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Shin J, Syme C, Wang D, Richer L, Pike GB, Gaudet D, Paus T, Pausova Z. Novel Genetic Locus of Visceral Fat and Systemic Inflammation. J Clin Endocrinol Metab 2019; 104:3735-3742. [PMID: 30942860 PMCID: PMC6642667 DOI: 10.1210/jc.2018-02656] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/28/2019] [Indexed: 11/19/2022]
Abstract
CONTEXT Visceral fat (VF), more than fat elsewhere in the body [mostly subcutaneous fat (SF)], promotes systemic inflammation and related disease. The mechanisms of preferentially visceral accumulation of body fat are largely unknown. OBJECTIVE To identify genetic loci and mechanistic pathways of preferential accumulation of VF and associated low-grade systemic inflammation. DESIGN Genome-wide association study (GWAS). SETTING AND PARTICIPANTS Population-based cohort of 1586 adolescents (aged 12 to 19 years) and adults (aged 36 to 65 years). MAIN OUTCOME MEASURES Abdominal VF and SF were measured with MRI, total body fat (TBF) was assessed with bioimpedance, and low-grade systemic inflammation was examined by serum C-reactive protein (CRP) measurement. RESULTS This GWAS of preferential accumulation of VF identified a significant locus on chromosome 6 at rs803522 (P = 1.1 × 10-9 or 4.3 × 10-10 for VF adjusted for SF or TBF, respectively). The major allele was associated with more VF; the association was similar in adolescents and adults. The allele was also associated with higher CRP level, but this association was stronger in adults than adolescents (P for interaction = 4.5 × 10-3). In adults, VF was a significant mediator (P = 1.9× 10-4) in the association between the locus and CRP, explaining 30% of the mediation. The locus was near ATG5, encoding an autophagy molecule reported to modulate adipocyte size and macrophage polarization. CONCLUSION A genetic locus near ATG5 regulates preferential accumulation of VF (vs SF) in youth and adulthood and contributes to the development of systemic inflammation in adulthood.
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Affiliation(s)
- Jean Shin
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Catriona Syme
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Dominic Wang
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Louis Richer
- Department of Health Sciences, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - G Bruce Pike
- Department of Radiology and Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Daniel Gaudet
- Lipidology Unit, Community Genomic Medicine Centre and ECOGENE-21, Department of Medicine, Université de Montréal, Saguenay, Quebec, Canada
| | - Tomas Paus
- Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
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Gene-Environment Interactions on Body Fat Distribution. Int J Mol Sci 2019; 20:ijms20153690. [PMID: 31357654 PMCID: PMC6696304 DOI: 10.3390/ijms20153690] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 02/08/2023] Open
Abstract
The prevalence of obesity has been increasing markedly in the U.S. and worldwide in the past decades; and notably, the obese populations are signified by not only the overall elevated adiposity but also particularly harmful accumulation of body fat in the central region of the body, namely, abdominal obesity. The profound shift from “traditional” to “obesogenic” environments, principally featured by the abundance of palatable, energy-dense diet, reduced physical activity, and prolonged sedentary time, promotes the obesity epidemics and detrimental body fat distribution. Recent advances in genomics studies shed light on the genetic basis of obesity and body fat distribution. In addition, growing evidence from investigations in large cohorts and clinical trials has lent support to interactions between genetic variations and environmental factors, e.g., diet and lifestyle factors, in relation to obesity and body fat distribution. This review summarizes the recent discoveries from observational studies and randomized clinical trials on the gene–environment interactions on obesity and body fat distribution.
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Mastrangelo S, Bahbahani H, Moioli B, Ahbara A, Al Abri M, Almathen F, da Silva A, Belabdi I, Portolano B, Mwacharo JM, Hanotte O, Pilla F, Ciani E. Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia. PLoS One 2019; 14:e0209632. [PMID: 31199810 PMCID: PMC6568386 DOI: 10.1371/journal.pone.0209632] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 05/28/2019] [Indexed: 01/24/2023] Open
Abstract
Genomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging to 23 sheep breeds of different geographic origins using the Rsb (extended haplotype homozygosity) and FST statistical approaches, to identify loci associated with the fat-tail phenotype. We also checked if these putative selection signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel signals and confirmed the presence of selection signature in genomic regions that harbor candidate genes known to affect fat deposition. Several genomic regions that frequently appeared in ROH were also identified within each breed, but only two ROH islands overlapped with the putative selection signatures. The results reported herein provide the most complete genome-wide study of selection signatures for fat-tail in African and Eurasian sheep breeds; they also contribute insights into the genetic basis for the fat tail phenotype in sheep, and confirm the great complexity of the mechanisms that underlie quantitative traits, such as the fat-tail.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Bianca Moioli
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), Monterotondo, Italy
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
| | - Mohammed Al Abri
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Oman
| | - Faisal Almathen
- Department of Public Health and Animal Welfare, College of Veterinary Medicine, King Faisal University, Alhufuf, Al-Ahsa, Saudi Arabia
| | - Anne da Silva
- Université de Limoges, INRA, PEREINE EA7500, USC1061 GAMAA, Limoges, France
| | - Ibrahim Belabdi
- Science Veterinary Institute, University of Blida, Blida, Algeria
- Laboratory of Biotechnology related to Animal Reproduction (LBRA), University of Blida, Blida, Algeria
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Joram M. Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- * E-mail:
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Ganeff IMM, Bos MM, van Heemst D, Noordam R. BMI-associated gene variants in FTO and cardiometabolic and brain disease: obesity or pleiotropy? Physiol Genomics 2019; 51:311-322. [PMID: 31199196 DOI: 10.1152/physiolgenomics.00040.2019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Obesity is a causal risk factor for the development of age-related disease conditions, which includes Type 2 diabetes mellitus, cardiovascular disease, and dementia. In genome-wide association studies, genetic variation in FTO is strongly associated with obesity and has been described across different ethnic backgrounds and life stages. To date, much work has been devoted on determining the biological mechanisms via which FTO affects body weight regulation and ultimately contributes to age-related cardiometabolic and brain disease. The main hypotheses of the involved biological mechanisms include the involvement of FTO in habitual food intake and energy expenditure. In this narrative review, our overall aim is to provide an overview on how FTO gene variants could increase the risk of developing age-related disease conditions. Specifically, we will discuss the state of the literature based on the different hypotheses how FTO regulates body weight and ultimately contributes to cardiometabolic disease and brain disease.
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Affiliation(s)
- Ingeborg M M Ganeff
- Department of Internal Medicine, Section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Maxime M Bos
- Department of Internal Medicine, Section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Diana van Heemst
- Department of Internal Medicine, Section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Raymond Noordam
- Department of Internal Medicine, Section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
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55
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Reese SE, Xu CJ, den Dekker HT, Lee MK, Sikdar S, Ruiz-Arenas C, Merid SK, Rezwan FI, Page CM, Ullemar V, Melton PE, Oh SS, Yang IV, Burrows K, Söderhäll C, Jima DD, Gao L, Arathimos R, Küpers LK, Wielscher M, Rzehak P, Lahti J, Laprise C, Madore AM, Ward J, Bennett BD, Wang T, Bell DA, Vonk JM, Håberg SE, Zhao S, Karlsson R, Hollams E, Hu D, Richards AJ, Bergström A, Sharp GC, Felix JF, Bustamante M, Gruzieva O, Maguire RL, Gilliland F, Baïz N, Nohr EA, Corpeleijn E, Sebert S, Karmaus W, Grote V, Kajantie E, Magnus MC, Örtqvist AK, Eng C, Liu AH, Kull I, Jaddoe VWV, Sunyer J, Kere J, Hoyo C, Annesi-Maesano I, Arshad SH, Koletzko B, Brunekreef B, Binder EB, Räikkönen K, Reischl E, Holloway JW, Jarvelin MR, Snieder H, Kazmi N, Breton CV, Murphy SK, Pershagen G, Anto JM, Relton CL, Schwartz DA, Burchard EG, Huang RC, Nystad W, Almqvist C, Henderson AJ, Melén E, Duijts L, Koppelman GH, London SJ. Epigenome-wide meta-analysis of DNA methylation and childhood asthma. J Allergy Clin Immunol 2019; 143:2062-2074. [PMID: 30579849 PMCID: PMC6556405 DOI: 10.1016/j.jaci.2018.11.043] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/01/2018] [Accepted: 11/16/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Epigenetic mechanisms, including methylation, can contribute to childhood asthma. Identifying DNA methylation profiles in asthmatic patients can inform disease pathogenesis. OBJECTIVE We sought to identify differential DNA methylation in newborns and children related to childhood asthma. METHODS Within the Pregnancy And Childhood Epigenetics consortium, we performed epigenome-wide meta-analyses of school-age asthma in relation to CpG methylation (Illumina450K) in blood measured either in newborns, in prospective analyses, or cross-sectionally in school-aged children. We also identified differentially methylated regions. RESULTS In newborns (8 cohorts, 668 cases), 9 CpGs (and 35 regions) were differentially methylated (epigenome-wide significance, false discovery rate < 0.05) in relation to asthma development. In a cross-sectional meta-analysis of asthma and methylation in children (9 cohorts, 631 cases), we identified 179 CpGs (false discovery rate < 0.05) and 36 differentially methylated regions. In replication studies of methylation in other tissues, most of the 179 CpGs discovered in blood replicated, despite smaller sample sizes, in studies of nasal respiratory epithelium or eosinophils. Pathway analyses highlighted enrichment for asthma-relevant immune processes and overlap in pathways enriched both in newborns and children. Gene expression correlated with methylation at most loci. Functional annotation supports a regulatory effect on gene expression at many asthma-associated CpGs. Several implicated genes are targets for approved or experimental drugs, including IL5RA and KCNH2. CONCLUSION Novel loci differentially methylated in newborns represent potential biomarkers of risk of asthma by school age. Cross-sectional associations in children can reflect both risk for and effects of disease. Asthma-related differential methylation in blood in children was substantially replicated in eosinophils and respiratory epithelium.
