinology, Necker Enfants Malades Hospital, Université Paris Descartes, Paris, France
| | | | - Louis Létourneau
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, and Genome Quebec Innovation Centre, Montreal, Canada
| | - Raphael Scharfmann
- Inserm-U845, Department of Pediatric Endocrinology, Necker Enfants Malades Hospital, Université Paris Descartes, Paris, France
| | | | - Robert Sladek
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, and Genome Quebec Innovation Centre, Montreal, Canada
| | - Michel Polak
- Inserm-U845, Department of Pediatric Endocrinology, Necker Enfants Malades Hospital, Université Paris Descartes, Paris, France
| | | | - Philippe Froguel
- CNRS-UMR-8199, Univ Lille Nord de France, UDSL, Lille, France
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, Hammersmith Hospital, London, United Kingdom
- * E-mail:
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Primeau V, Coderre L, Karelis AD, Brochu M, Lavoie ME, Messier V, Sladek R, Rabasa-Lhoret R. Characterizing the profile of obese patients who are metabolically healthy. Int J Obes (Lond) 2010; 35:971-81. [PMID: 20975726 DOI: 10.1038/ijo.2010.216] [Citation(s) in RCA: 452] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The presence of obesity-related metabolic disturbances varies widely among obese individuals. Accordingly, a unique subset of obese individuals has been described in the medical literature, which seems to be protected or more resistant to the development of metabolic abnormalities associated with obesity. These individuals, now known as 'metabolically healthy but obese' (MHO), despite having excessive body fatness, display a favorable metabolic profile characterized by high levels of insulin sensitivity, no hypertension as well as a favorable lipid, inflammation, hormonal, liver enzyme and immune profile. However, recent studies have indicated that this healthier metabolic profile may not translate into a lower risk for mortality. Mechanisms that could explain the favorable metabolic profile of MHO individuals are poorly understood. However, preliminary evidence suggests that differences in visceral fat accumulation, birth weight, adipose cell size and gene expression-encoding markers of adipose cell differentiation may favor the development of the MHO phenotype. Despite the uncertainty regarding the exact degree of protection related to the MHO status, identification of underlying factors and mechanisms associated with this phenotype will eventually be invaluable in helping us understand factors that predispose, delay or protect obese individuals from metabolic disturbances. Collectively, a greater understanding of the MHO individual has important implications for therapeutic decision making, the characterization of subjects in research protocols and medical education.
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Affiliation(s)
- V Primeau
- Research Center of the Centre Hospitalier de l'Université de Montréal, Montreal, Canada
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Hollmann A, Aloyz R, Baker K, Dirnhofer S, Owens T, Sladek R, Tzankov A. Vav-1 expression correlates with NFκB activation and CD40-mediated cell death in diffuse large B-cell lymphoma cell lines. Hematol Oncol 2010; 28:142-50. [PMID: 20155735 DOI: 10.1002/hon.935] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is an aggressive malignancy with a variable response to therapy. We have previously shown that DLBCL cell lines differ in their susceptibility to CD40-mediated cell death, and that resistance to CD40-targeted antibodies correlated with increased expression of markers of immature B-cell and absence of Vav-1 mRNA. We used gene expression profiling to investigate the mechanism of CD40 resistance in these cell lines, and found that resistance correlated with lack of Vav-1 and inability to activate NFκB upon CD40 ligation. Analysis of tissue microarrays of 213 DLBCL cases revealed that Vav-1 expression correlated with a higher proliferative index and the presence of the post-germinal centre marker Irf-4. Our results suggest that Vav-1 expression may be associated with activated B-cell DLBCL origin and higher proliferative activity, and indicate Vav-1 as a potential marker to identify tumours likely to respond to CD40-targeted therapies.
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Affiliation(s)
- Annette Hollmann
- Montreal Center for Experimental Therapeutics in Cancer, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montréal, Quebec, Canada.
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42
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El-Assaad W, Joly E, Barbeau A, Sladek R, Buteau J, Maestre I, Pepin E, Zhao S, Iglesias J, Roche E, Prentki M. Glucolipotoxicity alters lipid partitioning and causes mitochondrial dysfunction, cholesterol, and ceramide deposition and reactive oxygen species production in INS832/13 ss-cells. Endocrinology 2010; 151:3061-73. [PMID: 20444946 DOI: 10.1210/en.2009-1238] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Elevated glucose and saturated fatty acids synergize in inducing apoptosis in INS832/13 cells and in human islet cells. In order to gain insight into the molecular mechanism(s) of glucolipotoxicity (Gltox), gene profiling and metabolic analyses were performed in INS832/13 cells cultured at 5 or 20 mm glucose in the absence or presence of palmitate. Expression changes were observed for transcripts involved in mitochondrial, lipid, and glucose metabolism. At 24 h after Gltox, increased expression of lipid partitioning genes suggested a promotion of fatty acid esterification and reduced lipid oxidation/detoxification, whereas changes in the expression of energy metabolism genes suggested mitochondrial dysfunction. These changes were associated with decreased glucose-induced insulin secretion, total insulin content, ATP levels, AMP-kinase activity, mitochondrial membrane potential and fat oxidation, unchanged de novo fatty acid synthesis, and increased reactive oxygen species, cholesterol, ceramide, and triglyceride levels. However, the synergy between elevated glucose and palmitate to cause ss-cell toxicity in term of apoptosis and reduced glucose-induced insulin secretion only correlated with triglyceride and ceramide depositions. Overexpression of endoplasmic reticulum glycerol-3-phosphate acyl transferase to enhance lipid esterification amplified Gltox at intermediate glucose (11 mm), whereas reducing acetyl-coenzyme A carboxylase 1 expression by small interfering RNA to shift lipid partitioning to fat oxidation reduced Gltox. The results suggest that Gltox entails alterations in lipid partitioning, sterol and ceramide accumulation, mitochondrial dysfunction, and reactive oxygen species production, all contributing to altering ss-cell function. The data also suggest that the early promotion of lipid esterification processes is instrumental in the Gltox process.
