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Williamson A, Norris DM, Yin X, Broadaway KA, Moxley AH, Vadlamudi S, Wilson EP, Jackson AU, Ahuja V, Andersen MK, Arzumanyan Z, Bonnycastle LL, Bornstein SR, Bretschneider MP, Buchanan TA, Chang YC, Chuang LM, Chung RH, Clausen TD, Damm P, Delgado GE, de Mello VD, Dupuis J, Dwivedi OP, Erdos MR, Fernandes Silva L, Frayling TM, Gieger C, Goodarzi MO, Guo X, Gustafsson S, Hakaste L, Hammar U, Hatem G, Herrmann S, Højlund K, Horn K, Hsueh WA, Hung YJ, Hwu CM, Jonsson A, Kårhus LL, Kleber ME, Kovacs P, Lakka TA, Lauzon M, Lee IT, Lindgren CM, Lindström J, Linneberg A, Liu CT, Luan J, Aly DM, Mathiesen E, Moissl AP, Morris AP, Narisu N, Perakakis N, Peters A, Prasad RB, Rodionov RN, Roll K, Rundsten CF, Sarnowski C, Savonen K, Scholz M, Sharma S, Stinson SE, Suleman S, Tan J, Taylor KD, Uusitupa M, Vistisen D, Witte DR, Walther R, Wu P, Xiang AH, Zethelius B, Ahlqvist E, Bergman RN, Chen YDI, Collins FS, Fall T, Florez JC, Fritsche A, Grallert H, Groop L, Hansen T, Koistinen HA, Komulainen P, Laakso M, Lind L, Loeffler M, März W, Meigs JB, Raffel LJ, Rauramaa R, Rotter JI, Schwarz PEH, Stumvoll M, Sundström J, Tönjes A, Tuomi T, Tuomilehto J, Wagner R, Barroso I, Walker M, Grarup N, Boehnke M, Wareham NJ, Mohlke KL, Wheeler E, O'Rahilly S, Fazakerley DJ, Langenberg C. Genome-wide association study and functional characterization identifies candidate genes for insulin-stimulated glucose uptake. Nat Genet 2023; 55:973-983. [PMID: 37291194 PMCID: PMC7614755 DOI: 10.1038/s41588-023-01408-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 04/26/2023] [Indexed: 06/10/2023]
Abstract
Distinct tissue-specific mechanisms mediate insulin action in fasting and postprandial states. Previous genetic studies have largely focused on insulin resistance in the fasting state, where hepatic insulin action dominates. Here we studied genetic variants influencing insulin levels measured 2 h after a glucose challenge in >55,000 participants from three ancestry groups. We identified ten new loci (P < 5 × 10-8) not previously associated with postchallenge insulin resistance, eight of which were shown to share their genetic architecture with type 2 diabetes in colocalization analyses. We investigated candidate genes at a subset of associated loci in cultured cells and identified nine candidate genes newly implicated in the expression or trafficking of GLUT4, the key glucose transporter in postprandial glucose uptake in muscle and fat. By focusing on postprandial insulin resistance, we highlighted the mechanisms of action at type 2 diabetes loci that are not adequately captured by studies of fasting glycemic traits.
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Affiliation(s)
- Alice Williamson
- MRC Epidemiology Unit Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Metabolic Research Laboratories Wellcome Trust-MRC Institute of Metabolic Science, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK
| | - Dougall M Norris
- Metabolic Research Laboratories Wellcome Trust-MRC Institute of Metabolic Science, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK
| | - Xianyong Yin
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - K Alaine Broadaway
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Anne H Moxley
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | | | - Emma P Wilson
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Anne U Jackson
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Vasudha Ahuja
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mette K Andersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zorayr Arzumanyan
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Lori L Bonnycastle
- Center for Precision Health Research National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stefan R Bornstein
- Department of Internal Medicine III, Metabolic and Vascular Medicine, Medical Faculty Carl Gustav Carus, Dresden, Germany
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Maxi P Bretschneider
- Department of Internal Medicine III, Metabolic and Vascular Medicine, Medical Faculty Carl Gustav Carus, Dresden, Germany
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Thomas A Buchanan
- Department of Medicine, Division of Endocrinology and Diabetes, Keck School of Medicine USC, Los Angeles, CA, USA
| | - Yi-Cheng Chang
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei City, Taiwan
- Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Lee-Ming Chuang
- Department of Internal Medicine, Division of Endocrinology and Metabolism, National Taiwan University Hospital, Taipei City, Taiwan
| | - Ren-Hua Chung
- Institute of Population Health Sciences, National Health Research Institutes, Toufen, Taiwan
| | - Tine D Clausen
- Department of Gynecology and Obstetrics, Nordsjaellands Hospital, Hillerød, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Damm
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Pregnant Women with Diabetes, Rigshospitalet, Copenhagen, Denmark
- Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vanessa D de Mello
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
| | - Om P Dwivedi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Michael R Erdos
- Center for Precision Health Research National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Christian Gieger
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Mark O Goodarzi
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiuqing Guo
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stefan Gustafsson
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Liisa Hakaste
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Ulf Hammar
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Gad Hatem
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Sandra Herrmann
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- Department of Internal Medicine III, Prevention and Care of Diabetes, Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - Kurt Højlund
- Steno Diabetes Center Odense, Odense University Hospital, Odense, Denmark
| | - Katrin Horn
- Medical Faculty Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, Medical Faculty, Leipzig, Germany
| | - Willa A Hsueh
- Internal Medicine, Endocrinology, Diabetes and Metabolism, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Chii-Min Hwu
- Department of Medicine Section of Endocrinology and Metabolism, Taipei Veterans General Hospital, Taipei City, Taiwan
| | - Anna Jonsson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Line L Kårhus
- Center for Clinical Research and Prevention, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Marcus E Kleber
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Peter Kovacs