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Affiliation(s)
- Sarah E Reese
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Cheng-Jian Xu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Herman T den Dekker
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mi Kyeong Lee
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Sinjini Sikdar
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Carlos Ruiz-Arenas
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon K Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Phillip E Melton
- Curtin/UWA Centre for Genetic Origins of Health and Disease, Faculty of Health and Medical Sciences, University of Western Australia, Crawley, Australia; School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia
| | - Sam S Oh
- Department of Medicine, University of California San Francisco, San Francisco, Calif
| | - Ivana V Yang
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - Kimberley Burrows
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Dereje D Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC
| | - Lu Gao
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, Calif
| | - Ryan Arathimos
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Leanne K Küpers
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, United Kingdom
| | - Peter Rzehak
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland; Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
| | - Catherine Laprise
- Centre intégré universitaire de santé et de services sociaux du Saguenay, Saguenay, Quebec, Canada; Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Quebec, Canada
| | - Anne-Marie Madore
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Quebec, Canada
| | - James Ward
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Brian D Bennett
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Tianyuan Wang
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Douglas A Bell
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Judith M Vonk
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Siri E Håberg
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Shanshan Zhao
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Elysia Hollams
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, Calif
| | - Adam J Richards
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Gemma C Sharp
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mariona Bustamante
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC; Department of Community and Family Medicine, Duke University Medical Center, Durham, NC
| | - Frank Gilliland
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, Calif
| | - Nour Baïz
- Epidemiology of Allergic and Respiratory Diseases Department, IPLESP, INSERM and UPMC Sorbonne Université, Paris, France
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sylvain Sebert
- Biocenter Oulu, University of Oulu, Oulu, Finland; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland; Department of Genomics of Complex Diseases, School of Public Health, Imperial College London, London, United Kingdom
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, Tenn
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Eero Kajantie
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland; Department of Obstetrics and Gynaecology, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland; Hospital for Children and Adolescents, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Maria C Magnus
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Anne K Örtqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, Calif
| | | | - Inger Kull
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children's Hospital, Södersjukhuset, Stockholm, Sweden
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jordi Sunyer
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC; Department of Biological Sciences, North Carolina State University, Raleigh, NC
| | - Isabella Annesi-Maesano
- Epidemiology of Allergic and Respiratory Diseases Department, IPLESP, INSERM and UPMC Sorbonne Université, Paris, France
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; David Hide Asthma and Allergy Research Centre, Isle of Wight, United Kingdom
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Bert Brunekreef
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elisabeth B Binder
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Ga; Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Eva Reischl
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum Muenchen, Munich, Germany
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, United Kingdom; Biocenter Oulu, University of Oulu, Oulu, Finland; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nabila Kazmi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, Calif
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC; Nicholas School of the Environment, Duke University, Durham, NC
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Josep Maria Anto
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Caroline L Relton
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - David A Schwartz
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, Calif
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Wenche Nystad
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - A John Henderson
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Sachs' Children's Hospital, Södersjukhuset, Stockholm, Sweden
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephanie J London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC.
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Regional fat depot masses are influenced by protein-coding gene variants. PLoS One 2019; 14:e0217644. [PMID: 31145760 PMCID: PMC6542527 DOI: 10.1371/journal.pone.0217644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/15/2019] [Indexed: 12/23/2022] Open
Abstract
Waist-to-hip ratio (WHR) is a prominent cardiometabolic risk factor that increases cardio-metabolic disease risk independently of BMI and for which multiple genetic loci have been identified. However, WHR is a relatively crude proxy for fat distribution and it does not capture all variation in fat distribution. We here present a study of the role of coding genetic variants on fat mass in 6 distinct regions of the body, based on dual-energy X-ray absorptiometry imaging on more than 17k participants. We find that the missense variant CCDC92S70C, previously associated with WHR, is associated specifically increased leg fat mass and reduced visceral but not subcutaneous central fat. The minor allele-carrying transcript of CCDC92 is constitutively more highly expressed in adipose tissue samples. In addition, we identify two coding variants in SPATA20 and UQCC1 that are associated with arm fat mass. SPATA20K422R is a low-frequency variant with a large effect on arm fat only, and UQCC1R51Q is a common variant reaching significance for arm but showing similar trends in other subcutaneous fat depots. Our findings support the notion that different fat compartments are regulated by distinct genetic factors.
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Genetic variation in CADM2 as a link between psychological traits and obesity. Sci Rep 2019; 9:7339. [PMID: 31089183 PMCID: PMC6517397 DOI: 10.1038/s41598-019-43861-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 05/02/2019] [Indexed: 12/12/2022] Open
Abstract
CADM2 has been associated with a range of behavioural and metabolic traits, including physical activity, risk-taking, educational attainment, alcohol and cannabis use and obesity. Here, we set out to determine whether CADM2 contributes to mechanisms shared between mental and physical health disorders. We assessed genetic variants in the CADM2 locus for association with phenotypes in the UK Biobank, IMPROVE, PROCARDIS and SCARFSHEEP studies, before performing meta-analyses. A wide range of metabolic phenotypes were meta-analysed. Psychological phenotypes analysed in UK Biobank only were major depressive disorder, generalised anxiety disorder, bipolar disorder, neuroticism, mood instability and risk-taking behaviour. In UK Biobank, four, 88 and 172 genetic variants were significantly (p < 1 × 10−5) associated with neuroticism, mood instability and risk-taking respectively. In meta-analyses of 4 cohorts, we identified 362, 63 and 11 genetic variants significantly (p < 1 × 10−5) associated with BMI, SBP and CRP respectively. Genetic effects on BMI, CRP and risk-taking were all positively correlated, and were consistently inversely correlated with genetic effects on SBP, mood instability and neuroticism. Conditional analyses suggested an overlap in the signals for physical and psychological traits. Many significant variants had genotype-specific effects on CADM2 expression levels in adult brain and adipose tissues. CADM2 variants influence a wide range of both psychological and metabolic traits, suggesting common biological mechanisms across phenotypes via regulation of CADM2 expression levels in adipose tissue. Functional studies of CADM2 are required to fully understand mechanisms connecting mental and physical health conditions.
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Norheim F, Hasin-Brumshtein Y, Vergnes L, Chella Krishnan K, Pan C, Seldin MM, Hui ST, Mehrabian M, Zhou Z, Gupta S, Parks BW, Walch A, Reue K, Hofmann SM, Arnold AP, Lusis AJ. Gene-by-Sex Interactions in Mitochondrial Functions and Cardio-Metabolic Traits. Cell Metab 2019; 29:932-949.e4. [PMID: 30639359 PMCID: PMC6447452 DOI: 10.1016/j.cmet.2018.12.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/29/2018] [Accepted: 12/17/2018] [Indexed: 12/20/2022]
Abstract
We studied sex differences in over 50 cardio-metabolic traits in a panel of 100 diverse inbred strains of mice. The results clearly showed that the effects of sex on both clinical phenotypes and gene expression depend on the genetic background. In support of this, genetic loci associated with the traits frequently showed sex specificity. For example, Lyplal1, a gene implicated in human obesity, was shown to underlie a sex-specific locus for diet-induced obesity. Global gene expression analyses of tissues across the panel implicated adipose tissue "beiging" and mitochondrial functions in the sex differences. Isolated mitochondria showed gene-by-sex interactions in oxidative functions, such that some strains (C57BL/6J) showed similar function between sexes, whereas others (DBA/2J and A/J) showed increased function in females. Reduced adipose mitochondrial function in males as compared to females was associated with increased susceptibility to obesity and insulin resistance. Gonadectomy studies indicated that gonadal hormones acting in a tissue-specific manner were responsible in part for the sex differences.
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Affiliation(s)
- Frode Norheim
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Yehudit Hasin-Brumshtein
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurent Vergnes
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karthickeyan Chella Krishnan
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Calvin Pan
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Marcus M Seldin
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Simon T Hui
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Margarete Mehrabian
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zhiqiang Zhou
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sonul Gupta
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brian W Parks
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Karen Reue
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Susanna M Hofmann
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health (GmbH), Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, München 80336, Germany; Medizinische Klinik und Poliklinik IV, Klinikum der Ludwig Maximilian Universität (LMU), Munich, Germany
| | - Arthur P Arnold
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
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Lim U, Monroe KR, Buchthal S, Fan B, Cheng I, Kristal BS, Lampe JW, Hullar MA, Franke AA, Stram DO, Wilkens LR, Shepherd J, Ernst T, Marchand LL. Propensity for Intra-abdominal and Hepatic Adiposity Varies Among Ethnic Groups. Gastroenterology 2019; 156:966-975.e10. [PMID: 30445012 PMCID: PMC6409195 DOI: 10.1053/j.gastro.2018.11.021] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/17/2018] [Accepted: 11/01/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS We compared fat storage in the abdominal region among individuals from 5 different ethnic-racial groups to determine whether fat storage is associated with disparities observed in metabolic syndrome and other obesity-associated diseases. METHODS We collected data from 1794 participants in the Multiethnic Cohort Study (60-77 years old; of African, European [white], Japanese, Latino, or Native Hawaiian ancestry) with body mass index values of 17.1-46.2 kg/m2. From May 2013 through April 2016, participants visited the study clinic to undergo body measurements, an interview, and a blood collection. Participants were evaluated by dual-energy x-ray absorptiometry and abdominal magnetic resonance imaging. Among ethnic groups, we compared adiposity of the trunk, intra-abdominal visceral cavity, and liver, adjusting for total fat mass; we evaluated the association of adult weight change with abdominal adiposity; and we examined the prevalence of metabolic syndrome mediated by abdominal adiposity. RESULTS Relative amounts of trunk, visceral, and liver fat varied significantly with ethnicity-they were highest in Japanese Americans, lowest in African Americans, and intermediate in the other groups. Compared with African Americans, the mean visceral fat area was 45% and 73% greater in Japanese American men and women, respectively, and the mean measurements of liver fat were 61% and 122% greater in Japanese American men and women. The visceral and hepatic adiposity associated with weight gain since participants were 21 years old varied in a similar pattern among ethnic-racial groups. In the mediation analysis, visceral and liver fat jointly accounted for a statistically significant fraction of the difference in metabolic syndrome prevalence, compared with white persons, for African Americans, Japanese Americans, and Native Hawaiian women, independently of total fat mass. CONCLUSIONS In an analysis of data from the participants in the Multiethnic Cohort Study, we found extensive differences among ethnic-racial groups in the propensity to store fat intra-abdominally. This observation should be considered by clinicians in the prevention and early detection of metabolic disorders.