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Affiliation(s)
- Wissal El-Assaad
- Molecular Nutrition Unit and the Montreal Diabetes Research Center, the Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada H1W 4A4
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Dupuis J, Langenberg C, Prokopenko I, Saxena R, Soranzo N, Jackson AU, Wheeler E, Glazer NL, Bouatia-Naji N, Gloyn AL, Lindgren CM, Mägi R, Morris AP, Randall J, Johnson T, Elliott P, Rybin D, Thorleifsson G, Steinthorsdottir V, Henneman P, Grallert H, Dehghan A, Hottenga JJ, Franklin CS, Navarro P, Song K, Goel A, Perry JRB, Egan JM, Lajunen T, Grarup N, Sparsø T, Doney A, Voight BF, Stringham HM, Li M, Kanoni S, Shrader P, Cavalcanti-Proença C, Kumari M, Qi L, Timpson NJ, Gieger C, Zabena C, Rocheleau G, Ingelsson E, An P, O'Connell J, Luan J, Elliott A, McCarroll SA, Payne F, Roccasecca RM, Pattou F, Sethupathy P, Ardlie K, Ariyurek Y, Balkau B, Barter P, Beilby JP, Ben-Shlomo Y, Benediktsson R, Bennett AJ, Bergmann S, Bochud M, Boerwinkle E, Bonnefond A, Bonnycastle LL, Borch-Johnsen K, Böttcher Y, Brunner E, Bumpstead SJ, Charpentier G, Chen YDI, Chines P, Clarke R, Coin LJM, Cooper MN, Cornelis M, Crawford G, Crisponi L, Day INM, de Geus EJC, Delplanque J, Dina C, Erdos MR, Fedson AC, Fischer-Rosinsky A, Forouhi NG, Fox CS, Frants R, Franzosi MG, Galan P, Goodarzi MO, Graessler J, Groves CJ, Grundy S, Gwilliam R, Gyllensten U, Hadjadj S, Hallmans G, Hammond N, Han X, Hartikainen AL, Hassanali N, Hayward C, Heath SC, Hercberg S, Herder C, Hicks AA, Hillman DR, Hingorani AD, Hofman A, Hui J, Hung J, Isomaa B, Johnson PRV, Jørgensen T, Jula A, Kaakinen M, Kaprio J, Kesaniemi YA, Kivimaki M, Knight B, Koskinen S, Kovacs P, Kyvik KO, Lathrop GM, Lawlor DA, Le Bacquer O, Lecoeur C, Li Y, Lyssenko V, Mahley R, Mangino M, Manning AK, Martínez-Larrad MT, McAteer JB, McCulloch LJ, McPherson R, Meisinger C, Melzer D, Meyre D, Mitchell BD, Morken MA, Mukherjee S, Naitza S, Narisu N, Neville MJ, Oostra BA, Orrù M, Pakyz R, Palmer CNA, Paolisso G, Pattaro C, Pearson D, Peden JF, Pedersen NL, Perola M, Pfeiffer AFH, Pichler I, Polasek O, Posthuma D, Potter SC, Pouta A, Province MA, Psaty BM, Rathmann W, Rayner NW, Rice K, Ripatti S, Rivadeneira F, Roden M, Rolandsson O, Sandbaek A, Sandhu M, Sanna S, Sayer AA, Scheet P, Scott LJ, Seedorf U, Sharp SJ, Shields B, SigurÐsson G, Sijbrands EJG, Silveira A, Simpson L, Singleton A, Smith NL, Sovio U, Swift A, Syddall H, Syvänen AC, Tanaka T, Thorand B, Tichet J, Tönjes A, Tuomi T, Uitterlinden AG, van Dijk KW, van Hoek M, Varma D, Visvikis-Siest S, Vitart V, Vogelzangs N, Waeber G, Wagner PJ, Walley A, Walters GB, Ward KL, Watkins H, Weedon MN, Wild SH, Willemsen G, Witteman JCM, Yarnell JWG, Zeggini E, Zelenika D, Zethelius B, Zhai G, Zhao JH, Zillikens MC, Consortium DIAGRAM, Consortium GIANT, Consortium GBP, Borecki IB, Loos RJF, Meneton P, Magnusson PKE, Nathan DM, Williams GH, Hattersley AT, Silander K, Salomaa V, Smith GD, Bornstein SR, Schwarz P, Spranger J, Karpe F, Shuldiner AR, Cooper C, Dedoussis GV, Serrano-Ríos M, Morris AD, Lind L, Palmer LJ, Hu FB, Franks PW, Ebrahim S, Marmot M, Kao WHL, Pankow JS, Sampson MJ, Kuusisto J, Laakso M, Hansen T, Pedersen O, Pramstaller PP, Wichmann HE, Illig T, Rudan I, Wright AF, Stumvoll M, Campbell H, Wilson JF, Hamsten A, Bergman RN, Buchanan TA, Collins FS, Mohlke KL, Tuomilehto J, Valle TT, Altshuler D, Rotter JI, Siscovick DS, Penninx BWJH, Boomsma DI, Deloukas P, Spector TD, Frayling TM, Ferrucci L, Kong A, Thorsteinsdottir U, Stefansson K, van Duijn CM, Aulchenko YS, Cao A, Scuteri A, Schlessinger D, Uda M, Ruokonen A, Jarvelin MR, Waterworth DM, Vollenweider P, Peltonen L, Mooser V, Abecasis GR, Wareham NJ, Sladek R, Froguel P, Watanabe RM, Meigs JB, Groop L, Boehnke M, McCarthy MI, Florez JC, Barroso I. Erratum: New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat Genet 2010. [DOI: 10.1038/ng0510-464a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Walters RG, Jacquemont S, Valsesia A, de Smith AJ, Martinet D, Andersson J, Falchi M, Chen F, Andrieux J, Lobbens S, Delobel B, Stutzmann F, El-Sayed Moustafa JS, Chèvre JC, Lecoeur C, Vatin V, Bouquillon S, Buxton JL, Boute O, Holder-Espinasse M, Cuisset JM, Lemaitre MP, Ambresin AE, Brioschi A, Gaillard M, Giusti V, Fellmann F, Ferrarini A, Hadjikhani N, Campion D, Guilmatre A, Goldenberg A, Calmels N, Mandel JL, Le Caignec C, David A, Isidor B, Cordier MP, Dupuis-Girod S, Labalme A, Sanlaville D, Béri-Dexheimer M, Jonveaux P, Leheup B, Ounap K, Bochukova EG, Henning E, Keogh J, Ellis RJ, Macdermot KD, van Haelst MM, Vincent-Delorme C, Plessis G, Touraine R, Philippe A, Malan V, Mathieu-Dramard M, Chiesa J, Blaumeiser B, Kooy RF, Caiazzo R, Pigeyre M, Balkau B, Sladek R, Bergmann S, Mooser V, Waterworth D, Reymond A, Vollenweider P, Waeber G, Kurg A, Palta P, Esko T, Metspalu A, Nelis M, Elliott P, Hartikainen AL, McCarthy MI, Peltonen L, Carlsson L, Jacobson P, Sjöström L, Huang N, Hurles ME, O'Rahilly S, Farooqi IS, Männik K, Jarvelin MR, Pattou F, Meyre D, Walley AJ, Coin LJM, Blakemore AIF, Froguel P, Beckmann JS. A new highly penetrant form of obesity due to deletions on chromosome 16p11.2. Nature 2010; 463:671-5. [PMID: 20130649 PMCID: PMC2880448 DOI: 10.1038/nature08727] [Citation(s) in RCA: 345] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 12/01/2009] [Indexed: 01/04/2023]
Affiliation(s)
- R G Walters
- Section of Genomic Medicine, Imperial College London, London W12 0NN, UK
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Dupuis J, Langenberg C, Prokopenko I, Saxena R, Soranzo N, Jackson AU, Wheeler E, Glazer NL, Bouatia-Naji N, Gloyn AL, Lindgren CM, Mägi R, Morris AP, Randall J, Johnson T, Elliott P, Rybin D, Thorleifsson G, Steinthorsdottir V, Henneman P, Grallert H, Dehghan A, Hottenga JJ, Franklin CS, Navarro P, Song K, Goel A, Perry JRB, Egan JM, Lajunen T, Grarup N, Sparsø T, Doney A, Voight BF, Stringham HM, Li M, Kanoni S, Shrader P, Cavalcanti-Proença C, Kumari M, Qi L, Timpson NJ, Gieger C, Zabena C, Rocheleau G, Ingelsson E, An P, O’Connell J, Luan J, Elliott A, McCarroll SA, Payne F, Roccasecca RM, Pattou F, Sethupathy P, Ardlie K, Ariyurek Y, Balkau B, Barter P, Beilby JP, Ben-Shlomo Y, Benediktsson R, Bennett AJ, Bergmann S, Bochud M, Boerwinkle E, Bonnefond A, Bonnycastle LL, Borch-Johnsen K, Böttcher Y, Brunner E, Bumpstead SJ, Charpentier G, Chen YDI, Chines P, Clarke R, Coin LJM, Cooper MN, Cornelis M, Crawford G, Crisponi L, Day INM, de Geus E, Delplanque J, Dina C, Erdos MR, Fedson AC, Fischer-Rosinsky A, Forouhi NG, Fox CS, Frants R, Franzosi MG, Galan P, Goodarzi MO, Graessler J, Groves CJ, Grundy S, Gwilliam R, Gyllensten U, Hadjadj S, Hallmans G, Hammond N, Han X, Hartikainen AL, Hassanali N, Hayward C, Heath SC, Hercberg S, Herder C, Hicks AA, Hillman DR, Hingorani AD, Hofman A, Hui J, Hung J, Isomaa B, Johnson PRV, Jørgensen T, Jula A, Kaakinen M, Kaprio J, Kesaniemi YA, Kivimaki M, Knight B, Koskinen S, Kovacs P, Kyvik KO, Lathrop GM, Lawlor DA, Le Bacquer O, Lecoeur C, Li Y, Lyssenko V, Mahley R, Mangino M, Manning AK, Martínez-Larrad MT, McAteer JB, McCulloch LJ, McPherson R, Meisinger C, Melzer D, Meyre D, Mitchell BD, Morken MA, Mukherjee S, Naitza S, Narisu N, Neville MJ, Oostra BA, Orrù M, Pakyz R, Palmer CNA, Paolisso G, Pattaro C, Pearson D, Peden JF, Pedersen NL, Perola M, Pfeiffer AFH, Pichler I, Polasek O, Posthuma D, Potter SC, Pouta A, Province MA, Psaty BM, Rathmann W, Rayner NW, Rice K, Ripatti S, Rivadeneira F, Roden M, Rolandsson O, Sandbaek A, Sandhu M, Sanna S, Sayer AA, Scheet P, Scott LJ, Seedorf U, Sharp SJ, Shields B, Sigurðsson G, Sijbrands EJG, Silveira A, Simpson L, Singleton A, Smith NL, Sovio U, Swift A, Syddall H, Syvänen AC, Tanaka T, Thorand B, Tichet J, Tönjes A, Tuomi T, Uitterlinden AG, van Dijk KW, van Hoek M, Varma D, Visvikis-Siest S, Vitart V, Vogelzangs N, Waeber G, Wagner PJ, Walley A, Walters GB, Ward KL, Watkins H, Weedon MN, Wild SH, Willemsen G, Witteman JCM, Yarnell JWG, Zeggini E, Zelenika D, Zethelius B, Zhai G, Zhao JH, Zillikens MC, Borecki IB, Loos RJF, Meneton P, Magnusson PKE, Nathan DM, Williams GH, Hattersley AT, Silander K, Salomaa V, Smith GD, Bornstein SR, Schwarz P, Spranger J, Karpe F, Shuldiner AR, Cooper C, Dedoussis GV, Serrano-Ríos M, Morris AD, Lind L, Palmer LJ, Hu FB, Franks PW, Ebrahim S, Marmot M, Kao WHL, Pankow JS, Sampson MJ, Kuusisto J, Laakso M, Hansen T, Pedersen O, Pramstaller PP, Wichmann HE, Illig T, Rudan I, Wright AF, Stumvoll M, Campbell H, Wilson JF, Hamsten A, Bergman RN, Buchanan TA, Collins FS, Mohlke KL, Tuomilehto J, Valle TT, Altshuler D, Rotter JI, Siscovick DS, Penninx BWJH, Boomsma D, Deloukas P, Spector TD, Frayling TM, Ferrucci L, Kong A, Thorsteinsdottir U, Stefansson K, van Duijn CM, Aulchenko YS, Cao A, Scuteri A, Schlessinger D, Uda M, Ruokonen A, Jarvelin MR, Waterworth DM, Vollenweider P, Peltonen L, Mooser V, Abecasis GR, Wareham NJ, Sladek R, Froguel P, Watanabe RM, Meigs JB, Groop L, Boehnke M, McCarthy MI, Florez JC, Barroso I. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat Genet 2010; 42:105-16. [PMID: 20081858 PMCID: PMC3018764 DOI: 10.1038/ng.520] [Citation(s) in RCA: 1655] [Impact Index Per Article: 118.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 10/14/2009] [Indexed: 02/08/2023]