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Marie Lauzon
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - I-Te Lee
- Department of Internal Medicine Division of Endocrinology and Metabolism, Taichung Veterans General Hospital, Taichung City, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung City, Taiwan
| | - Cecilia M Lindgren
- Big Data Institute Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Wellcome Trust Centre Human Genetics, University of Oxford, Oxford, UK
- Broad Institute, Cambridge, MA, USA
| | | | - Allan Linneberg
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Research and Prevention, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jian'an Luan
- MRC Epidemiology Unit Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Dina Mansour Aly
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Elisabeth Mathiesen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Pregnant Women with Diabetes, Rigshospitalet, Copenhagen, Denmark
- Department of Endocrinology Rigshospitalet, Copenhagen, Denmark
| | - Angela P Moissl
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Institute of Nutritional Sciences, Friedrich-Schiller-University, Jena, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena, Jena, Germany
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Narisu Narisu
- Center for Precision Health Research National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nikolaos Perakakis
- Department of Internal Medicine III, Metabolic and Vascular Medicine, Medical Faculty Carl Gustav Carus, Dresden, Germany
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Annette Peters
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Rashmi B Prasad
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Roman N Rodionov
- Department of Internal Medicine III, University Center for Vascular Medicine, Medical Faculty Carl Gustav Carus, Dresden, Germany
- College of Medicine and Public Health, Flinders University and Flinders Medical Centre, Adelaide, Australia
| | - Kathryn Roll
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Carsten F Rundsten
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chloé Sarnowski
- Department of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center, Houston, TX, USA
| | - Kai Savonen
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Markus Scholz
- Medical Faculty Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, Medical Faculty, Leipzig, Germany
| | - Sapna Sharma
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Food Chemistry and Molecular and Sensory Science, Technical University of Munich, Freising-Weihenstephan, München, Germany
| | - Sara E Stinson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sufyan Suleman
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jingyi Tan
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Matti Uusitupa
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Dorte Vistisen
- Clinical Research, Steno Diabetes Center Copenhagen, Herlev, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Daniel R Witte
- Steno Diabetes Center Aarhus, Aarhus, Denmark
- Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Romy Walther
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- Department of Internal Medicine III, Pathobiochemistry, Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Anny H Xiang
- Research and Evaluation, Division of Biostatistics, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Björn Zethelius
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, Sweden
| | - Emma Ahlqvist
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Richard N Bergman
- Diabetes and Obesity Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yii-Der Ida Chen
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Francis S Collins
- Center for Precision Health Research National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Jose C Florez
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, The Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andreas Fritsche
- Department of Internal Medicine IV, University Hospital Tübingen, Tübingen, Germany
| | - Harald Grallert
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Leif Groop
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Lund, Sweden
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heikki A Koistinen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Pirjo Komulainen
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Lars Lind
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Markus Loeffler
- Medical Faculty Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, Medical Faculty, Leipzig, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Synlab Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany
| | - James B Meigs
- Department of Internal Medicine IV, University Hospital Tübingen, Tübingen, Germany
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Lund, Sweden
- Department of Medicine Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Leslie J Raffel
- Department of Pediatrics, Genetic and Genomic Medicine, University of California, Irvine, CA, USA
| | - Rainer Rauramaa
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - 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, USA
| | - Peter E H Schwarz
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Department of Internal Medicine III, Prevention and Care of Diabetes, Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - Michael Stumvoll
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Johan Sundström
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Anke Tönjes
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Jaakko Tuomilehto
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Robert Wagner
- Department of Internal Medicine IV, University Hospital Tübingen, Tübingen, Germany
| | - Inês Barroso
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Mark Walker
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Boehnke
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas J Wareham
- MRC Epidemiology Unit Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
| | - Eleanor Wheeler
- MRC Epidemiology Unit Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK.
| | - Stephen O'Rahilly
- Metabolic Research Laboratories Wellcome Trust-MRC Institute of Metabolic Science, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK.
| | - Daniel J Fazakerley
- Metabolic Research Laboratories Wellcome Trust-MRC Institute of Metabolic Science, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK.
| | - Claudia Langenberg
- MRC Epidemiology Unit Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK.
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin, Berlin, Germany.
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK.