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Affiliation(s)
- Unhee Lim
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii.
| | - Kristine R. Monroe
- Keck School of Medicine, University of Southern California, Los Angeles, California, U.S.A
| | - Steve Buchthal
- John A. Burns School of Medicine, University of Hawaii at Mānoa, Honolulu, Hawaii, U.S.A
| | - Bo Fan
- School of Medicine, University of California San Francisco, San Francisco, California, U.S.A
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, U.S.A
| | - Bruce S. Kristal
- Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, U.S.A
| | - Johanna W. Lampe
- Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | | | - Adrian A. Franke
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, U.S.A
| | - Daniel O. Stram
- Keck School of Medicine, University of Southern California, Los Angeles, California, U.S.A
| | - Lynne R. Wilkens
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, U.S.A
| | - John Shepherd
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, U.S.A
| | - Thomas Ernst
- University of Maryland School of Medicine, Baltimore, Maryland, U.S.A
| | - Loïc Le Marchand
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, U.S.A
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Morenikeji OB, Akinyemi MO, Wheto M, Ogunshola OJ, Badejo AA, Chineke CA. Transcriptome profiling of four candidate milk genes in milk and tissue samples of temperate and tropical cattle. J Genet 2019; 98:25. [PMID: 30945671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The expression of four genes involved in milk regulation and production in bovine milk and tissue samples profiled using quantitative PCR to identify differential gene expression. Our goal focussed on the differential mRNA expression of milk genes (KCN, PRL, BLG and PIT-1) in milk samples and different tissues from four different breeds of ecologically adapted and geographically separated cattle species. The mRNA expression identified the four milk genes under studied most upregulated in mammary gland and milk samples as compared with other tissues. The expression of PIT-1 gene in the brain identified to have influenced the expression of PRL and K-CN in the mammary and milk samples. Among the four genes, PRL had the highest mRNA expression (144.19-fold change) in Holstein followed by K-CN with 100.89-fold change, while the smallest relative expression for most genes in this study are in the range from 0.79 to 7.35-fold difference. White Fulani cattle was identified to have a higher expression for K-CN, PRL and BLG compared with Angus and Ndama cattle, while Holstein cattle is on top of the list on the basis of the gene expression and gene regulation for all the four genes in this study. Also, White Fulani and Holstein are in the same cluster based on their mRNA expression for milk genes. Our data showed the first evidence of the molecular identification of indigenous White Fulani cattle ofhaving potential for higher milk production.
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Affiliation(s)
- Olanrewaju B Morenikeji
- Department of Animal Production and Health, Federal University of Technology, Akure 340252, Nigeria. ,
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Irvin MR, Sitlani CM, Noordam R, Avery CL, Bis JC, Floyd JS, Li J, Limdi NA, Srinivasasainagendra V, Stewart J, de Mutsert R, Mook-Kanamori DO, Lipovich L, Kleinbrink EL, Smith A, Bartz TM, Whitsel EA, Uitterlinden AG, Wiggins KL, Wilson JG, Zhi D, Stricker BH, Rotter JI, Arnett DK, Psaty BM, Lange LA. Genome-wide meta-analysis of SNP-by9-ACEI/ARB and SNP-by-thiazide diuretic and effect on serum potassium in cohorts of European and African ancestry. THE PHARMACOGENOMICS JOURNAL 2019; 19:97-108. [PMID: 29855607 PMCID: PMC6274589 DOI: 10.1038/s41397-018-0021-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 12/21/2017] [Accepted: 02/12/2018] [Indexed: 12/22/2022]
Abstract
We evaluated interactions of SNP-by-ACE-I/ARB and SNP-by-TD on serum potassium (K+) among users of antihypertensive treatments (anti-HTN). Our study included seven European-ancestry (EA) (N = 4835) and four African-ancestry (AA) cohorts (N = 2016). We performed race-stratified, fixed-effect, inverse-variance-weighted meta-analyses of 2.5 million SNP-by-drug interaction estimates; race-combined meta-analysis; and trans-ethnic fine-mapping. Among EAs, we identified 11 significant SNPs (P < 5 × 10-8) for SNP-ACE-I/ARB interactions on serum K+ that were located between NR2F1-AS1 and ARRDC3-AS1 on chromosome 5 (top SNP rs6878413 P = 1.7 × 10-8; ratio of serum K+ in ACE-I/ARB exposed compared to unexposed is 1.0476, 1.0280, 1.0088 for the TT, AT, and AA genotypes, respectively). Trans-ethnic fine mapping identified the same group of SNPs on chromosome 5 as genome-wide significant for the ACE-I/ARB analysis. In conclusion, SNP-by-ACE-I /ARB interaction analyses uncovered loci that, if replicated, could have future implications for the prevention of arrhythmias due to anti-HTN treatment-related hyperkalemia. Before these loci can be identified as clinically relevant, future validation studies of equal or greater size in comparison to our discovery effort are needed.
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Affiliation(s)
| | | | - Raymond Noordam
- Department of Epidemiology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Christie L Avery
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Joshua C Bis
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - James S Floyd
- Departments of Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | - Jin Li
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Nita A Limdi
- Department of Neurology, University of Alabama, Birmingham, AL, USA
| | | | - James Stewart
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, USA
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology and Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Leonard Lipovich
- Department of Neurology, Wayne State University, Detroit, MI, USA
| | - Erica L Kleinbrink
- Center Molecular Medicine/Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Albert Smith
- Icelandic Heart Association, Kopavogur, Iceland, University of Iceland, Reykjavik, Iceland
| | - Traci M Bartz
- Departments of Biostatistics and Medicine, University of Washington, Seattle, WA, USA
| | - Eric A Whitsel
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, USA
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Kerri L Wiggins
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Degui Zhi
- School of Biomedical Informatics, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
- Inspectorate of Health Care, Utrecht, The Netherlands
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences and Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, Health Services, University of Washington, Seattle, WA, USA
- Group Health Research Institute, Group Health Cooperatives, Seattle, WA, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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Tam V, Turcotte M, Meyre D. Established and emerging strategies to crack the genetic code of obesity. Obes Rev 2019; 20:212-240. [PMID: 30353704 DOI: 10.1111/obr.12770] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 12/11/2022]
Abstract
Tremendous progress has been made in the genetic elucidation of obesity over the past two decades, driven largely by technological, methodological and organizational innovations. Current strategies for identifying obesity-predisposing loci/genes, including cytogenetics, linkage analysis, homozygosity mapping, admixture mapping, candidate gene studies, genome-wide association studies, custom genotyping arrays, whole-exome sequencing and targeted exome sequencing, have achieved differing levels of success, and the identified loci in aggregate explain only a modest fraction of the estimated heritability of obesity. This review outlines the successes and limitations of these approaches and proposes novel strategies, including the use of exceptionally large sample sizes, the study of diverse ethnic groups and deep phenotypes and the application of innovative methods and study designs, to identify the remaining obesity-predisposing genes. The use of both established and emerging strategies has the potential to crack the genetic code of obesity in the not-too-distant future. The resulting knowledge is likely to yield improvements in obesity prediction, prevention and care.
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Affiliation(s)
- V Tam
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - M Turcotte
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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HONG MINWOOK, CHOI SOYOUNG, SINGH NARESHKUMAR, KIM HUN, YANG SONGYI, KWAK KYEONGROK, KIM JONGBOK, LEE SUNGJIN. Genome-wide association analysis to identify QTL for carcass traits in Hanwoo (Korean native cattle). THE INDIAN JOURNAL OF ANIMAL SCIENCES 2019. [DOI: 10.56093/ijans.v89i1.86384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A genome-wide association study (GWAS) was performed to investigate the genetic markers associated with carcass traits of Hanwoo (Bos taurus coreanae) steer in the Gangwon region of Korea. Hanwoo steer (139) from the Gangwon region were genotyped with Bovine SNP50K BeadChip, and 35,769 SNPs were analyzed for five specific carcass traits after applying several filters. A total of seven quantitative trait loci were detected, of which four, one, and 2 SNPs were detected on various B. taurus autosomal chromosomes (BTA) by the respective model. The four significant SNPs associated with backfat thickness were ARS-BFGL-NGS–41475 on BTA 5, ARS-BFGLNGS- 36359 on BTA 19, ARS-BFGL-NGS-56813 on BTA 22, and Hapmap25048-BTA-138242 on BTA 25. Among the detected SNPs, one and two SNPs were associated with marbling score (ARS-BFGL-NGS-110066 on BTA 23) and meat colour (BTB-01920239 on BTA 15 and ARS-BFGL-NGS-24934 on BTA 18). In this GWAS, we identified three positional candidate genes for carcass traits, backfat thickness (Fibulin-2, FBLN2; Sorting nexin 29, SNX29) and meat colour (WW domain containing oxidoreductase, WWOX). Our results suggest that the candidate SNP markers do affect the genomic selection of associated carcass traits for Hanwoo in the Gangwon region.