Abstract
Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes.
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Affiliation(s)
- Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02118, USA
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts 01702, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Inga Prokopenko
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Twin Research & Genetic Epidemiology Department, King’s College London, St Thomas' Hospital Campus, Lambeth Palace Rd, London SE1 7EH, UK
| | - Anne U Jackson
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, USA
| | - Eleanor Wheeler
- Metabolic Disease Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Nicole L Glazer
- Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Nabila Bouatia-Naji
- CNRS-UMR8090, Pasteur Institute, Lille 2-Droit et Santé University, F-59000 Lille, France
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
| | - Cecilia M Lindgren
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Reedik Mägi
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Joshua Randall
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Toby Johnson
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland
- University Institute of Social and Preventative Medicine, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, 1005 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Switzerland
| | - Paul Elliott
- Department of Epidemiology and Public Health, Imperial College of London, Faculty of Medicine, Norfolk Place, London W2 1PG, UK
| | - Denis Rybin
- Boston University Data Coordinating Center, Boston, Massachusetts 02118, USA
| | | | | | - Peter Henneman
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Harald Grallert
- Institute of Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC Rotterdam, 3000 CA, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, VU, Van der Boechorststraat 1, 1081 BT Amsterdam, The Netherlands
| | | | - Pau Navarro
- MRC Human Genetics Unit, IGMM, Edinburgh EH4 2XU, UK
| | - Kijoung Song
- Division of Genetics, R&D, Glaxo SmithKline, King of Prussia, Pennsylvania 19406, USA
| | - Anuj Goel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - John R B Perry
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter EX1 2LU, UK
| | - Josephine M Egan
- Laboratory of Clinical Investigation, National Institute of Aging, Baltimore, Maryland 21250, USA
| | - Taina Lajunen
- Unit for Child and Adolescent Health and Welfare, National Institute for Health and Welfare, Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
| | - Niels Grarup
- Hagedorn Research Institute, 2820 Gentofte, Denmark
| | | | - Alex Doney
- Department of Medicine & Therapeutics, Level 7, Ninewells Hospital & Medical School, Dundee DD1 9SY, UK
| | - Benjamin F Voight
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Heather M Stringham
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, USA
| | - Man Li
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Stavroula Kanoni
- Department of Nutrition - Dietetics, Harokopio University, 17671 Athens, Greece
| | - Peter Shrader
- General Medicine Division, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Meena Kumari
- Department of Epidemiology and Public Health, University College London, UK
| | - Lu Qi
- Depts. of Nutrition and Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Nicholas J Timpson
- MRC Centre for Causal Analyses in Translational Epidemiology, University of Bristol, Bristol BS8 2PR, UK
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Carina Zabena
- Fundación para la Investigación Biomédica del Hospital Clínico San Carlos, Madrid, Spain
| | - Ghislain Rocheleau
- Departments of Medicine and Human Genetics, McGill University, Montreal, Canada
- Genome Quebec Innovation Centre, Montreal H3A 1A4, Canada
| | - Erik Ingelsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Ping An
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey O’Connell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Amanda Elliott
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Felicity Payne
- Metabolic Disease Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Rosa Maria Roccasecca
- Metabolic Disease Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - François Pattou
- INSERM U859, Universite de Lille-Nord de France, F-59000 Lille, France
| | - Praveen Sethupathy
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Kristin Ardlie
- The Broad Institute, Cambridge, Massachusetts 02141, USA
| | - Yavuz Ariyurek
- Leiden Genome Technology Center, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Beverley Balkau
- INSERM U780-IFR69, Paris Sud University, F-94807 Villejuif, France
| | - Philip Barter
- The Heart Research Institute, Sydney, New South Wales, Australia
| | - John P Beilby
- PathWest Laboratory of Western Australia, Department of Molecular Genetics, J Block, QEII Medical Centre, NEDLANDS WA 6009, Australia
- School of Surgery and Pathology, University of Western Australia, Nedlands WA 6009, Australia
| | - Yoav Ben-Shlomo
- Department of Social Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Rafn Benediktsson
- Landspitali University Hospital, 101 Reykjavik, Iceland
- Icelandic Heart Association, 201 Kopavogur, Iceland
| | - Amanda J Bennett
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
| | - Sven Bergmann
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland
- University Institute of Social and Preventative Medicine, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, 1005 Lausanne, Switzerland
| | - Murielle Bochud
- University Institute of Social and Preventative Medicine, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne, 1005 Lausanne, Switzerland
| | - Eric Boerwinkle
- The Human Genetics Center and Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Amélie Bonnefond
- CNRS-UMR8090, Pasteur Institute, Lille 2-Droit et Santé University, F-59000 Lille, France
| | - Lori L Bonnycastle
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Knut Borch-Johnsen
- Steno Diabetes Center, DK-2820 Gentofte, Copenhagen, Denmark
- Faculty of Health Science, University of Aarhus, Aarhus DK-8000, Denmark
| | - Yvonne Böttcher
- Department of Medicine, University of Leipzig, Liebigstr. 18, 04103 Leipzig, Germany
| | - Eric Brunner
- Department of Epidemiology and Public Health, University College London, UK
| | | | | | - Yii-Der Ida Chen
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Peter Chines
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Robert Clarke
- Clinical Trial Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Lachlan J M Coin
- Department of Epidemiology and Public Health, Imperial College of London, Faculty of Medicine, Norfolk Place, London W2 1PG, UK
| | - Matthew N Cooper
- Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Perth, Australia
| | - Marilyn Cornelis
- Depts. of Nutrition and Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Gabe Crawford
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Laura Crisponi
- Istituto di Neurogenetica e Neurofarmacologia (INN), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari 09042, Italy
| | - Ian N M Day
- MRC Centre for Causal Analyses in Translational Epidemiology, University of Bristol, Bristol BS8 2PR, UK
| | - Eco de Geus
- Department of Biological Psychology, VU, Van der Boechorststraat 1, 1081 BT Amsterdam, The Netherlands
| | - Jerome Delplanque
- CNRS-UMR8090, Pasteur Institute, Lille 2-Droit et Santé University, F-59000 Lille, France
| | - Christian Dina