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A novel splice-affecting HNF1A variant with large population impact on diabetes in Greenland. THE LANCET REGIONAL HEALTH. EUROPE 2022; 24:100529. [PMID: 36649380 PMCID: PMC9832271 DOI: 10.1016/j.lanepe.2022.100529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/15/2022] [Accepted: 10/03/2022] [Indexed: 11/12/2022]
Abstract
Background The genetic disease architecture of Inuit includes a large number of common high-impact variants. Identification of such variants contributes to our understanding of the genetic aetiology of diseases and improves global equity in genomic personalised medicine. We aimed to identify and characterise novel variants in genes associated with Maturity Onset Diabetes of the Young (MODY) in the Greenlandic population. Methods Using combined data from Greenlandic population cohorts of 4497 individuals, including 448 whole genome sequenced individuals, we screened 14 known MODY genes for previously identified and novel variants. We functionally characterised an identified novel variant and assessed its association with diabetes prevalence and cardiometabolic traits and population impact. Findings We identified a novel variant in the known MODY gene HNF1A with an allele frequency of 1.9% in the Greenlandic Inuit and absent elsewhere. Functional assays indicate that it prevents normal splicing of the gene. The variant caused lower 30-min insulin (β = -232 pmol/L, βSD = -0.695, P = 4.43 × 10-4) and higher 30-min glucose (β = 1.20 mmol/L, βSD = 0.441, P = 0.0271) during an oral glucose tolerance test. Furthermore, the variant was associated with type 2 diabetes (OR 4.35, P = 7.24 × 10-6) and HbA1c (β = 0.113 HbA1c%, βSD = 0.205, P = 7.84 × 10-3). The variant explained 2.5% of diabetes variance in Greenland. Interpretation The reported variant has the largest population impact of any previously reported variant within a MODY gene. Together with the recessive TBC1D4 variant, we show that close to 1 in 5 cases of diabetes (18%) in Greenland are associated with high-impact genetic variants compared to 1-3% in large populations. Funding Novo Nordisk Foundation, Independent Research Fund Denmark, and Karen Elise Jensen's Foundation.
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O’Connor MJ, Schroeder P, Huerta-Chagoya A, Cortés-Sánchez P, Bonàs-Guarch S, Guindo-Martínez M, Cole JB, Kaur V, Torrents D, Veerapen K, Grarup N, Kurki M, Rundsten CF, Pedersen O, Brandslund I, Linneberg A, Hansen T, Leong A, Florez JC, Mercader JM. Recessive Genome-Wide Meta-analysis Illuminates Genetic Architecture of Type 2 Diabetes. Diabetes 2022; 71:554-565. [PMID: 34862199 PMCID: PMC8893948 DOI: 10.2337/db21-0545] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/28/2021] [Indexed: 11/13/2022]
Abstract
Most genome-wide association studies (GWAS) of complex traits are performed using models with additive allelic effects. Hundreds of loci associated with type 2 diabetes have been identified using this approach. Additive models, however, can miss loci with recessive effects, thereby leaving potentially important genes undiscovered. We conducted the largest GWAS meta-analysis using a recessive model for type 2 diabetes. Our discovery sample included 33,139 case subjects and 279,507 control subjects from 7 European-ancestry cohorts, including the UK Biobank. We identified 51 loci associated with type 2 diabetes, including five variants undetected by prior additive analyses. Two of the five variants had minor allele frequency of <5% and were each associated with more than a doubled risk in homozygous carriers. Using two additional cohorts, FinnGen and a Danish cohort, we replicated three of the variants, including one of the low-frequency variants, rs115018790, which had an odds ratio in homozygous carriers of 2.56 (95% CI 2.05-3.19; P = 1 × 10-16) and a stronger effect in men than in women (for interaction, P = 7 × 10-7). The signal was associated with multiple diabetes-related traits, with homozygous carriers showing a 10% decrease in LDL cholesterol and a 20% increase in triglycerides; colocalization analysis linked this signal to reduced expression of the nearby PELO gene. These results demonstrate that recessive models, when compared with GWAS using the additive approach, can identify novel loci, including large-effect variants with pathophysiological consequences relevant to type 2 diabetes.
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Affiliation(s)
- Mark J. O’Connor
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Endocrine Division, Massachusetts General Hospital, Boston, MA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Philip Schroeder
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Alicia Huerta-Chagoya
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | | | | | - Joanne B. Cole
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Center for Basic and Translations Obesity Research, Boston Children’s Hospital, Boston, MA
| | - Varinderpal Kaur
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Kumar Veerapen
- Department of Medicine, Harvard Medical School, Boston, MA
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mitja Kurki
- Department of Medicine, Harvard Medical School, Boston, MA
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Carsten F. Rundsten
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivan Brandslund
- Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Aaron Leong
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Endocrine Division, Massachusetts General Hospital, Boston, MA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Jose C. Florez
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Endocrine Division, Massachusetts General Hospital, Boston, MA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Josep M. Mercader
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
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4
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Lu Y, Gentiluomo M, Macauda A, Gioffreda D, Gazouli M, Petrone MC, Kelemen D, Ginocchi L, Morelli L, Papiris K, Greenhalf W, Izbicki JR, Kiudelis V, Mohelníková-Duchoňová B, Bueno-de-Mesquita B, Vodicka P, Brenner H, Diener MK, Pezzilli R, Ivanauskas A, Salvia R, Szentesi A, Aoki MN, Németh BC, Sperti C, Jamroziak K, Chammas R, Oliverius M, Archibugi L, Ermini S, Novák J, Kupcinskas J, Strouhal O, Souček P, Cavestro GM, Milanetto AC, Vanella G, Neoptolemos JP, Theodoropoulos GE, van Laarhoven HWM, Mambrini A, Moz S, Kala Z, Loveček M, Basso D, Uzunoglu FG, Hackert T, Testoni SGG, Hlaváč V, Andriulli A, Lucchesi M, Tavano F, Carrara S, Hegyi P, Arcidiacono PG, Busch OR, Lawlor RT, Puzzono M, Boggi U, Guo F, Małecka-Panas E, Capurso G, Landi S, Talar-Wojnarowska R, Strobel O, Gao X, Vashist Y, Campa D, Canzian F. Identification of Recessively Inherited Genetic Variants Potentially Linked to Pancreatic Cancer Risk. Front Oncol 2021; 11:771312. [PMID: 34926279 PMCID: PMC8678088 DOI: 10.3389/fonc.2021.771312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/16/2021] [Indexed: 02/05/2023] Open