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Rask-Andersen M, Karlsson T, Ek WE, Johansson Å. Genome-wide association study of body fat distribution identifies adiposity loci and sex-specific genetic effects. Nat Commun 2019; 10:339. [PMID: 30664634 PMCID: PMC6341104 DOI: 10.1038/s41467-018-08000-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/11/2018] [Indexed: 12/12/2022] Open
Abstract
Body mass and body fat composition are of clinical interest due to their links to cardiovascular- and metabolic diseases. Fat stored in the trunk has been suggested to be more pathogenic compared to fat stored in other compartments. In this study, we perform genome-wide association studies (GWAS) for the proportion of body fat distributed to the arms, legs and trunk estimated from segmental bio-electrical impedance analysis (sBIA) for 362,499 individuals from the UK Biobank. 98 independent associations with body fat distribution are identified, 29 that have not previously been associated with anthropometric traits. A high degree of sex-heterogeneity is observed and the effects of 37 associated variants are stronger in females compared to males. Our findings also implicate that body fat distribution in females involves mesenchyme derived tissues and cell types, female endocrine tissues as well as extracellular matrix maintenance and remodeling. Obesity and the distribution of fat within the body are risk factors for cardiometabolic diseases. Here, Rask-Andersen et al. perform GWAS for bio-electrical impedance measurements in UK Biobank participants and identify 29 novel independent loci for fat distribution and a high degree of sex-heterogeneity.
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Affiliation(s)
- Mathias Rask-Andersen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 256, 751 05, Uppsala, Sweden.
| | - Torgny Karlsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 256, 751 05, Uppsala, Sweden
| | - Weronica E Ek
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 256, 751 05, Uppsala, Sweden
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 256, 751 05, Uppsala, Sweden.
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Karpe F, Vasan SK, Humphreys SM, Miller J, Cheeseman J, Dennis AL, Neville MJ. Cohort Profile: The Oxford Biobank. Int J Epidemiol 2019; 47:21-21g. [PMID: 29040543 PMCID: PMC5837504 DOI: 10.1093/ije/dyx132] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2017] [Indexed: 11/18/2022] Open
Affiliation(s)
- Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford.,Oxford National Institute for Health Research, Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Senthil K Vasan
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford
| | - Sandy M Humphreys
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford.,Oxford National Institute for Health Research, Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - John Miller
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford.,Oxford National Institute for Health Research, Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Jane Cheeseman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford.,Oxford National Institute for Health Research, Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - A Louise Dennis
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford.,Oxford National Institute for Health Research, Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Matt J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford.,Oxford National Institute for Health Research, Biomedical Research Centre, Churchill Hospital, Oxford, UK
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Aldehyde Dehydrogenases Genetic Polymorphism and Obesity: From Genomics to Behavior and Health. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1193:135-154. [PMID: 31368102 DOI: 10.1007/978-981-13-6260-6_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Obesity is multifactorial and complex. Remarkable progress has been made recently in search for polygenic obesity through genome-wide association study (GWAS), but biology of polygenic effects on obesity is largely poor. This review summarizes the available evidence and provides an overview of the links between ALDH2 variants and adiposity, which were firstly and mainly derived from studies of polygenic obesity and also indirectly investigated by using cell lines and mice. The genetic association studies have observed consistent associations of ALDH2 variants with obesity-related traits including BMI, waist circumference (WC), waist-to-hip ratio (WHR), and visceral fat accumulation. In consideration of ALDH2 variants with enzyme activity and alcohol consumption behavior in physiological mechanism studies, we proposed a model by which the physiological and behavioral consequences of alcohol consumption serve as an intermediary process between polymorphisms in ALDH2 and obesity.
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Choe EK, Rhee H, Lee S, Shin E, Oh SW, Lee JE, Choi SH. Metabolic Syndrome Prediction Using Machine Learning Models with Genetic and Clinical Information from a Nonobese Healthy Population. Genomics Inform 2018; 16:e31. [PMID: 30602092 PMCID: PMC6440667 DOI: 10.5808/gi.2018.16.4.e31] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023] Open
Abstract
The prevalence of metabolic syndrome (MS) in the nonobese population is not low. However, the identification and risk mitigation of MS are not easy in this population. We aimed to develop an MS prediction model using genetic and clinical factors of nonobese Koreans through machine learning methods. A prediction model for MS was designed for a nonobese population using clinical and genetic polymorphism information with five machine learning algorithms, including naïve Bayes classification (NB). The analysis was performed in two stages (training and test sets). Model A was designed with only clinical information (age, sex, body mass index, smoking status, alcohol consumption status, and exercise status), and for model B, genetic information (for 10 polymorphisms) was added to model A. Of the 7,502 nonobese participants, 647 (8.6%) had MS. In the test set analysis, for the maximum sensitivity criterion, NB showed the highest sensitivity: 0.38 for model A and 0.42 for model B. The specificity of NB was 0.79 for model A and 0.80 for model B. In a comparison of the performances of models A and B by NB, model B (area under the receiver operating characteristic curve [AUC] = 0.69, clinical and genetic information input) showed better performance than model A (AUC = 0.65, clinical information only input). We designed a prediction model for MS in a nonobese population using clinical and genetic information. With this model, we might convince nonobese MS individuals to undergo health checks and adopt behaviors associated with a preventive lifestyle.
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Affiliation(s)
- Eun Kyung Choe
- Department of Surgery, Seoul National University Hospital, Healthcare System Gangnam Center, Seoul 06236, Korea
| | | | | | | | - Seung-Won Oh
- Department of Family Medicine, Seoul National University Hospital, Healthcare System Gangnam Center, Seoul 06236, Korea
| | | | - Seung Ho Choi
- Department of Internal Medicine, Seoul National University Hospital, Healthcare System Gangnam Center, Seoul 06236, Korea
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69
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Coletta AM, Sanchez B, O'Connor A, Dalton R, Springer S, Koozehchian MS, Murano PS, Woodman CR, Rasmussen C, Kreider RB. Alignment of diet prescription to genotype does not promote greater weight loss success in women with obesity participating in an exercise and weight loss program. Obes Sci Pract 2018; 4:554-574. [PMID: 30574349 PMCID: PMC6298313 DOI: 10.1002/osp4.305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/03/2018] [Accepted: 10/11/2018] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE Genetics contribute to variability in individual response to weight-loss interventions. The objective of this study was to determine the efficacy of a commercially available exercise and weight-loss program and whether alignment of diet to genotype related to lipid metabolism promotes greater success. DESIGN Sedentary women with obesity (n = 63) had genotype (FABP2rs1799883, PPARG2rs1801282, ADRB3rs4994C3, ADRB2rs1042713, rs1042714) determined using a direct-to-consumer genetic screening kit purported to promote greater weight-loss success through dietary recommendations based on these genes. Participants were randomly assigned to follow a moderate carbohydrate (MC) or lower carbohydrate (LC) hypo-energetic diet that aligned (A) or did not align (NA) with genotype for 24 weeks while participating in a resistance training and walking program. Data were analysed by general linear model repeated measures adjusted for baseline variables and are presented as mean (95% confidence interval) changes from baseline. RESULTS Participants in the LC group experienced greater improvements (p = 0.051, ηp 2 = 0.025) in per cent changes in body composition (weight: MC -3.32 [-1.4, -5.2], LC -5.82 [-4.1, -7.6]; fat mass: MC -7.25 [-3.2, -11.2], LC -10.93 [-7.3, -14.5]; fat-free mass: MC -0.32 [1.4, -2.0], LC -1.48 [0.7, -3.0]; and body fat percentage: MC -4.19 [-1.6, -6.8], LC -5.60 [-3.3, -7.9] %). No significant differences were observed between genotype groups (weight: A -5.00 [-3.3, -6.7], NA -4.14 [-2.2, -6.1]; fat mass: A -10.15 [-7.0, -13.6], NA -8.02 [-4.0, -12.0]; fat-free mass: A -1.23 [0.3, -2.8], NA -0.56 [1.12, -2.3]; and body fat: A -5.28 [-3.0, -7.6], NA -4.51 [-1.9, -7.1] %). CONCLUSIONS Adherence to this exercise and weight-loss program promoted improvements in body composition and health outcomes. While individuals following the LC diet experienced greater benefits, alignment of these diets to this genetic profile did not promote greater health outcomes.