- CNRS-UMR8090, Pasteur Institute, Lille 2-Droit et Santé University, F-59000 Lille, France
| | - Michael R Erdos
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Annette C Fedson
- Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Perth, Australia
- Western Australian Sleep Disorders Research Institute, Queen Elizabeth Medical Centre II, Perth, Australia
| | - Antje Fischer-Rosinsky
- Department of Endocrinology, Diabetes and Nutrition, Charite-Universitaetsmedizin Berlin, Berlin, Germany
- Department of Clinical Nutrition, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Nita G Forouhi
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Caroline S Fox
- National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts 01702, USA
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rune Frants
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Maria Grazia Franzosi
- Department of Cardiovascular Research, Istituto di Ricerche Farmacologiche 'Mario Negri', Milan, Italy
| | - Pilar Galan
- U557 Institut National de la Santé et de la Recherche Médicale, U1125 Institut National de la Recherche Agronomique, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny Cedex, France
| | - Mark O Goodarzi
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jürgen Graessler
- Department of Medicine III, Division Prevention and Care of Diabetes, University of Dresden, 01307 Dresden
| | - Christopher J Groves
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
| | - Scott Grundy
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Rhian Gwilliam
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Ulf Gyllensten
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, S-751 85 Uppsala, Sweden
| | - Samy Hadjadj
- CHU de Poitiers, Endocrinologie Diabetologie, CIC INSERM 0802, INSERM U927, Université de Poitiers, UFR, Médecine Pharmacie, Poitiers, France
| | - Göran Hallmans
- Department of Public Health & Clinical Medicine, Section for Nutritional Research, Umeå University, Umeå, Sweden
| | - Naomi Hammond
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Xijing Han
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, USA
| | - Anna-Liisa Hartikainen
- Department of Clinical Sciences, Obstetrics and Gynecology, University of Oulu, Box 5000, Fin-90014 University of Oulu, Finland
| | - Neelam Hassanali
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
| | | | - Simon C Heath
- Centre National de Génotypage/IG/CEA, 2 rue Gaston Crémieux CP 5721, 91057 Evry Cedex, France
| | - Serge Hercberg
- U872 Institut National de la Santé et de la Recherche Médicale, Faculté de Médecine Paris Descartes, 15 rue de l’Ecole de Médecine, 75270 Paris Cedex, France
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Andrew A Hicks
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Viale Druso 1, 39100 Bolzano, Italy, Affiliated Institute of the University Lübeck, Germany
| | - David R Hillman
- Western Australian Sleep Disorders Research Institute, Queen Elizabeth Medical Centre II, Perth, Australia
- Department of Pulmonary Physiology, Sir Charles Gairdner Hospital, Perth, Australia
| | - Aroon D Hingorani
- Department of Epidemiology and Public Health, University College London, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC Rotterdam, 3000 CA, The Netherlands
| | - Jennie Hui
- PathWest Laboratory of Western Australia, Department of Molecular Genetics, J Block, QEII Medical Centre, NEDLANDS WA 6009, Australia
- Busselton Population Medical Research Foundation, Sir Charles Gairdner Hospital, Perth, Australia
| | - Joe Hung
- Heart Institute of Western Australia, Sir Charles Gairdner Hospital, Nedlands WA 6009, Australia
- School of Medicine and Pharmacology, University of Western Australia, Nedlands, WA 6009, Australia
| | - Bo Isomaa
- Folkhalsan Research Centre, Helsinki, Finland
- Malmska Municipal Health Care Center and Hospital, Jakobstad, Finland
| | - Paul R V Johnson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
- Nuffield Department of Surgery, University of Oxford, Oxford OX3 9DU, UK
| | - Torben Jørgensen
- Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark
- Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Antti Jula
- National Institute for Health and Welfare, Unit of Population Studies, Turku, Finland
| | - Marika Kaakinen
- Institute of Health Sciences and Biocenter Oulu, Box 5000, Fin-90014 University of Oulu, Finland
| | - Jaakko Kaprio
- Department of Public Health, Faculty of Medicine, P.O. Box 41 (Mannerheimintie 172), University of Helsinki, 00014 Helsinki, Finland
- National Institute for Health and Welfare, Unit for Child and Adolescent Mental Health, Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | | | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, UK
| | - Beatrice Knight
- Diabetes Genetics, Institute of Biomedical and Clinical Science, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter EX2 5DW, UK
| | - Seppo Koskinen
- National Institute for Health and Welfare, Unit of Living Conditions, Health and Wellbeing, Helsinki, Finland
| | - Peter Kovacs
- Interdisciplinary Centre for Clinical Research, University of Leipzig, Inselstr. 22, 04103 Leipzig, Germany
| | - Kirsten Ohm Kyvik
- The Danish Twin Registry, Epidemiology, Institute of Public Health, University of Southern Denmark, J.B. Winsløws Vej 9B, 5000 Odense, Denmark
| | - G Mark Lathrop
- Centre National de Génotypage/IG/CEA, 2 rue Gaston Crémieux CP 5721, 91057 Evry Cedex, France
| | - Debbie A Lawlor
- MRC Centre for Causal Analyses in Translational Epidemiology, University of Bristol, Bristol BS8 2PR, UK
| | - Olivier Le Bacquer
- CNRS-UMR8090, Pasteur Institute, Lille 2-Droit et Santé University, F-59000 Lille, France
| | - Cécile Lecoeur
- CNRS-UMR8090, Pasteur Institute, Lille 2-Droit et Santé University, F-59000 Lille, France
| | - Yun Li
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, USA
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Malmo, Malmo, Sweden
| | - Robert Mahley
- Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, California, USA
| | - Massimo Mangino
- Twin Research & Genetic Epidemiology Department, King’s College London, St Thomas' Hospital Campus, Lambeth Palace Rd, London SE1 7EH, UK
| | - Alisa K Manning
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts 02118, USA
| | | | - Jarred B McAteer
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Laura J McCulloch
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
| | - Ruth McPherson
- Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Christa Meisinger
- Institute of Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - David Melzer
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter EX1 2LU, UK
| | - David Meyre
- CNRS-UMR8090, Pasteur Institute, Lille 2-Droit et Santé University, F-59000 Lille, France
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Mario A Morken
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Sutapa Mukherjee
- Western Australian Sleep Disorders Research Institute, Queen Elizabeth Medical Centre II, Perth, Australia
- Department of Pulmonary Physiology, Sir Charles Gairdner Hospital, Perth, Australia
| | - Silvia Naitza
- Istituto di Neurogenetica e Neurofarmacologia (INN), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari 09042, Italy
| | - Narisu Narisu
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Matthew J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Ben A Oostra
- Department of Clinical Genetics, Erasmus MC Rotterdam, 3000 CA, The Netherlands
| | - Marco Orrù
- Istituto di Neurogenetica e Neurofarmacologia (INN), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari 09042, Italy
| | - Ruth Pakyz
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Colin N A Palmer
- Biomedical Research Institute, University of Dundee, Ninewells Hospital & Medical School, Dundee DD1 9SY, UK
| | - Giuseppe Paolisso
- Department of Geriatric Medicine and Metabolic Disease, Second University of Naples, Naples, Italy
| | - Cristian Pattaro
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Viale Druso 1, 39100 Bolzano, Italy, Affiliated Institute of the University Lübeck, Germany
| | - Daniel Pearson
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - John F Peden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Markus Perola
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Unit of Public Health Genomics, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Andreas F H Pfeiffer