Abstract
Although 21 pancreatic cancer susceptibility loci have been identified in individuals of European ancestry through genome-wide association studies (GWASs), much of the heritability of pancreatic cancer risk remains unidentified. A recessive genetic model could be a powerful tool for identifying additional risk variants. To discover recessively inherited pancreatic cancer risk loci, we performed a re-analysis of the largest pancreatic cancer GWAS, the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4), including 8,769 cases and 7,055 controls of European ancestry. Six single nucleotide polymorphisms (SNPs) showed associations with pancreatic cancer risk according to a recessive model of inheritance. We replicated these variants in 3,212 cases and 3,470 controls collected from the PANcreatic Disease ReseArch (PANDoRA) consortium. The results of the meta-analyses confirmed that rs4626538 (7q32.2), rs7008921 (8p23.2) and rs147904962 (17q21.31) showed specific recessive effects (p<10-5) compared with the additive effects (p>10-3), although none of the six SNPs reached the conventional threshold for genome-wide significance (p < 5×10-8). Additional bioinformatic analysis explored the functional annotations of the SNPs and indicated a possible relationship between rs36018702 and expression of the BCL2L11 and BUB1 genes, which are known to be involved in pancreatic biology. Our findings, while not conclusive, indicate the importance of considering non-additive genetic models when performing GWAS analysis. The SNPs associated with pancreatic cancer in this study could be used for further meta-analysis for recessive association of SNPs and pancreatic cancer risk and might be a useful addiction to improve the performance of polygenic risk scores.
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Affiliation(s)
- Ye Lu
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, University of Heidelberg, Heidelberg, Germany
| | | | - Angelica Macauda
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Domenica Gioffreda
- Division of Gastroenterology and Research Laboratory, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria C. Petrone
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Dezső Kelemen
- Department of Surgery, Medical School, University of Pécs, Pécs, Hungary
| | - Laura Ginocchi
- Oncological Department, Oncological Unit of Massa Carrara, Azienda Unità Sanitaria Locale (USL) Toscana Nord Ovest, Carrara, Italy
| | - Luca Morelli
- General Surgery, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Konstantinos Papiris
- Endoscopic Surgery Department, Hippocratio General Hospital of Athens, Athens, Greece
| | - William Greenhalf
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Jakob R. Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vytautas Kiudelis
- Department of Gastroenterology, Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Beatrice Mohelníková-Duchoňová
- Department of Oncology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czechia
| | - Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases (DCD), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University, Pilsen, Czechia
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Prague, Czechia
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Markus K. Diener
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | | | - Audrius Ivanauskas
- Department of Gastroenterology, Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Roberto Salvia
- Department of General and Pancreatic Surgery, The Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Szentesi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- Centre for Translational Medicine, Department of Medicine, University of Szeged, Szeged, Hungary
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Curitiba, Brazil
| | - Balázs C. Németh
- First Department of Medicine, University of Szeged, Szeged, Hungary
| | - Cosimo Sperti
- Department of Surgery-Dipartimento di Scienze Chirurgiche Oncologiche e Gastroenterologiche (DiSCOG), Padua University Hospital, Padua, Italy
| | - Krzysztof Jamroziak
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Roger Chammas
- Department of Radiology and Oncology, Institute of Cancer of São Paulo (ICESP), São Paulo, Brazil
- Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Martin Oliverius
- Department of Surgery, Faculty Hospital Kralovske Vinohrady and Third Faculty of Medicine, Charles University, Prague, Czechia
| | - Livia Archibugi
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Digestive and Liver Disease Unit, Sant’ Andrea Hospital, Rome, Italy
- Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Stefano Ermini
- Blood Transfusion Service, Children’s Hospital, Azienda Ospedaliero-Universitaria Meyer, Florence, Italy
| | - János Novák
- Pándy Kálmán Hospital of Békés County, Gyula, Hungary
| | - Juozas Kupcinskas
- Department of Gastroenterology, Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ondřej Strouhal
- Department of Oncology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czechia
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czechia
| | - Pavel Souček
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Giulia M. Cavestro
- Division of Experimental Oncology, Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Anna C. Milanetto
- Department of Surgery-Dipartimento di Scienze Chirurgiche Oncologiche e Gastroenterologiche (DiSCOG), Padua University Hospital, Padua, Italy
| | - Giuseppe Vanella
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Digestive and Liver Disease Unit, Sant’ Andrea Hospital, Rome, Italy
- Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - John P. Neoptolemos
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - George E. Theodoropoulos
- First Propaedeutic University Surgery Clinic, Hippocratio General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Hanneke W. M. van Laarhoven
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Andrea Mambrini
- Oncological Department, Oncological Unit of Massa Carrara, Azienda Unità Sanitaria Locale (USL) Toscana Nord Ovest, Carrara, Italy
| | - Stefania Moz
- Department of Medicine (DIMED), Padua University Hospital, Padua, Italy
| | - Zdenek Kala
- Department of Surgery, University Hospital Brno Bohunice, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Martin Loveček
- Department of Surgery I, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czechia
| | - Daniela Basso
- Department of Medicine (DIMED), Padua University Hospital, Padua, Italy
| | - Faik G. Uzunoglu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thilo Hackert
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - Sabrina G. G. Testoni
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Viktor Hlaváč
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Angelo Andriulli
- Division of Gastroenterology and Research Laboratory, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Maurizio Lucchesi