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Affiliation(s)
- A. M. Coletta
- Exercise and Sport Nutrition Laboratory, Human Clinical Research Facility, Department of Health and KinesiologyTexas A&M UniversityCollege StationTXUSA
- Cancer Control and Population Sciences ProgramHuntsman Cancer InstituteSalt Lake CityUTUSA
- Department of Health, Kinesiology, and RecreationThe University of UtahSalt Lake CityUTUSA
| | - B. Sanchez
- Exercise and Sport Nutrition Laboratory, Human Clinical Research Facility, Department of Health and KinesiologyTexas A&M UniversityCollege StationTXUSA
| | - A. O'Connor
- Exercise and Sport Nutrition Laboratory, Human Clinical Research Facility, Department of Health and KinesiologyTexas A&M UniversityCollege StationTXUSA
| | - R. Dalton
- Exercise and Sport Nutrition Laboratory, Human Clinical Research Facility, Department of Health and KinesiologyTexas A&M UniversityCollege StationTXUSA
| | - S. Springer
- Exercise and Sport Nutrition Laboratory, Human Clinical Research Facility, Department of Health and KinesiologyTexas A&M UniversityCollege StationTXUSA
| | - M. S. Koozehchian
- Exercise and Sport Nutrition Laboratory, Human Clinical Research Facility, Department of Health and KinesiologyTexas A&M UniversityCollege StationTXUSA
| | - P. S. Murano
- Institute for Obesity Research and Program Evaluation, Department of Nutrition and Food ScienceTexas A&M UniversityCollege StationTXUSA
| | - C. R. Woodman
- Vascular Biology Laboratory, Department of Health and KinesiologyTexas A&M UniversityCollege StationTXUSA
| | - C. Rasmussen
- Exercise and Sport Nutrition Laboratory, Human Clinical Research Facility, Department of Health and KinesiologyTexas A&M UniversityCollege StationTXUSA
| | - R. B. Kreider
- Exercise and Sport Nutrition Laboratory, Human Clinical Research Facility, Department of Health and KinesiologyTexas A&M UniversityCollege StationTXUSA
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70
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Hughes MF, Lenighan YM, Godson C, Roche HM. Exploring Coronary Artery Disease GWAs Targets With Functional Links to Immunometabolism. Front Cardiovasc Med 2018; 5:148. [PMID: 30460244 PMCID: PMC6232936 DOI: 10.3389/fcvm.2018.00148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/01/2018] [Indexed: 12/24/2022] Open
Abstract
Finding genetic variants that cause functional disruption or regulatory change among the many implicated GWAs variants remains a key challenge to translating the findings from GWAs to therapeutic treatments. Defining the causal mechanisms behind the variants require functional screening experiments that can be complex and costly. Prioritizing variants for functional characterization using techniques that capture important functional and regulatory elements can assist this. The genetic architecture of complex traits such as cardiovascular disease and type II diabetes comprise an enormously large number of variants of small effect contributing to heritability and spread throughout the genome. This makes it difficult to distinguish which variants or core genes are most relevant for prioritization and how they contribute to the regulatory networks that become dysregulated leading to disease. Despite these challenges, recent GWAs for CAD prioritized genes associated with lipid metabolism, coagulation and adhesion along with novel signals related to innate immunity, adipose tissue and, vascular function as important core drivers of risk. We focus on three examples of novel signals associated with CAD which affect risk through missense or UTR mutations indicating their potential for therapeutic modification. These variants play roles in adipose tissue function vascular function and innate immunity which form the cornerstones of immuno-metabolism. In addition we have explored the putative, but potentially important interactions between the environment, specifically food and nutrition, with respect to key processes.
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Affiliation(s)
- Maria F Hughes
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,Nutrigenomics Research Group, UCD Institute of Food and Health, School of Public Health Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,Centre of Excellence for Public Health, Queen's University Belfast, Belfast, United Kingdom.,UCD Institute of Food and Health, School of Public Health Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Yvonne M Lenighan
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,UCD Institute of Food and Health, School of Public Health Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Catherine Godson
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland
| | - Helen M Roche
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,Nutrigenomics Research Group, UCD Institute of Food and Health, School of Public Health Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Institute of Food and Health, School of Public Health Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
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Abstract
Obesity prevalence continues to rise worldwide, posing a substantial burden on people's health. However, up to 45% of obese individuals do not suffer from cardiometabolic complications, also called the metabolically healthy obese (MHO). Concurrently, up to 30% of normal-weight individuals demonstrate cardiometabolic risk factors that are generally observed in obese individuals, the metabolically obese normal weight (MONW). Besides lifestyle, environmental factors and demographic factors, innate biological mechanisms are known to contribute to the aetiology of the MHO and MONW phenotypes, as well. Experimental studies in animal models have shown that adipose tissue expandability, fat distribution, adipogenesis, adipose tissue vascularization, inflammation and fibrosis, and mitochondrial function are the main mechanisms that uncouple adiposity from its cardiometabolic comorbidities. We reviewed current genetic association studies to expand insights into the biology of MHO/MONW phenotypes. At least four genetic loci were identified through genome-wide association studies for body fat percentage (BF%) of which the BF%-increasing allele was associated with a protective effect on glycemic and lipid outcomes. For some, this association was mediated through favourable effects on body fat distribution. Other studies that characterized the genetic susceptibility of insulin resistance found that a higher susceptibility was associated with lower overall adiposity due to less fat accumulation at hips and legs, suggesting that an impaired capacity to store fat subcutaneously or a preferential storage in the intra-abdominal cavity may be metabolically harmful. Clearly, more work remains to be done in this field, first through gene discovery and subsequently through functional follow-up of identified genes.
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Affiliation(s)
- R J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Copenhagen, Denmark
| | - T O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Umano GR, Shabanova V, Pierpont B, Mata M, Nouws J, Tricò D, Galderisi A, Santoro N, Caprio S. A low visceral fat proportion, independent of total body fat mass, protects obese adolescent girls against fatty liver and glucose dysregulation: a longitudinal study. Int J Obes (Lond) 2018; 43:673-682. [PMID: 30337653 DOI: 10.1038/s41366-018-0227-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 08/13/2018] [Accepted: 08/29/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND The relative proportion of visceral fat (VAT) to subcutaneous fat (SAT) has been described as a major determinant of insulin resistance (IR). Our study sought to evaluate the effect of body fat distribution on glucose metabolism and intrahepatic fat content over time in a multiethnic cohort of obese adolescents. SUBJECTS/METHODS We examined markers of glucose metabolism by oral glucose tolerance test, and body fat distribution by abdominal MRI at baseline and after 19.2 ± 11.4 months in a cohort of 151 obese adolescents (88 girls, 63 boys; mean age 13.3 ± 3.4 years; mean BMI z-score 2.15 ± 0.70). Hepatic fat content was assessed by fast-gradient MRI in a subset of 93 subjects. We used the median value of VAT/(VAT + SAT) ratio within each gender at baseline to stratify our sample into high and low ratio groups (median value 0.0972 in girls and 0.118 in boys). RESULTS Female subjects tended to remain in their VAT/(VAT + SAT) category over time (change over follow-up P = 0.14 among girls, and P = 0.04 among boys). Baseline VAT/(VAT + SAT) strongly predicted the hepatic fat content, fasting insulin, 2-h glucose, and whole-body insulin sensitivity index at follow-up among girls, but not in boys. CONCLUSIONS The VAT/(VAT + SAT) ratio is a major determinant of impaired glucose metabolism and hepatic fat accumulation over time, and its effects are more pronounced in girls than in boys.
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Affiliation(s)
- Giuseppina R Umano
- Department of Pediatrics, Division of Pediatric Endocrinology, Yale University School of Medicine, New Haven, CT, 06520, USA.,Department of the Woman, the Child, of General and Specialized Surgery, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Veronika Shabanova
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Bridget Pierpont
- Department of Pediatrics, Division of Pediatric Endocrinology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Mariana Mata
- Department of Pediatrics, Division of Pediatric Endocrinology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Jessica Nouws
- Department of Pediatrics, Division of Pediatric Endocrinology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Domenico Tricò
- Department of Internal Medicine, Section of Endocrinology, Yale University School of Medicine, New Haven, CT, 06520, USA.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Alfonso Galderisi
- Department of Pediatrics, Division of Pediatric Endocrinology, Yale University School of Medicine, New Haven, CT, 06520, USA.,Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Nicola Santoro
- Department of Pediatrics, Division of Pediatric Endocrinology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Sonia Caprio
- Department of Pediatrics, Division of Pediatric Endocrinology, Yale University School of Medicine, New Haven, CT, 06520, USA.
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Renner S, Blutke A, Dobenecker B, Dhom G, Müller TD, Finan B, Clemmensen C, Bernau M, Novak I, Rathkolb B, Senf S, Zöls S, Roth M, Götz A, Hofmann SM, Hrabĕ de Angelis M, Wanke R, Kienzle E, Scholz AM, DiMarchi R, Ritzmann M, Tschöp MH, Wolf E. Metabolic syndrome and extensive adipose tissue inflammation in morbidly obese Göttingen minipigs. Mol Metab 2018; 16:180-190. [PMID: 30017782 PMCID: PMC6157610 DOI: 10.1016/j.molmet.2018.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 06/16/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE The worldwide prevalence of obesity has increased to 10% in men and 15% in women and is associated with severe comorbidities such as diabetes, cancer, and cardiovascular disease. Animal models of obesity are central to experimental studies of disease mechanisms and therapeutic strategies. Diet-induced obesity (DIO) models in rodents have provided important insights into the pathophysiology of obesity and, in most instances, are the first in line for exploratory pharmacology studies. To deepen the relevance towards translation to human patients, we established a corresponding DIO model in Göttingen minipigs (GM). METHODS Young adult female ovariectomized GM were fed a high-fat/high-energy diet for a period of 70 weeks. The ration was calculated to meet the requirements and maintain body weight (BW) of lean adult minipigs (L-GM group) or increased stepwise to achieve an obese state (DIO-GM group). Body composition, blood parameters and intravenous glucose tolerance were determined at regular intervals. A pilot chronic treatment trial with a GLP1 receptor agonist was conducted in DIO-GM. At the end of the study, the animals were necropsied and a biobank of selected tissues was established. RESULTS DIO-GM developed severe subcutaneous and visceral adiposity (body fat >50% of body mass vs. 22% in L-GM), increased plasma cholesterol, triglyceride, and free fatty acid levels, insulin resistance (HOMA-IR >5 vs. 2 in L-GM), impaired glucose tolerance and increased heart rate when resting and active. However, fasting glucose concentrations stayed within normal range throughout the study. Treatment with a long-acting GLP1 receptor agonist revealed substantial reduction of food intake and body weight within four weeks, with increased drug sensitivity relative to observations in other DIO animal models. Extensive adipose tissue inflammation and adipocyte necrosis was observed in visceral, but not subcutaneous, adipose tissue of DIO-GM. CONCLUSIONS The Munich DIO-GM model resembles hallmarks of the human metabolic syndrome with extensive adipose tissue inflammation and adipocyte necrosis reported for the first time. DIO-GM may be used for evaluating novel treatments of obesity and associated comorbidities. They may help to identify triggers and mechanisms of fat tissue inflammation and mechanisms preventing complete metabolic decompensation despite morbid obesity.