- Department of Endocrinology, Diabetes and Nutrition, Charite-Universitaetsmedizin Berlin, Berlin, Germany
- Department of Clinical Nutrition, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Irene Pichler
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Viale Druso 1, 39100 Bolzano, Italy, Affiliated Institute of the University Lübeck, Germany
| | - Ozren Polasek
- Department of Medical Statistics, Epidemiology and Medical Informatics, Andrija Stampar School of Public Health, Medical School, University of Zagreb, Rockefellerova 4, 10000 Zagreb, Croatia
| | - Danielle Posthuma
- Department of Biological Psychology, VU, Van der Boechorststraat 1, 1081 BT Amsterdam, The Netherlands
- Department of Clinical Genetics, VUMC, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Simon C Potter
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Anneli Pouta
- Department of Obstetrics and Gynaecology, Oulu University Hospital, Oulu, Finland
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bruce M Psaty
- Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, Washington, USA
- Group Health Center for Health Studies, Seattle, Washington, USA
| | - Wolfgang Rathmann
- Institute of Biometrics and Epidemiology, German Diabetes Centre, Leibniz Centre at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nigel W Rayner
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Unit of Public Health Genomics, Helsinki, Finland
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus MC Rotterdam, 3000 CA, The Netherlands
- Department of Internal Medicine, Erasmus MC Rotterdam, 3000 CA, The Netherlands
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Department of Medicine/Metabolic Diseases, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Olov Rolandsson
- Department of Public Health & Clinical Medicine, Section for Family Medicine, Umeå University Hospital, Umeå, Sweden
| | - Annelli Sandbaek
- School of Public Health, Department of General Practice, University of Aarhus, Aarhus DK-8000, Denmark
| | - Manjinder Sandhu
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
- Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
| | - Serena Sanna
- Istituto di Neurogenetica e Neurofarmacologia (INN), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari 09042, Italy
| | - Avan Aihie Sayer
- MRC Epidemiology Resource Centre, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Paul Scheet
- Department of Epidemiology, University of Texas, M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Laura J Scott
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, USA
| | - Udo Seedorf
- Leibniz-Institut für Arterioskleroseforschung an der Universität Münster,Münster, Germany
| | - Stephen J Sharp
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Beverley Shields
- Diabetes Genetics, Institute of Biomedical and Clinical Science, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter EX2 5DW, UK
| | - Gunnar Sigurðsson
- Landspitali University Hospital, 101 Reykjavik, Iceland
- Icelandic Heart Association, 201 Kopavogur, Iceland
| | - Erik J G Sijbrands
- Department of Epidemiology, Erasmus MC Rotterdam, 3000 CA, The Netherlands
- Department of Internal Medicine, Erasmus MC Rotterdam, 3000 CA, The Netherlands
| | - Angela Silveira
- Atherosclerosis Research Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Laila Simpson
- Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Perth, Australia
- Western Australian Sleep Disorders Research Institute, Queen Elizabeth Medical Centre II, Perth, Australia
| | - Andrew Singleton
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland 20892, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, Washington 98195, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, Washington, USA
| | - Ulla Sovio
- Department of Epidemiology and Public Health, Imperial College of London, Faculty of Medicine, Norfolk Place, London W2 1PG, UK
| | - Amy Swift
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Holly Syddall
- MRC Epidemiology Resource Centre, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
| | | | - Toshiko Tanaka
- Medstar Research Institute, Baltimore, Maryland 21250, USA
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland 21250, USA
| | - Barbara Thorand
- Institute of Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Jean Tichet
- Institut interrégional pour la santé (IRSA), F-37521 La Riche, France
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Liebigstr. 18, 04103 Leipzig, Germany
- Coordination Centre for Clinical Trials, University of Leipzig, Härtelstr. 16-18, 04103 Leipzig, Germany
| | - Tiinamaija Tuomi
- Folkhalsan Research Centre, Helsinki, Finland
- Department of Medicine, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC Rotterdam, 3000 CA, The Netherlands
- Department of Internal Medicine, Erasmus MC Rotterdam, 3000 CA, The Netherlands
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
- Department of Internal Medicine, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Mandy van Hoek
- Department of Internal Medicine, Erasmus MC Rotterdam, 3000 CA, The Netherlands
| | - Dhiraj Varma
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Sophie Visvikis-Siest
- Research Unit, Cardiovascular Genetics, Nancy University Henri Poincaré, Nancy, France
| | | | - Nicole Vogelzangs
- EMGO Institute/Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands
| | - Gérard Waeber
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Peter J Wagner
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Unit of Public Health Genomics, Helsinki, Finland
| | - Andrew Walley
- Genomic Medicine, Imperial College London, Hammersmith Hospital, W12 0NN, London, UK
| | | | - Kim L Ward
- Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Perth, Australia
- Western Australian Sleep Disorders Research Institute, Queen Elizabeth Medical Centre II, Perth, Australia
| | - Hugh Watkins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Cardiovascular Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Michael N Weedon
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter EX1 2LU, UK
| | - Sarah H Wild
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Gonneke Willemsen
- Department of Biological Psychology, VU, Van der Boechorststraat 1, 1081 BT Amsterdam, The Netherlands
| | | | - John W G Yarnell
- Epidemiology & Public Health, Queen's University Belfast, Belfast BT12 6BJ, UK
| | - Eleftheria Zeggini
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Diana Zelenika
- Centre National de Génotypage/IG/CEA, 2 rue Gaston Crémieux CP 5721, 91057 Evry Cedex, France
| | - Björn Zethelius
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
- Medical Products Agency, Uppsala, Sweden
| | - Guangju Zhai
- Twin Research & Genetic Epidemiology Department, King’s College London, St Thomas' Hospital Campus, Lambeth Palace Rd, London SE1 7EH, UK
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus MC Rotterdam, 3000 CA, The Netherlands
| | | | | | | | - Ingrid B Borecki
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ruth J F Loos
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Pierre Meneton
- U872 Institut National de la Santé et de la Recherche Médicale, Faculté de Médecine Paris Descartes, 15 rue de l’Ecole de Médecine, 75270 Paris Cedex, France
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - David M Nathan
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Gordon H Williams
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Andrew T Hattersley
- Diabetes Genetics, Institute of Biomedical and Clinical Science, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter EX2 5DW, UK
| | - Kaisa Silander
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Unit of Public Health Genomics, Helsinki, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Unit of Chronic Disease Epidemiology and Prevention, Helsinki, Finland
| | - George Davey Smith
- MRC Centre for Causal Analyses in Translational Epidemiology, University of Bristol, Bristol BS8 2PR, UK
| | - Stefan R Bornstein
- Department of Medicine III, Division Prevention and Care of Diabetes, University of Dresden, 01307 Dresden
| | - Peter Schwarz
- Department of Medicine III, Division Prevention and Care of Diabetes, University of Dresden, 01307 Dresden
| | - Joachim Spranger
- Department of Endocrinology, Diabetes and Nutrition, Charite-Universitaetsmedizin Berlin, Berlin, Germany