- Oncological Department, Oncological Unit of Massa Carrara, Azienda Unità Sanitaria Locale (USL) Toscana Nord Ovest, Carrara, Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Silvia Carrara
- Division of Gastroenterology and Digestive Endoscopy, Department of Gastroenterology, Humanitas Clinical and Research Center Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Péter Hegyi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- Centre for Translational Medicine, Department of Medicine, University of Szeged, Szeged, Hungary
| | - Paolo G. Arcidiacono
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Olivier R. Busch
- Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Rita T. Lawlor
- Applied Research on Cancer (ARC)-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Marta Puzzono
- Division of Experimental Oncology, Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Ugo Boggi
- Division of General and Transplant Surgery, Pisa University Hospital, Pisa, Italy
| | - Feng Guo
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ewa Małecka-Panas
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Gabriele Capurso
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Digestive and Liver Disease Unit, Sant’ Andrea Hospital, Rome, Italy
- Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | | | - Oliver Strobel
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - Xin Gao
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yogesh Vashist
- Centre for Surgical Oncology, Medias Klinikum Burghausen, Burghausen, Germany
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
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5
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Chiang CWK. The Opportunities and Challenges of Integrating Population Histories Into Genetic Studies for Diverse Populations: A Motivating Example From Native Hawaiians. Front Genet 2021; 12:643883. [PMID: 34646295 PMCID: PMC8503554 DOI: 10.3389/fgene.2021.643883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 08/19/2021] [Indexed: 11/25/2022] Open
Abstract
There is a well-recognized need to include diverse populations in genetic studies, but several obstacles continue to be prohibitive, including (but are not limited to) the difficulty of recruiting individuals from diverse populations in large numbers and the lack of representation in available genomic references. These obstacles notwithstanding, studying multiple diverse populations would provide informative, population-specific insights. Using Native Hawaiians as an example of an understudied population with a unique evolutionary history, I will argue that by developing key genomic resources and integrating evolutionary thinking into genetic epidemiology, we will have the opportunity to efficiently advance our knowledge of the genetic risk factors, ameliorate health disparity, and improve healthcare in this underserved population.
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Affiliation(s)
- Charleston W K Chiang
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, United States
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6
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Wang M, Tao H, Huang P. Clinical significance of LARGE1 in progression of liver cancer and the underlying mechanism. Gene 2021; 779:145493. [PMID: 33588034 DOI: 10.1016/j.gene.2021.145493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/26/2022]
Abstract
Liver cancer is a malignant disease and causes thousands of death each year. The prognosis is dismal for patients with metastasis and recurrence. It is urgent to disclose the cause and mechanism underlying liver cancer. LARGE1 encodes a glycosyltransferase and was reported to promote progression in cancer. But its role in liver cancer is unknown. In this study, LARGE1 displayed upregulated expression in liver cancer cells. When LARGE1 was knocked down in SMMC-7721 and Huh-7 cells, the ability of cell proliferation and colony formation were decreased significantly. Cell migration and invasion were suppressed. The number of cells in G1 phase increased but decreased in S phase. Cell apoptosis was not affected. Tumor growth in vivo was also inhibited. Tumor volume was decreased from 1270 mm3 to 721 mm3 (p < 0.05) and tumor weight from 0.95 g to 0.63 g (p < 0.05). Furthermore, the expression of β-catenin, TCF and Cyclin D1 was reduced when LARGE1 was knocked down but increased in LARGE1-overexpressed cells. LGK-974, a specific inhibitor in canonical Wnt signaling, inhibited cell proliferation even when LARGE1 was over-expressed. In tumor tissues, LARGE1 was increased by 4.8 folds compared to paratumoral tissues. And higher LARGE1 expression caused shorter survival. Clinicopathological analysis demonstrated that LARGE1 was associated with TNM stage (Ⅰ/Ⅱ vs III/IV, p = 0.005). Therefore, LARGE1 promotes progression and regulates Wnt/β-catenin signaling pathway in liver cancer.
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Affiliation(s)
- Min Wang
- Medical Research & Laboratory Diagnostic Center, Central Hospital affiliated to Shandong First Medical University, Jinan 250013, China
| | - Haiyan Tao
- Department of Acupuncture & Massage, Central Hospital affiliated to Shandong First Medical University, Jinan 250013, China
| | - Ping Huang
- Medical Research & Laboratory Diagnostic Center, Central Hospital affiliated to Shandong First Medical University, Jinan 250013, China.
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7
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Guindo-Martínez M, Amela R, Bonàs-Guarch S, Puiggròs M, Salvoro C, Miguel-Escalada I, Carey CE, Cole JB, Rüeger S, Atkinson E, Leong A, Sanchez F, Ramon-Cortes C, Ejarque J, Palmer DS, Kurki M, Aragam K, Florez JC, Badia RM, Mercader JM, Torrents D. The impact of non-additive genetic associations on age-related complex diseases. Nat Commun 2021; 12:2436. [PMID: 33893285 PMCID: PMC8065056 DOI: 10.1038/s41467-021-21952-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 02/09/2021] [Indexed: 01/19/2023] Open
Abstract
Genome-wide association studies (GWAS) are not fully comprehensive, as current strategies typically test only the additive model, exclude the X chromosome, and use only one reference panel for genotype imputation. We implement an extensive GWAS strategy, GUIDANCE, which improves genotype imputation by using multiple reference panels and includes the analysis of the X chromosome and non-additive models to test for association. We apply this methodology to 62,281 subjects across 22 age-related diseases and identify 94 genome-wide associated loci, including 26 previously unreported. Moreover, we observe that 27.7% of the 94 loci are missed if we use standard imputation strategies with a single reference panel, such as HRC, and only test the additive model. Among the new findings, we identify three novel low-frequency recessive variants with odds ratios larger than 4, which need at least a three-fold larger sample size to be detected under the additive model. This study highlights the benefits of applying innovative strategies to better uncover the genetic architecture of complex diseases.