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Affiliation(s)
- Simone Renner
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany; Center for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, Hackerstr. 27, 85764, Oberschleißheim, Germany; German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
| | - Andreas Blutke
- Institute of Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, Veterinärstr. 13, 80539, Munich, Germany
| | - Britta Dobenecker
- Chair of Animal Nutrition and Dietetics, Department of Veterinary Sciences, LMU Munich, Schönleutnerstr. 8, 85764, Oberschleißheim, Germany
| | - Georg Dhom
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany; Center for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, Hackerstr. 27, 85764, Oberschleißheim, Germany
| | - Timo D Müller
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Division of Metabolic Diseases, Department of Medicine, Technische Universität, Ismaninger Str. 22, 81675, Munich, Germany
| | - Brian Finan
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Division of Metabolic Diseases, Department of Medicine, Technische Universität, Ismaninger Str. 22, 81675, Munich, Germany
| | - Christoffer Clemmensen
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Division of Metabolic Diseases, Department of Medicine, Technische Universität, Ismaninger Str. 22, 81675, Munich, Germany
| | - Maren Bernau
- Livestock Center of the Veterinary Faculty, LMU Munich, St.-Hubertus-Str. 12, 85764, Oberschleißheim, Germany
| | - Istvan Novak
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany; Center for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, Hackerstr. 27, 85764, Oberschleißheim, Germany
| | - Birgit Rathkolb
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany; Center for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, Hackerstr. 27, 85764, Oberschleißheim, Germany; German Mouse Clinic (GMC), Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Steffanie Senf
- Clinic for Swine, Center for Clinical Veterinary Medicine, LMU Munich, Sonnenstr. 16, 85764, Oberschleißheim, Germany
| | - Susanne Zöls
- Clinic for Swine, Center for Clinical Veterinary Medicine, LMU Munich, Sonnenstr. 16, 85764, Oberschleißheim, Germany
| | - Mirjam Roth
- Animal aspects, 88400, Biberach an der Riss, Germany
| | - Anna Götz
- Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Department of Internal Medicine I, University Hospital RWTH Aachen, Pauwelstr. 30, 52074, Aachen, Germany
| | - Susanna M Hofmann
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Institute of Diabetes and Regeneration Research (IDR), Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Medizinische Klinik und Poliklinik IV, Klinikum der LMU, Ziemssenstr, 180336, Munich, Germany
| | - Martin Hrabĕ de Angelis
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; German Mouse Clinic (GMC), Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Genome Analysis Center (GAC), Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health and Chair of Experimental Genetics, Technische Universität, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Rüdiger Wanke
- Institute of Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, Veterinärstr. 13, 80539, Munich, Germany
| | - Ellen Kienzle
- Chair of Animal Nutrition and Dietetics, Department of Veterinary Sciences, LMU Munich, Schönleutnerstr. 8, 85764, Oberschleißheim, Germany
| | - Armin M Scholz
- Livestock Center of the Veterinary Faculty, LMU Munich, St.-Hubertus-Str. 12, 85764, Oberschleißheim, Germany
| | - Richard DiMarchi
- Novo Nordisk Research Center Indianapolis, 5225 Exploration Drive, Indianapolis, IN, 46241, USA; Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN, 47405-7102, USA
| | - Mathias Ritzmann
- Clinic for Swine, Center for Clinical Veterinary Medicine, LMU Munich, Sonnenstr. 16, 85764, Oberschleißheim, Germany
| | - Matthias H Tschöp
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Institute for Diabetes and Obesity (IDO), Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Division of Metabolic Diseases, Department of Medicine, Technische Universität, Ismaninger Str. 22, 81675, Munich, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany; Center for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, Hackerstr. 27, 85764, Oberschleißheim, Germany; German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany; Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany
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Wang L, Perez J, Heard-Costa N, Chu AY, Joehanes R, Munson PJ, Levy D, Fox CS, Cupples LA, Liu CT. Integrating genetic, transcriptional, and biological information provides insights into obesity. Int J Obes (Lond) 2018; 43:457-467. [PMID: 30232418 PMCID: PMC6405310 DOI: 10.1038/s41366-018-0190-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 07/18/2018] [Accepted: 07/22/2018] [Indexed: 02/07/2023]
Abstract
Objective: Indices of body fat distribution are heritable, but few genetic signals have been reported from genome-wide association studies (GWAS) of computed tomography (CT) imaging measurements of body fat distribution. We aimed to identify genes associated with adiposity traits and the key drivers that are central to adipose regulatory networks. Subjects: We analyzed gene transcript expression data in blood from participants in the Framingham Heart Study, a large community-based cohort (n up to 4,303), as well as implemented an integrative analysis of these data and existing biological information. Results: Our association analyses identified unique and common gene expression signatures across several adiposity traits, including body mass index, waist-hip ratio, waist circumference, and CT-measured indices, including volume and quality of visceral and subcutaneous adipose tissues. We identified six enriched KEGG pathways and two co-expression modules for further exploration of adipose regulatory networks. The integrative analysis revealed four gene sets (Apoptosis, p53 signaling pathway, Proteasome, Ubiquitin mediated proteolysis) and two co-expression modules with significant genetic variants and 94 key drivers/genes whose local networks were enriched with adiposity-associated genes, suggesting that these enriched pathways or modules have genetic effects on adiposity. Most identified key driver genes are involved in essential biological processes such as controlling cell cycle, DNA repair and degradation of regulatory proteins and are cancer related. Conclusion: Our integrative analysis of genetic, transcriptional and biological information provides a list of compelling candidates for further follow-up functional studies to uncover the biological mechanisms underlying obesity. These candidates highlight the value of examining CT-derived and central adiposity traits.
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Affiliation(s)
- Lan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Jeremiah Perez
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | | | - Audrey Y Chu
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,The Framingham Heart Study, Framingham, MA, 01702, USA
| | - Roby Joehanes
- Hebrew SeniorLife, Harvard Medical School, Boston, MA, 02131, USA
| | - Peter J Munson
- Mathematical and Statistical Computing Laboratory, Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,The Framingham Heart Study, Framingham, MA, 01702, USA
| | - Caroline S Fox
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,The Framingham Heart Study, Framingham, MA, 01702, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA.,The Framingham Heart Study, Framingham, MA, 01702, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA.
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Strawbridge RJ, Ward J, Lyall LM, Tunbridge EM, Cullen B, Graham N, Ferguson A, Johnston KJA, Lyall DM, Mackay D, Cavanagh J, Howard DM, Adams MJ, Deary I, Escott-Price V, O'Donovan M, McIntosh AM, Bailey MES, Pell JP, Harrison PJ, Smith DJ. Genetics of self-reported risk-taking behaviour, trans-ethnic consistency and relevance to brain gene expression. Transl Psychiatry 2018; 8:178. [PMID: 30181555 PMCID: PMC6123450 DOI: 10.1038/s41398-018-0236-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/05/2018] [Indexed: 12/25/2022] Open
Abstract
Risk-taking behaviour is an important component of several psychiatric disorders, including attention-deficit hyperactivity disorder, schizophrenia and bipolar disorder. Previously, two genetic loci have been associated with self-reported risk taking and significant genetic overlap with psychiatric disorders was identified within a subsample of UK Biobank. Using the white British participants of the full UK Biobank cohort (n = 83,677 risk takers versus 244,662 controls) for our primary analysis, we conducted a genome-wide association study of self-reported risk-taking behaviour. In secondary analyses, we assessed sex-specific effects, trans-ethnic heterogeneity and genetic overlap with psychiatric traits. We also investigated the impact of risk-taking-associated SNPs on both gene expression and structural brain imaging. We identified 10 independent loci for risk-taking behaviour, of which eight were novel and two replicated previous findings. In addition, we found two further sex-specific risk-taking loci. There were strong positive genetic correlations between risk-taking and attention-deficit hyperactivity disorder, bipolar disorder and schizophrenia. Index genetic variants demonstrated effects generally consistent with the discovery analysis in individuals of non-British White, South Asian, African-Caribbean or mixed ethnicity. Polygenic risk scores comprising alleles associated with increased risk taking were associated with lower white matter integrity. Genotype-specific expression pattern analyses highlighted DPYSL5, CGREF1 and C15orf59 as plausible candidate genes. Overall, our findings substantially advance our understanding of the biology of risk-taking behaviour, including the possibility of sex-specific contributions, and reveal consistency across ethnicities. We further highlight several putative novel candidate genes, which may mediate these genetic effects.
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Affiliation(s)
- Rona J Strawbridge
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK.
- Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden.
| | - Joey Ward
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Laura M Lyall
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Elizabeth M Tunbridge
- Department of Psychiatry, University of Oxford, Oxford, UK
- Oxford Health NHS Foundation Trust, Oxford, UK
| | - Breda Cullen
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Nicholas Graham
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Amy Ferguson
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Keira J A Johnston
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Division of Psychiatry, College of Medicine, University of Edinburgh, Edinburgh, UK
| | - Donald M Lyall
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Daniel Mackay
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Jonathan Cavanagh
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - David M Howard
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF, UK
| | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF, UK
| | - Ian Deary
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9YL, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9YL, UK
| | | | - Michael O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF, UK
| | - Mark E S Bailey
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jill P Pell
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Paul J Harrison
- Department of Psychiatry, University of Oxford, Oxford, UK
- Oxford Health NHS Foundation Trust, Oxford, UK
| | - Daniel J Smith
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
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76
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Frank AP, de Souza Santos R, Palmer BF, Clegg DJ. Determinants of body fat distribution in humans may provide insight about obesity-related health risks. J Lipid Res 2018; 60:1710-1719. [PMID: 30097511 DOI: 10.1194/jlr.r086975] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/07/2018] [Indexed: 12/24/2022] Open
Abstract
Obesity increases the risks of developing cardiovascular and metabolic diseases and degrades quality of life, ultimately increasing the risk of death. However, not all forms of obesity are equally dangerous: some individuals, despite higher percentages of body fat, are at less risk for certain chronic obesity-related complications. Many open questions remain about why this occurs. Data suggest that the physical location of fat and the overall health of fat dramatically influence disease risk; for example, higher concentrations of visceral relative to subcutaneous adipose tissue are associated with greater metabolic risks. As such, understanding the determinants of the location and health of adipose tissue can provide insight about the pathological consequences of obesity and can begin to outline targets for novel therapeutic approaches to combat the obesity epidemic. Although age and sex hormones clearly play roles in fat distribution and location, much remains unknown about gene regulation at the level of adipose tissue or how genetic variants regulate fat distribution. In this review, we discuss what is known about the determinants of body fat distribution, and we highlight the important roles of sex hormones, aging, and genetic variation in the determination of body fat distribution and its contribution to obesity-related comorbidities.
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Affiliation(s)
- Aaron P Frank
- Diabetes, Obesity, and Wellness Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Roberta de Souza Santos
- Diabetes, Obesity, and Wellness Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Biff F Palmer
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Deborah J Clegg
- Diabetes, Obesity, and Wellness Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
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AMPK activation negatively regulates GDAP1, which influences metabolic processes and circadian gene expression in skeletal muscle. Mol Metab 2018; 16:12-23. [PMID: 30093355 PMCID: PMC6157647 DOI: 10.1016/j.molmet.2018.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/26/2018] [Accepted: 07/01/2018] [Indexed: 12/31/2022] Open
Abstract
Objective We sought to identify AMPK-regulated genes via bioinformatic analysis of microarray data generated from skeletal muscle of animal models with genetically altered AMPK activity. We hypothesized that such genes would play a role in metabolism. Ganglioside-induced differentiation-associated protein 1 (GDAP1), a gene which plays a role in mitochondrial fission and peroxisomal function in neuronal cells but whose function in skeletal muscle is undescribed, was identified and further validated. AMPK activation reduced GDAP1 expression in skeletal muscle. GDAP1 expression was elevated in skeletal muscle from type 2 diabetic patients but decreased after acute exercise. Methods The metabolic impact of GDAP1 silencing was determined in primary skeletal muscle cells via siRNA-transfections. Confocal microscopy was used to visualize whether silencing GDAP1 impacted mitochondrial network morphology and membrane potential. Results GDAP1 silencing increased mitochondrial protein abundance, decreased palmitate oxidation, and decreased non-mitochondrial respiration. Mitochondrial morphology was unaltered by GDAP1 silencing. GDAP1 silencing and treatment of cells with AMPK agonists altered several genes in the core molecular clock machinery. Conclusion We describe a role for GDAP1 in regulating mitochondrial proteins, circadian genes, and metabolic flux in skeletal muscle. Collectively, our results implicate GDAP1 in the circadian control of metabolism. Transcriptomic studies reveal GDAP1 mRNA is inversely associated with AMPK activity. GDAP1 silencing increases mitochondrial protein abundance in skeletal muscle. GDAP1 silencing influences expression of core molecular clock machinery. GDAP1 is a AMPK target involved in metabolism and circadian gene expression.
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78
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Berry A, Bucci M, Raggi C, Eriksson JG, Guzzardi MA, Nuutila P, Huovinen V, Iozzo P, Cirulli F. Dynamic changes in p66Shc mRNA expression in peripheral blood mononuclear cells following resistance training intervention in old frail women born to obese mothers: a pilot study. Aging Clin Exp Res 2018; 30:871-876. [PMID: 28952131 DOI: 10.1007/s40520-017-0834-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/14/2017] [Indexed: 01/28/2023]
Abstract
The p66Shc gerontogene may affect healthspan by promoting fat accumulation. We assessed changes of p66Shc-mRNA in peripheral tissues in relation to maternal obesity and the moderating effects of resistance-training (RT) exercise in elderly frail women. Thirty-seven women participated in a 4-month RT program. Twenty were offspring of lean/normal weight mothers and 17 were offspring of overweight/obese mothers (OOM). P66Shc was assessed in peripheral blood mononuclear cells (PBMC) and in subcutaneous adipose tissue (SAT) before and after RT. Overall, OOM showed elevated p66Shc mRNA levels in the PBMC. Independently from maternal obesity, following RT there was a decrease in p66Shc expression in PBMC but not in SAT, particularly in subjects with a high body mass index. Results suggest that maternal obesity has long-term effects on the expression of genes involved in mitochondrial function and fat deposition and that RT modifies p66Shc expression in PBMC with greater effects in obese subjects.ClinicalTrials.gov ID: NCT01931540.
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Affiliation(s)
- Alessandra Berry
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy.
| | - Marco Bucci
- Turku PET Centre, University of Turku, Turku, Finland
| | - Carla Raggi
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Johan G Eriksson
- Department of Chronic Disease Prevention, National Institute of Health and Welfare, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Pirjo Nuutila
- Turku PET Centre, University of Turku, Turku, Finland
- Department of Endocrinology, Turku University Hospital, Turku, Finland
| | - Ville Huovinen
- Turku PET Centre, University of Turku, Turku, Finland
- Department of Radiology, University of Turku, Turku, Finland
- Department of Radiology, Turku University Hospital, Turku, Finland
| | - Patricia Iozzo
- Institute of Clinical Physiology, National Research Council, Pisa, Italy
| | - Francesca Cirulli
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
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Dong SS, Zhang YJ, Chen YX, Yao S, Hao RH, Rong Y, Niu HM, Chen JB, Guo Y, Yang TL. Comprehensive review and annotation of susceptibility SNPs associated with obesity-related traits. Obes Rev 2018. [PMID: 29527783 DOI: 10.1111/obr.12677] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We aimed to summarize the results of genetic association studies for obesity and provide a comprehensive annotation of all susceptibility single nucleotide polymorphisms (SNPs). A total of 72 studies were summarized, resulting in 90,361 susceptibility SNPs (738 index SNPs and 89,623 linkage disequilibrium SNPs). Over 90% of the susceptibility SNPs are located in non-coding regions, and it is challenging to understand their functional significance. Therefore, we annotated these SNPs by using various functional databases. We identified 24,623 functional SNPs, including 4 nonsense SNPs, 479 missense SNPs, 399 untranslated region SNPs which might affect microRNA binding, 262 promoter and 5,492 enhancer SNPs which might affect transcription factor binding, 7 splicing sites, 76 SNPs which might affect gene methylation levels, 1,839 SNPs under natural selection and 17,351 SNPs which might modify histone binding. Expression quantitative trait loci analyses for functional SNPs identified 98 target genes, including 69 protein coding genes, 27 long non-coding RNAs and 3 processed transcripts. The percentage of protein coding genes that could be correlated with obesity-related pathways directly or through gene-gene interaction is 75.36 (52/69). Our results may serve as an encyclopaedia of obesity susceptibility SNPs and offer guide for functional experiments.
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Affiliation(s)
- S-S Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Y-J Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Y-X Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - S Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - R-H Hao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Y Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - H-M Niu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - J-B Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Y Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - T-L Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
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80
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An Association Mapping Framework To Account for Potential Sex Difference in Genetic Architectures. Genetics 2018; 209:685-698. [PMID: 29752291 DOI: 10.1534/genetics.117.300501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 04/12/2018] [Indexed: 01/29/2023] Open
Abstract
Over the past few years, genome-wide association studies have identified many trait-associated loci that have different effects on females and males, which increased attention to the genetic architecture differences between the sexes. The between-sex differences in genetic architectures can cause a variety of phenomena such as differences in the effect sizes at trait-associated loci, differences in the magnitudes of polygenic background effects, and differences in the phenotypic variances. However, current association testing approaches for dealing with sex, such as including sex as a covariate, cannot fully account for these phenomena and can be suboptimal in statistical power. We present a novel association mapping framework, MetaSex, that can comprehensively account for the genetic architecture differences between the sexes. Through simulations and applications to real data, we show that our framework has superior performance than previous approaches in association mapping.