- Department of Clinical Nutrition, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Alan R Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Cyrus Cooper
- MRC Epidemiology Resource Centre, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
| | - George V Dedoussis
- Department of Nutrition - Dietetics, Harokopio University, 17671 Athens, Greece
| | - Manuel Serrano-Ríos
- Fundación para la Investigación Biomédica del Hospital Clínico San Carlos, Madrid, Spain
| | - Andrew D Morris
- Biomedical Research Institute, University of Dundee, Ninewells Hospital & Medical School, Dundee DD1 9SY, UK
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Lyle J Palmer
- Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Perth, Australia
- Western Australian Sleep Disorders Research Institute, Queen Elizabeth Medical Centre II, Perth, Australia
- Busselton Population Medical Research Foundation, Sir Charles Gairdner Hospital, Perth, Australia
| | - Frank B. Hu
- Departments of Nutrition and Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Paul W Franks
- Genetic Epidemiology & Clinical Research Group, Department of Public Health & Clinical Medicine, Section for Medicine, Umeå University Hospital, Umeå, Sweden
| | - Shah Ebrahim
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Michael Marmot
- Department of Epidemiology and Public Health, University College London, UK
| | - W H Linda Kao
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21287, USA
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21287, USA
- The Welch Center for Prevention, Epidemiology, and Clinical Research, School of Medicine and Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55454, USA
| | - Michael J Sampson
- Department of Endocrinology and Diabetes, Norfolk and Norwich University Hospital NHS Trust, Norwich, NR1 7UY, UK
| | - Johanna Kuusisto
- Department of Medicine, University of Kuopio and Kuopio University Hospital, Kuopio 70210, Finland
| | - Markku Laakso
- Department of Medicine, University of Kuopio and Kuopio University Hospital, Kuopio 70210, Finland
| | - Torben Hansen
- Hagedorn Research Institute, 2820 Gentofte, Denmark
- Faculty of Health Science, University of Southern Denmark, Odense, Denmark
| | - Oluf Pedersen
- Hagedorn Research Institute, 2820 Gentofte, Denmark
- Faculty of Health Science, University of Aarhus, Aarhus DK-8000, Denmark
- Institute of Biomedical Science, Faculty of Health Science, University of Copenhagen, Denmark
| | - Peter Paul Pramstaller
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Viale Druso 1, 39100 Bolzano, Italy, Affiliated Institute of the University Lübeck, Germany
- Department of Neurology, General Central Hospital, 39100 Bolzano, Italy
- Department of Neurology, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - H Erich Wichmann
- Institute of Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Klinikum Grosshadern, Munich, Germany
| | - Thomas Illig
- Institute of Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
- School of Medicine, University of Split, Soltanska 2, 21000 Split, Croatia
- Gen-Info Ltd, Ruzmarinka 17, 10000 Zagreb, Croatia
| | - Alan F Wright
- MRC Human Genetics Unit, IGMM, Edinburgh EH4 2XU, UK
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Liebigstr. 18, 04103 Leipzig, Germany
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - James F Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Anders Hamsten
- Atherosclerosis Research Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Richard N Bergman
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Thomas A Buchanan
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
- Department of Medicine, Division of Endocrinology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Francis S Collins
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jaakko Tuomilehto
- Department of Public Health, Faculty of Medicine, P.O. Box 41 (Mannerheimintie 172), University of Helsinki, 00014 Helsinki, Finland
- National Institute for Health and Welfare, Unit of Diabetes Prevention, Helsinki, Finland
| | - Timo T Valle
- National Institute for Health and Welfare, Unit of Diabetes Prevention, Helsinki, Finland
| | - David Altshuler
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jerome I Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - David S Siscovick
- Departments of Medicine and Epidemiology, University of Washington, Seattle, Washington, USA
| | - Brenda W J H Penninx
- EMGO Institute/Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands
| | - Dorret Boomsma
- Department of Biological Psychology, VU, Van der Boechorststraat 1, 1081 BT Amsterdam, The Netherlands
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Timothy D Spector
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Twin Research & Genetic Epidemiology Department, King’s College London, St Thomas' Hospital Campus, Lambeth Palace Rd, London SE1 7EH, UK
| | - Timothy M Frayling
- Genetics of Complex Traits, Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter EX1 2LU, UK
| | - Luigi Ferrucci
- Longitudinal Studies Section, Clinical Research Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | | | - Unnur Thorsteinsdottir
- deCODE Genetics, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavík, Iceland
| | - Kari Stefansson
- deCODE Genetics, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavík, Iceland
| | | | - Yurii S Aulchenko
- Department of Epidemiology, Erasmus MC Rotterdam, 3000 CA, The Netherlands
| | - Antonio Cao
- Istituto di Neurogenetica e Neurofarmacologia (INN), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari 09042, Italy
| | - Angelo Scuteri
- Istituto di Neurogenetica e Neurofarmacologia (INN), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari 09042, Italy
- Lab of Cardiovascular Sciences, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - David Schlessinger
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Manuela Uda
- Istituto di Neurogenetica e Neurofarmacologia (INN), Consiglio Nazionale delle Ricerche, c/o Cittadella Universitaria di Monserrato, Monserrato, Cagliari 09042, Italy
| | - Aimo Ruokonen
- Department of Clinical Sciences/Clinical Chemistry, University of Oulu, Box 5000, Fin-90014 University of Oulu, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Public Health, Imperial College of London, Faculty of Medicine, Norfolk Place, London W2 1PG, UK
- Institute of Health Sciences and Biocenter Oulu, Box 5000, Fin-90014 University of Oulu, Finland
- National Institute of Health and Welfare, Aapistie 1, P.O. Box 310, Fin-90101 Oulu, Finland
| | - Dawn M Waterworth
- Division of Genetics, R&D, Glaxo SmithKline, King of Prussia, Pennsylvania 19406, USA
| | - Peter Vollenweider
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Leena Peltonen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- The Broad Institute, Cambridge, Massachusetts 02141, USA
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Unit of Public Health Genomics, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Vincent Mooser
- Division of Genetics, R&D, Glaxo SmithKline, King of Prussia, Pennsylvania 19406, USA
| | - Goncalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, USA
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Robert Sladek
- Departments of Medicine and Human Genetics, McGill University, Montreal, Canada
- Genome Quebec Innovation Centre, Montreal H3A 1A4, Canada
| | - Philippe Froguel
- CNRS-UMR8090, Pasteur Institute, Lille 2-Droit et Santé University, F-59000 Lille, France
- Genomic Medicine, Imperial College London, Hammersmith Hospital, W12 0NN, London, UK
| | - Richard M Watanabe
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA
| | - James B Meigs
- General Medicine Division, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Malmo, Malmo, Sweden
| | - Michael Boehnke
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan 48109, USA
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Inês Barroso