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Affiliation(s)
| | - Ramon Amela
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Silvia Bonàs-Guarch
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | | | | | - Irene Miguel-Escalada
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Madrid, Spain
| | - Caitlin E Carey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joanne B Cole
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Sina Rüeger
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Elizabeth Atkinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron Leong
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Jorge Ejarque
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Duncan S Palmer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- GENOMICS plc, Oxford, UK
| | - Mitja Kurki
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Krishna Aragam
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jose C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Rosa M Badia
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Josep M Mercader
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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8
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Yaghootkar H, Whitcher B, Bell JD, Thomas EL. Ethnic differences in adiposity and diabetes risk - insights from genetic studies. J Intern Med 2020; 288:271-283. [PMID: 32367627 DOI: 10.1111/joim.13082] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Type 2 diabetes is more common in non-Europeans and starts at a younger age and at lower BMI cut-offs. This review discusses the insights from genetic studies about pathophysiological mechanisms which determine risk of disease with a focus on the role of adiposity and body fat distribution in ethnic disparity in risk of type 2 diabetes. During the past decade, genome-wide association studies (GWAS) have identified more than 400 genetic variants associated with the risk of type 2 diabetes. The Eurocentric nature of these genetic studies has made them less effective in identifying mechanisms that make non-Europeans more susceptible to higher risk of disease. One possible mechanism suggested by epidemiological studies is the role of ethnic difference in body fat distribution. Using genetic variants associated with an ability to store extra fat in a safe place, which is subcutaneous adipose tissue, we discuss how different ethnic groups could be genetically less susceptible to type 2 diabetes by developing a more favourable fat distribution.
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Affiliation(s)
- H Yaghootkar
- From the, Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK.,School of Life Sciences, College of Liberal Arts and Science, University of Westminster, London, UK.,Division of Medical Sciences, Department of Health Sciences, Luleå University of Technology, Luleå, Sweden
| | - B Whitcher
- School of Life Sciences, College of Liberal Arts and Science, University of Westminster, London, UK
| | - J D Bell
- School of Life Sciences, College of Liberal Arts and Science, University of Westminster, London, UK
| | - E L Thomas
- School of Life Sciences, College of Liberal Arts and Science, University of Westminster, London, UK
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9
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The derived allele of a novel intergenic variant at chromosome 11 associates with lower body mass index and a favorable metabolic phenotype in Greenlanders. PLoS Genet 2020; 16:e1008544. [PMID: 31978080 PMCID: PMC7001991 DOI: 10.1371/journal.pgen.1008544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 02/05/2020] [Accepted: 11/27/2019] [Indexed: 11/19/2022] Open
Abstract
The genetic architecture of the small and isolated Greenlandic population is advantageous for identification of novel genetic variants associated with cardio-metabolic traits. We aimed to identify genetic loci associated with body mass index (BMI), to expand the knowledge of the genetic and biological mechanisms underlying obesity. Stage 1 BMI-association analyses were performed in 4,626 Greenlanders. Stage 2 replication and meta-analysis were performed in additional cohorts comprising 1,058 Yup'ik Alaska Native people, and 1,529 Greenlanders. Obesity-related traits were assessed in the stage 1 study population. We identified a common variant on chromosome 11, rs4936356, where the derived G-allele had a frequency of 24% in the stage 1 study population. The derived allele was genome-wide significantly associated with lower BMI (beta (SE), -0.14 SD (0.03), p = 3.2x10-8), corresponding to 0.64 kg/m2 lower BMI per G allele in the stage 1 study population. We observed a similar effect in the Yup'ik cohort (-0.09 SD, p = 0.038), and a non-significant effect in the same direction in the independent Greenlandic stage 2 cohort (-0.03 SD, p = 0.514). The association remained genome-wide significant in meta-analysis of the Arctic cohorts (-0.10 SD (0.02), p = 4.7x10-8). Moreover, the variant was associated with a leaner body type (weight, -1.68 (0.37) kg; waist circumference, -1.52 (0.33) cm; hip circumference, -0.85 (0.24) cm; lean mass, -0.84 (0.19) kg; fat mass and percent, -1.66 (0.33) kg and -1.39 (0.27) %; visceral adipose tissue, -0.30 (0.07) cm; subcutaneous adipose tissue, -0.16 (0.05) cm, all p<0.0002), lower insulin resistance (HOMA-IR, -0.12 (0.04), p = 0.00021), and favorable lipid levels (triglyceride, -0.05 (0.02) mmol/l, p = 0.025; HDL-cholesterol, 0.04 (0.01) mmol/l, p = 0.0015). In conclusion, we identified a novel variant, where the derived G-allele possibly associated with lower BMI in Arctic populations, and as a consequence also leaner body type, lower insulin resistance, and a favorable lipid profile.