- Metabolic Disease Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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Saxena R, Hivert MF, Langenberg C, Tanaka T, Pankow JS, Vollenweider P, Lyssenko V, Bouatia-Naji N, Dupuis J, Jackson AU, Kao WHL, Li M, Glazer NL, Manning AK, Luan J, Stringham HM, Prokopenko I, Johnson T, Grarup N, Boesgaard TW, Lecoeur C, Shrader P, O'Connell J, Ingelsson E, Couper DJ, Rice K, Song K, Andreasen CH, Dina C, Köttgen A, Le Bacquer O, Pattou F, Taneera J, Steinthorsdottir V, Rybin D, Ardlie K, Sampson M, Qi L, van Hoek M, Weedon MN, Aulchenko YS, Voight BF, Grallert H, Balkau B, Bergman RN, Bielinski SJ, Bonnefond A, Bonnycastle LL, Borch-Johnsen K, Böttcher Y, Brunner E, Buchanan TA, Bumpstead SJ, Cavalcanti-Proença C, Charpentier G, Chen YDI, Chines PS, Collins FS, Cornelis M, J Crawford G, Delplanque J, Doney A, Egan JM, Erdos MR, Firmann M, Forouhi NG, Fox CS, Goodarzi MO, Graessler J, Hingorani A, Isomaa B, Jørgensen T, Kivimaki M, Kovacs P, Krohn K, Kumari M, Lauritzen T, Lévy-Marchal C, Mayor V, McAteer JB, Meyre D, Mitchell BD, Mohlke KL, Morken MA, Narisu N, Palmer CNA, Pakyz R, Pascoe L, Payne F, Pearson D, Rathmann W, Sandbaek A, Sayer AA, Scott LJ, Sharp SJ, Sijbrands E, Singleton A, Siscovick DS, Smith NL, Sparsø T, Swift AJ, Syddall H, Thorleifsson G, Tönjes A, Tuomi T, Tuomilehto J, Valle TT, Waeber G, Walley A, Waterworth DM, Zeggini E, Zhao JH, Illig T, Wichmann HE, Wilson JF, van Duijn C, Hu FB, Morris AD, Frayling TM, Hattersley AT, Thorsteinsdottir U, Stefansson K, Nilsson P, Syvänen AC, Shuldiner AR, Walker M, Bornstein SR, Schwarz P, Williams GH, Nathan DM, Kuusisto J, Laakso M, Cooper C, Marmot M, Ferrucci L, Mooser V, Stumvoll M, Loos RJF, Altshuler D, Psaty BM, Rotter JI, Boerwinkle E, Hansen T, Pedersen O, Florez JC, McCarthy MI, Boehnke M, Barroso I, Sladek R, Froguel P, Meigs JB, Groop L, Wareham NJ, Watanabe RM. Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge. Nat Genet 2010; 42:142-8. [PMID: 20081857 PMCID: PMC2922003 DOI: 10.1038/ng.521] [Citation(s) in RCA: 481] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 12/10/2009] [Indexed: 12/18/2022]
Abstract
Glucose levels 2 h after an oral glucose challenge are a clinical measure of glucose tolerance used in the diagnosis of type 2 diabetes. We report a meta-analysis of nine genome-wide association studies (n = 15,234 nondiabetic individuals) and a follow-up of 29 independent loci (n = 6,958-30,620). We identify variants at the GIPR locus associated with 2-h glucose level (rs10423928, beta (s.e.m.) = 0.09 (0.01) mmol/l per A allele, P = 2.0 x 10(-15)). The GIPR A-allele carriers also showed decreased insulin secretion (n = 22,492; insulinogenic index, P = 1.0 x 10(-17); ratio of insulin to glucose area under the curve, P = 1.3 x 10(-16)) and diminished incretin effect (n = 804; P = 4.3 x 10(-4)). We also identified variants at ADCY5 (rs2877716, P = 4.2 x 10(-16)), VPS13C (rs17271305, P = 4.1 x 10(-8)), GCKR (rs1260326, P = 7.1 x 10(-11)) and TCF7L2 (rs7903146, P = 4.2 x 10(-10)) associated with 2-h glucose. Of the three newly implicated loci (GIPR, ADCY5 and VPS13C), only ADCY5 was found to be associated with type 2 diabetes in collaborating studies (n = 35,869 cases, 89,798 controls, OR = 1.12, 95% CI 1.09-1.15, P = 4.8 x 10(-18)).
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Affiliation(s)
- Richa Saxena
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Richards JB, Waterworth D, O'Rahilly S, Hivert MF, Loos RJF, Perry JRB, Tanaka T, Timpson NJ, Semple RK, Soranzo N, Song K, Rocha N, Grundberg E, Dupuis J, Florez JC, Langenberg C, Prokopenko I, Saxena R, Sladek R, Aulchenko Y, Evans D, Waeber G, Erdmann J, Burnett MS, Sattar N, Devaney J, Willenborg C, Hingorani A, Witteman JCM, Vollenweider P, Glaser B, Hengstenberg C, Ferrucci L, Melzer D, Stark K, Deanfield J, Winogradow J, Grassl M, Hall AS, Egan JM, Thompson JR, Ricketts SL, König IR, Reinhard W, Grundy S, Wichmann HE, Barter P, Mahley R, Kesaniemi YA, Rader DJ, Reilly MP, Epstein SE, Stewart AFR, Van Duijn CM, Schunkert H, Burling K, Deloukas P, Pastinen T, Samani NJ, McPherson R, Davey Smith G, Frayling TM, Wareham NJ, Meigs JB, Mooser V, Spector TD. A genome-wide association study reveals variants in ARL15 that influence adiponectin levels. PLoS Genet 2009; 5:e1000768. [PMID: 20011104 PMCID: PMC2781107 DOI: 10.1371/journal.pgen.1000768] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 11/12/2009] [Indexed: 12/22/2022] Open
Abstract
The adipocyte-derived protein adiponectin is highly heritable and inversely associated with risk of type 2 diabetes mellitus (T2D) and coronary heart disease (CHD). We meta-analyzed 3 genome-wide association studies for circulating adiponectin levels (n = 8,531) and sought validation of the lead single nucleotide polymorphisms (SNPs) in 5 additional cohorts (n = 6,202). Five SNPs were genome-wide significant in their relationship with adiponectin (P< or =5x10(-8)). We then tested whether these 5 SNPs were associated with risk of T2D and CHD using a Bonferroni-corrected threshold of P< or =0.011 to declare statistical significance for these disease associations. SNPs at the adiponectin-encoding ADIPOQ locus demonstrated the strongest associations with adiponectin levels (P-combined = 9.2x10(-19) for lead SNP, rs266717, n = 14,733). A novel variant in the ARL15 (ADP-ribosylation factor-like 15) gene was associated with lower circulating levels of adiponectin (rs4311394-G, P-combined = 2.9x10(-8), n = 14,733). This same risk allele at ARL15 was also associated with a higher risk of CHD (odds ratio [OR] = 1.12, P = 8.5x10(-6), n = 22,421) more nominally, an increased risk of T2D (OR = 1.11, P = 3.2x10(-3), n = 10,128), and several metabolic traits. Expression studies in humans indicated that ARL15 is well-expressed in skeletal muscle. These findings identify a novel protein, ARL15, which influences circulating adiponectin levels and may impact upon CHD risk.
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Affiliation(s)
- J Brent Richards
- Departments of Medicine, Human Genetics, and Epidemiology and Biostatistics, Jewish General Hospital, McGill University, Montréal, Québec, Canada.
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48
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Bonnefond A, Vaxillaire M, Labrune Y, Lecoeur C, Chèvre JC, Bouatia-Naji N, Cauchi S, Balkau B, Marre M, Tichet J, Riveline JP, Hadjadj S, Gallois Y, Czernichow S, Hercberg S, Kaakinen M, Wiesner S, Charpentier G, Lévy-Marchal C, Elliott P, Jarvelin MR, Horber F, Dina C, Pedersen O, Sladek R, Meyre D, Froguel P. Genetic variant in HK1 is associated with a proanemic state and A1C but not other glycemic control-related traits. Diabetes 2009; 58:2687-97. [PMID: 19651813 PMCID: PMC2768183 DOI: 10.2337/db09-0652] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OBJECTIVE A1C is widely considered the gold standard for monitoring effective blood glucose levels. Recently, a genome-wide association study reported an association between A1C and rs7072268 within HK1 (encoding hexokinase 1), which catalyzes the first step of glycolysis. HK1 deficiency in erythrocytes (red blood cells [RBCs]) causes severe nonspherocytic hemolytic anemia in both humans and mice. RESEARCH DESIGN AND METHODS The contribution of rs7072268 to A1C and the RBC-related traits was assessed in 6,953 nondiabetic European participants. We additionally analyzed the association with hematologic traits in 5,229 nondiabetic European individuals (in whom A1C was not measured) and 1,924 diabetic patients. Glucose control-related markers other than A1C were analyzed in 18,694 nondiabetic European individuals. A type 2 diabetes case-control study included 7,447 French diabetic patients. RESULTS Our study confirms a strong association between the rs7072268-T allele and increased A1C (beta = 0.029%; P = 2.22 x 10(-7)). Surprisingly, despite adequate study power, rs7072268 showed no association with any other markers of glucose control (fasting- and 2-h post-OGTT-related parameters, n = 18,694). In contrast, rs7072268-T allele decreases hemoglobin levels (n = 13,416; beta = -0.054 g/dl; P = 3.74 x 10(-6)) and hematocrit (n = 11,492; beta = -0.13%; P = 2.26 x 10(-4)), suggesting a proanemic effect. The T allele also increases risk for anemia (836 cases; odds ratio 1.13; P = 0.018). CONCLUSIONS HK1 variation, although strongly associated with A1C, does not seem to be involved in blood glucose control. Since HK1 rs7072268 is associated with reduced hemoglobin levels and favors anemia, we propose that HK1 may influence A1C levels through its anemic effect or its effect on glucose metabolism in RBCs. These findings may have implications for type 2 diabetes diagnosis and clinical management because anemia is a frequent complication of the diabetes state.