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10
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Camacho-Mejorado R, Gómez R, Torres-Sánchez LE, Alhelí Hernández-Tobías E, Noris G, Santana C, Magaña JJ, Orozco L, de la Peña-Díaz A, de la Luz Arenas-Sordo M, Meraz-Ríos MA, Majluf-Cruz A. ALOX5, LPA, MMP9 and TPO gene polymorphisms increase atherothrombosis susceptibility in middle-aged Mexicans. ROYAL SOCIETY OPEN SCIENCE 2020; 7:190775. [PMID: 32218930 PMCID: PMC7029922 DOI: 10.1098/rsos.190775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Atherothrombosis is the cornerstone of cardiovascular diseases and the primary cause of death worldwide. Genetic contribution to disturbances in lipid metabolism, coagulation, inflammation and oxidative stress increase the susceptibility to its development and progression. Given its multifactorial nature, the multiloci studies have been proposed as potential predictors of susceptibility. A cross-sectional study was conducted to explore the contribution of nine genes involved in oxidative stress, inflammatory and thrombotic processes in 204 subjects with atherothrombosis matched by age and gender with a healthy group (n = 204). To evaluate the possibility of spurious associations owing to the Mexican population genetic heterogeneity as well as its ancestral origins, 300 unrelated mestizo individuals and 329 Native Americans were also included. ALOX5, LPA, MMP9 and TPO gene polymorphisms, as well as their multiallelic combinations, were twice to four times more frequent in those individuals with clinical manifestations of atherothrombosis than in the healthy group. Once adjusting for population stratification was done, these differences remained. Our results add further evidence on the contribution of ALOX5, LPA, MMP9 and TPO polymorphisms to atherothrombosis development in the middle-aged group, emphasizing the multiethnic studies in search of gene risk polymorphisms.
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Affiliation(s)
| | - Rocío Gómez
- Departamento de Toxicología, Cinvestav-IPN, Mexico City 07360, Mexico
| | - Luisa E. Torres-Sánchez
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | | | - Gino Noris
- Laboratorio Biología Molecular Diagnóstica, Querétaro, Qro, Mexico
| | - Carla Santana
- Laboratorio Biología Molecular Diagnóstica, Querétaro, Qro, Mexico
| | | | - Lorena Orozco
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, INMEGEN, Mexico City, Mexico
| | - Aurora de la Peña-Díaz
- Facultad de Medicina, Departamento de Farmacología, Universidad Nacional Autónoma de México, Mexico
- Departamento de Biología Molecular, Instituto Nacional de Cardiología, Mexico City, Mexico
| | | | | | - Abraham Majluf-Cruz
- Unidad de Investigación Médica en Trombosis, Hemostasia y Aterogénesis, IMSS, Mexico City, Mexico
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11
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Wang X, Sterr M, Ansarullah, Burtscher I, Böttcher A, Beckenbauer J, Siehler J, Meitinger T, Häring HU, Staiger H, Cernilogar FM, Schotta G, Irmler M, Beckers J, Wright CVE, Bakhti M, Lickert H. Point mutations in the PDX1 transactivation domain impair human β-cell development and function. Mol Metab 2019; 24:80-97. [PMID: 30930126 PMCID: PMC6531841 DOI: 10.1016/j.molmet.2019.03.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/04/2019] [Accepted: 03/13/2019] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVE Hundreds of missense mutations in the coding region of PDX1 exist; however, if these mutations predispose to diabetes mellitus is unknown. METHODS In this study, we screened a large cohort of subjects with increased risk for diabetes and identified two subjects with impaired glucose tolerance carrying common, heterozygous, missense mutations in the PDX1 coding region leading to single amino acid exchanges (P33T, C18R) in its transactivation domain. We generated iPSCs from patients with heterozygous PDX1P33T/+, PDX1C18R/+ mutations and engineered isogenic cell lines carrying homozygous PDX1P33T/P33T, PDX1C18R/C18R mutations and a heterozygous PDX1 loss-of-function mutation (PDX1+/-). RESULTS Using an in vitro β-cell differentiation protocol, we demonstrated that both, heterozygous PDX1P33T/+, PDX1C18R/+ and homozygous PDX1P33T/P33T, PDX1C18R/C18R mutations impair β-cell differentiation and function. Furthermore, PDX1+/- and PDX1P33T/P33T mutations reduced differentiation efficiency of pancreatic progenitors (PPs), due to downregulation of PDX1-bound genes, including transcription factors MNX1 and PDX1 as well as insulin resistance gene CES1. Additionally, both PDX1P33T/+ and PDX1P33T/P33T mutations in PPs reduced the expression of PDX1-bound genes including the long-noncoding RNA, MEG3 and the imprinted gene NNAT, both involved in insulin synthesis and secretion. CONCLUSIONS Our results reveal mechanistic details of how common coding mutations in PDX1 impair human pancreatic endocrine lineage formation and β-cell function and contribute to the predisposition for diabetes.