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Affiliation(s)
- Amélie Bonnefond
- CNRS-UMR-8090, Institute of Biology and Lille 2 University, Pasteur Institute, Lille, France
| | - Martine Vaxillaire
- CNRS-UMR-8090, Institute of Biology and Lille 2 University, Pasteur Institute, Lille, France
| | - Yann Labrune
- CNRS-UMR-8090, Institute of Biology and Lille 2 University, Pasteur Institute, Lille, France
| | - Cécile Lecoeur
- CNRS-UMR-8090, Institute of Biology and Lille 2 University, Pasteur Institute, Lille, France
| | - Jean-Claude Chèvre
- CNRS-UMR-8090, Institute of Biology and Lille 2 University, Pasteur Institute, Lille, France
| | - Nabila Bouatia-Naji
- CNRS-UMR-8090, Institute of Biology and Lille 2 University, Pasteur Institute, Lille, France
| | - Stéphane Cauchi
- CNRS-UMR-8090, Institute of Biology and Lille 2 University, Pasteur Institute, Lille, France
| | - Beverley Balkau
- INSERM U780, Villejuif, France, and University Paris-Sud, Orsay, France
| | - Michel Marre
- Department of Endocrinology, Diabetology and Nutrition, Bichat-Claude Bernard University Hospital, Assistance Publique des Hôpitaux de Paris, Paris, France
- INSERM U695, Université Paris 7, Paris, France
| | - Jean Tichet
- Institut Inter-Régional Pour la Santé, La Riche, France
| | | | - Samy Hadjadj
- CHU de Poitiers, Endocrinologie Diabétologie, CIC INSERM 0802, INSERM U927, Université de Poitiers, UFR Médecine Pharmacie, Poitiers, France
| | - Yves Gallois
- CHU d'Angers, the Biochemistry Laboratory, Angers, France
| | - Sébastien Czernichow
- Unité de Recherche en Epidémiologie Nutritionnelle, INSERM U557, INRA U1125, CNAM, UP13, CRNH-IdF, and the Public Health Department, Hôpital Avicenne (AP-HP), Bobigny, France
| | - Serge Hercberg
- Unité de Recherche en Epidémiologie Nutritionnelle, INSERM U557, INRA U1125, CNAM, UP13, CRNH-IdF, and the Public Health Department, Hôpital Avicenne (AP-HP), Bobigny, France
| | - Marika Kaakinen
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Susanne Wiesner
- Klinik Lindberg, Winterthur, Switzerland
- University Berne, Berne, Switzerland
| | | | - Claire Lévy-Marchal
- INSERM U690, Robert Debré Hospital, Paris, France
- Paris Diderot University, Paris, France
| | - Paul Elliott
- Department of Epidemiology and Public Health, Imperial College London, London, U.K
| | - Marjo-Riitta Jarvelin
- Unité de Recherche en Epidémiologie Nutritionnelle, INSERM U557, INRA U1125, CNAM, UP13, CRNH-IdF, and the Public Health Department, Hôpital Avicenne (AP-HP), Bobigny, France
- Department of Epidemiology and Public Health, Imperial College London, London, U.K
| | - Fritz Horber
- Klinik Lindberg, Winterthur, Switzerland
- University Berne, Berne, Switzerland
| | - Christian Dina
- CNRS-UMR-8090, Institute of Biology and Lille 2 University, Pasteur Institute, Lille, France
| | - Oluf Pedersen
- Steno Diabetes Center, Gentofte, Denmark
- Department of Health Sciences, University of Aarhus, Aarhus, Denmark
- Department of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Robert Sladek
- Department of Human Genetics, McGill University, Montreal, Canada
- Genome Quebec Innovation Centre, Montreal, Canada
| | - David Meyre
- CNRS-UMR-8090, Institute of Biology and Lille 2 University, Pasteur Institute, Lille, France
| | - Philippe Froguel
- CNRS-UMR-8090, Institute of Biology and Lille 2 University, Pasteur Institute, Lille, France
- Genomic Medicine, Hammersmith Hospital, Imperial College London, London, U.K
- Corresponding author: Philippe Froguel,
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Rung J, Cauchi S, Albrechtsen A, Shen L, Rocheleau G, Cavalcanti-Proença C, Bacot F, Balkau B, Belisle A, Borch-Johnsen K, Charpentier G, Dina C, Durand E, Elliott P, Hadjadj S, Järvelin MR, Laitinen J, Lauritzen T, Marre M, Mazur A, Meyre D, Montpetit A, Pisinger C, Posner B, Poulsen P, Pouta A, Prentki M, Ribel-Madsen R, Ruokonen A, Sandbaek A, Serre D, Tichet J, Vaxillaire M, Wojtaszewski JFP, Vaag A, Hansen T, Polychronakos C, Pedersen O, Froguel P, Sladek R. Erratum: Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia. Nat Genet 2009. [DOI: 10.1038/ng1009-1156c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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Rung J, Cauchi S, Albrechtsen A, Shen L, Rocheleau G, Cavalcanti-Proença C, Bacot F, Balkau B, Belisle A, Borch-Johnsen K, Charpentier G, Dina C, Durand E, Elliott P, Hadjadj S, Järvelin MR, Laitinen J, Lauritzen T, Marre M, Mazur A, Meyre D, Montpetit A, Pisinger C, Posner B, Poulsen P, Pouta A, Prentki M, Ribel-Madsen R, Ruokonen A, Sandbaek A, Serre D, Tichet J, Vaxillaire M, Wojtaszewski JFP, Vaag A, Hansen T, Polychronakos C, Pedersen O, Froguel P, Sladek R. Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia. Nat Genet 2009; 41:1110-5. [PMID: 19734900 DOI: 10.1038/ng.443] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 07/13/2009] [Indexed: 12/22/2022]
Abstract
Genome-wide association studies have identified common variants that only partially explain the genetic risk for type 2 diabetes (T2D). Using genome-wide association data from 1,376 French individuals, we identified 16,360 SNPs nominally associated with T2D and studied these SNPs in an independent sample of 4,977 French individuals. We then selected the 28 best hits for replication in 7,698 Danish subjects and identified 4 SNPs showing strong association with T2D, one of which (rs2943641, P = 9.3 x 10(-12), OR = 1.19) was located adjacent to the insulin receptor substrate 1 gene (IRS1). Unlike previously reported T2D risk loci, which predominantly associate with impaired beta cell function, the C allele of rs2943641 was associated with insulin resistance and hyperinsulinemia in 14,358 French, Danish and Finnish participants from population-based cohorts; this allele was also associated with reduced basal levels of IRS1 protein and decreased insulin induction of IRS1-associated phosphatidylinositol-3-OH kinase activity in human skeletal muscle biopsies.
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Affiliation(s)
- Johan Rung
- McGill University and Génome Québec Innovation Centre, Montréal, Canada
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