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Affiliation(s)
- Xianming Wang
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany
| | - Ansarullah
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Julia Beckenbauer
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Johanna Siehler
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Hans-Ulrich Häring
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany; Department of Internal Medicine, Division of Endocrinology, Diabetology, Vascular Medicine, Nephrology and Clinical Chemistry, University of Tübingen, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Harald Staiger
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum München at the University of Tübingen, 72076 Tübingen, Germany; Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Filippo M Cernilogar
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Gunnar Schotta
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Johannes Beckers
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Christopher V E Wright
- Vanderbilt University Program in Developmental Biology, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technische Universität München, Ismaningerstraße 22, 81675 München, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
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12
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Suzuki K, Akiyama M, Ishigaki K, Kanai M, Hosoe J, Shojima N, Hozawa A, Kadota A, Kuriki K, Naito M, Tanno K, Ishigaki Y, Hirata M, Matsuda K, Iwata N, Ikeda M, Sawada N, Yamaji T, Iwasaki M, Ikegawa S, Maeda S, Murakami Y, Wakai K, Tsugane S, Sasaki M, Yamamoto M, Okada Y, Kubo M, Kamatani Y, Horikoshi M, Yamauchi T, Kadowaki T. Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet 2019. [DOI: 10.1038/s41588-018-0332-4 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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13
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Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet 2019. [DOI: 10.1038/s41588-018-0332-4 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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14
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Suzuki K, Akiyama M, Ishigaki K, Kanai M, Hosoe J, Shojima N, Hozawa A, Kadota A, Kuriki K, Naito M, Tanno K, Ishigaki Y, Hirata M, Matsuda K, Iwata N, Ikeda M, Sawada N, Yamaji T, Iwasaki M, Ikegawa S, Maeda S, Murakami Y, Wakai K, Tsugane S, Sasaki M, Yamamoto M, Okada Y, Kubo M, Kamatani Y, Horikoshi M, Yamauchi T, Kadowaki T. Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet 2019. [DOI: 10.1038/s41588-018-0332-4 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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15
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Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet 2019. [DOI: 10.1038/s41588-018-0332-4 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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16
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Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet 2019. [DOI: 10.1038/s41588-018-0332-4 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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17
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Suzuki K, Akiyama M, Ishigaki K, Kanai M, Hosoe J, Shojima N, Hozawa A, Kadota A, Kuriki K, Naito M, Tanno K, Ishigaki Y, Hirata M, Matsuda K, Iwata N, Ikeda M, Sawada N, Yamaji T, Iwasaki M, Ikegawa S, Maeda S, Murakami Y, Wakai K, Tsugane S, Sasaki M, Yamamoto M, Okada Y, Kubo M, Kamatani Y, Horikoshi M, Yamauchi T, Kadowaki T. Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet 2019. [DOI: 10.1038/s41588-018-0332-4 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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18
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Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet 2019. [DOI: 10.1038/s41588-018-0332-4 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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19
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Suzuki K, Akiyama M, Ishigaki K, Kanai M, Hosoe J, Shojima N, Hozawa A, Kadota A, Kuriki K, Naito M, Tanno K, Ishigaki Y, Hirata M, Matsuda K, Iwata N, Ikeda M, Sawada N, Yamaji T, Iwasaki M, Ikegawa S, Maeda S, Murakami Y, Wakai K, Tsugane S, Sasaki M, Yamamoto M, Okada Y, Kubo M, Kamatani Y, Horikoshi M, Yamauchi T, Kadowaki T. Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet 2019; 51:379-386. [PMID: 30718926 DOI: 10.1038/s41588-018-0332-4] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/10/2018] [Indexed: 12/22/2022]
Abstract
To understand the genetics of type 2 diabetes in people of Japanese ancestry, we conducted A meta-analysis of four genome-wide association studies (GWAS; 36,614 cases and 155,150 controls of Japanese ancestry). We identified 88 type 2 diabetes-associated loci (P < 5.0 × 10-8) with 115 independent signals (P < 5.0 × 10-6), of which 28 loci with 30 signals were novel. Twenty-eight missense variants were in linkage disequilibrium (r2 > 0.6) with the lead variants. Among the 28 missense variants, three previously unreported variants had distinct minor allele frequency (MAF) spectra between people of Japanese and European ancestry (MAFJPN > 0.05 versus MAFEUR < 0.01), including missense variants in genes related to pancreatic acinar cells (GP2) and insulin secretion (GLP1R). Transethnic comparisons of the molecular pathways identified from the GWAS results highlight both ethnically shared and heterogeneous effects of a series of pathways on type 2 diabetes (for example, monogenic diabetes and beta cells).
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Affiliation(s)
- Ken Suzuki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan.,Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masahiro Kanai
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jun Hosoe
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuhiro Shojima
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Aya Kadota
- Center for Epidemiologic Research in Asia, Shiga University of Medical Science, Otsu, Japan.,Department of Public Health, Shiga University of Medical Science, Otsu, Japan
| | - Kiyonori Kuriki
- Laboratory of Public Health, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Mariko Naito
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Oral Epidemiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kozo Tanno
- Division of Clinical Research and Epidemiology, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Iwate, Japan.,Department of Hygiene and Preventive Medicine, School of Medicine, Iwate Medical University, Iwate, Japan
| | - Yasushi Ishigaki
- Division of Innovation & Education, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Iwate, Japan.,Division of Diabetes, Metabolism and Endocrinology, Department of Internal Medicine, Iwate Medical University, Iwate, Japan
| | - Makoto Hirata
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Koichi Matsuda
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - Norie Sawada
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Shiro Maeda
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan.,Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan.,Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shoichiro Tsugane
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Iwate, Japan.,Division of Ultrahigh Field MRI, Institute for Biomedical Sciences, Iwate Medical University, Iwate, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. .,Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Momoko Horikoshi
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan.
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. .,Department of Prevention of Diabetes and Lifestyle-Related Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. .,Department of Metabolism and Nutrition, Mizonokuchi Hospital, Faculty of Medicine, Teikyo University, Tokyo, Japan.
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