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81
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Huckins LM, Hatzikotoulas K, Southam L, Thornton LM, Steinberg J, Aguilera-McKay F, Treasure J, Schmidt U, Gunasinghe C, Romero A, Curtis C, Rhodes D, Moens J, Kalsi G, Dempster D, Leung R, Keohane A, Burghardt R, Ehrlich S, Hebebrand J, Hinney A, Ludolph A, Walton E, Deloukas P, Hofman A, Palotie A, Palta P, van Rooij FJA, Stirrups K, Adan R, Boni C, Cone R, Dedoussis G, van Furth E, Gonidakis F, Gorwood P, Hudson J, Kaprio J, Kas M, Keski-Rahonen A, Kiezebrink K, Knudsen GP, Slof-Op 't Landt MCT, Maj M, Monteleone AM, Monteleone P, Raevuori AH, Reichborn-Kjennerud T, Tozzi F, Tsitsika A, van Elburg A, Collier DA, Sullivan PF, Breen G, Bulik CM, Zeggini E. Investigation of common, low-frequency and rare genome-wide variation in anorexia nervosa. Mol Psychiatry 2018; 23:1169-1180. [PMID: 29155802 PMCID: PMC5828108 DOI: 10.1038/mp.2017.88] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 12/12/2022]
Abstract
Anorexia nervosa (AN) is a complex neuropsychiatric disorder presenting with dangerously low body weight, and a deep and persistent fear of gaining weight. To date, only one genome-wide significant locus associated with AN has been identified. We performed an exome-chip based genome-wide association studies (GWAS) in 2158 cases from nine populations of European origin and 15 485 ancestrally matched controls. Unlike previous studies, this GWAS also probed association in low-frequency and rare variants. Sixteen independent variants were taken forward for in silico and de novo replication (11 common and 5 rare). No findings reached genome-wide significance. Two notable common variants were identified: rs10791286, an intronic variant in OPCML (P=9.89 × 10-6), and rs7700147, an intergenic variant (P=2.93 × 10-5). No low-frequency variant associations were identified at genome-wide significance, although the study was well-powered to detect low-frequency variants with large effect sizes, suggesting that there may be no AN loci in this genomic search space with large effect sizes.
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Affiliation(s)
- L M Huckins
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - K Hatzikotoulas
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - L Southam
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - L M Thornton
- Department of Psychiatry and Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J Steinberg
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - F Aguilera-McKay
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - J Treasure
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - U Schmidt
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - C Gunasinghe
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - A Romero
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - C Curtis
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - D Rhodes
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - J Moens
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - G Kalsi
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - D Dempster
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - R Leung
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - A Keohane
- Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC SLaM BioResource for Mental Health, SGDP Centre & Centre for Neuroimaging Sciences, Section of Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - R Burghardt
- Klinik für Kinder- und Jugendpsychiatrie, Psychotherapie und Psychosomatik Klinikum Frankfurt, Frankfurt, Germany
| | - S Ehrlich
- Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine, TU Dresden, Dresden, Germany
- Eating Disorders Research and Treatment Center, Department of Child and Adolescent Psychiatry, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - J Hebebrand
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - A Hinney
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - A Ludolph
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - E Walton
- Division of Psychological & Social Medicine and Developmental Neurosciences, Technische Universität Dresden, Faculty of Medicine, University Hospital C.G. Carus, Dresden, Germany
- Department of Psychology, Georgia State University, Atlanta, GA, USA
| | - P Deloukas
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - A Hofman
- Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A Palotie
- Center for Human Genome Research at the Massachusetts General Hospital, Boston, MA, USA
- Department of Public Health & Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - P Palta
- Department of Public Health & Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - F J A van Rooij
- Erasmus University Medical Center, Rotterdam, The Netherlands
| | - K Stirrups
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - R Adan
- Brain Center Rudolf Magnus, Department of Neuroscience and Pharmacology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C Boni
- INSERM U984, Centre of Psychiatry and Neuroscience, Paris, France
| | - R Cone
- Mary Sue Coleman Director, Life Sciences Institute, Professor of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - G Dedoussis
- Department of Dietetics-Nutrition, Harokopio University, Athens, Greece
| | - E van Furth
- Rivierduinen Eating Disorders Ursula, Leiden, Zuid-Holland, The Netherlands
| | - F Gonidakis
- Eating Disorders Unit, 1st Department of Psychiatry, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - P Gorwood
- INSERM U984, Centre of Psychiatry and Neuroscience, Paris, France
| | - J Hudson
- Department of Psychiatry, McLean Hospital/Harvard Medical School, Belmont, MA, USA
| | - J Kaprio
- Department of Public Health & Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - M Kas
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - A Keski-Rahonen
- Department of Public Health, Clinicum, University of Helsinki, Helsinki, Finland
| | - K Kiezebrink
- Institute of Applied Health Sciences, University of Aberdeen, Aberdeen, UK
| | - G-P Knudsen
- Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | | | - M Maj
- Department of Psychiatry, University of Naples SUN, Naples, Italy
| | - A M Monteleone
- Department of Psychiatry, University of Naples SUN, Naples, Italy
| | - P Monteleone
- Department of Medicine and Surgery, Section of Neurosciences, University of Salerno, Salerno, Italy
| | - A H Raevuori
- Department of Public Health, Clinicum, University of Helsinki, Helsinki, Finland
| | - T Reichborn-Kjennerud
- Department of Genetics, Environment and Mental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - F Tozzi
- eHealth Lab-Computer Science Department, University of Cyprus, Nicosia, Cyprus
| | - 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
| | - A van Elburg
- Center for Eating Disorders Rintveld, University of Utrecht, Utrecht, The Netherlands
| | - D A Collier
- Eli Lilly and Company, Erl Wood Manor, Windlesham, UK
| | - P F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinksa Institutet, Stockholm, Sweden
| | - G Breen
- Social Genetic and Developmental Psychiatry, King's College London, London, UK
| | - C M Bulik
- Department of Psychiatry and Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinksa Institutet, Stockholm, Sweden
| | - E Zeggini
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Rausch JC, Lavine JE, Chalasani N, Guo X, Kwon S, Schwimmer JB, Molleston JP, Loomba R, Brunt EM, da Chen YDI, Goodarzi MO, Taylor KD, Yates KP, Rotter JI. Genetic Variants Associated With Obesity and Insulin Resistance in Hispanic Boys With Nonalcoholic Fatty Liver Disease. J Pediatr Gastroenterol Nutr 2018; 66:789-796. [PMID: 29470286 PMCID: PMC5916321 DOI: 10.1097/mpg.0000000000001926] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND OBJECTIVES Nonalcoholic fatty liver disease (NAFLD) disproportionately affects Hispanic boys. Further, obesity and insulin resistance are major risk factors for NAFLD. No gene localization studies had been performed on children with biopsy-proven NAFLD. This study aims to identify genomic variants associated with increased adiposity and insulin resistance in a population of children with varying histologic severity of NAFLD. METHODS We conducted a genome-wide association scan (GWAS) including 624,297 single-nucleotide polymorphisms (SNPs) distributed among all 22 autosomal chromosomes in 234 Hispanic boys (up to 18 years of age) who were consecutively recruited in a prospective cohort study in the Nonalcoholic Steatohepatitis Clinical Research Network Studies. Traits were examined quantitatively using linear regression. SNPs with P value <10 and a minor allele frequency >5% were considered potentially significant. RESULTS Evaluated subjects had a median age of 12.0 years, body mass index (BMI) of 31.4, and hemoglobin A1C (Hgb A1C) of 5.3. The prevalence of NAFL, borderline NASH, and definite NASH were 23%, 53%, and 22%, respectively. The GWAS identified 10 SNPs that were associated with BMI z score, 6 within chromosome 2, and 1 within CAMK1D, which has a potential role in liver gluconeogenesis. In addition, the GWAS identified 9 novel variants associated with insulin resistance: HOMA-IR (6) and HbA1c (3). CONCLUSIONS This study of Hispanic boys with biopsy-proven NAFLD with increased risk for the metabolic syndrome revealed novel genetic variants that are associated with obesity and insulin resistance.
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Affiliation(s)
| | | | | | - Xiuqing Guo
- Institute for Translational Genomics and Population Science and Pediatrics, LA BioMed at Harbor-UCLA Medical Center, Los Angeles, CA
| | - Soonil Kwon
- Institute for Translational Genomics and Population Science and Pediatrics, LA BioMed at Harbor-UCLA Medical Center, Los Angeles, CA
| | | | | | - Rohit Loomba
- Medicine, University of California, San Diego, San Diego, CA
| | | | - Yii-Der I da Chen
- Institute for Translational Genomics and Population Science and Pediatrics, LA BioMed at Harbor-UCLA Medical Center, Los Angeles, CA
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Science and Pediatrics, LA BioMed at Harbor-UCLA Medical Center, Los Angeles, CA
| | - Katherine P Yates
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Science and Pediatrics, LA BioMed at Harbor-UCLA Medical Center, Los Angeles, CA
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83
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Abstract
Big Data promises huge benefits for medical research. Looking beyond superficial increases in the amount of data collected, we identify three key areas where Big Data differs from conventional analyses of data samples: (i) data are captured more comprehensively relative to the phenomenon under study; this reduces some bias but surfaces important trade-offs, such as between data quantity and data quality; (ii) data are often analysed using machine learning tools, such as neural networks rather than conventional statistical methods resulting in systems that over time capture insights implicit in data, but remain black boxes, rarely revealing causal connections; and (iii) the purpose of the analyses of data is no longer simply answering existing questions, but hinting at novel ones and generating promising new hypotheses. As a consequence, when performed right, Big Data analyses can accelerate research. Because Big Data approaches differ so fundamentally from small data ones, research structures, processes and mindsets need to adjust. The latent value of data is being reaped through repeated reuse of data, which runs counter to existing practices not only regarding data privacy, but data management more generally. Consequently, we suggest a number of adjustments such as boards reviewing responsible data use, and incentives to facilitate comprehensive data sharing. As data's role changes to a resource of insight, we also need to acknowledge the importance of collecting and making data available as a crucial part of our research endeavours, and reassess our formal processes from career advancement to treatment approval.
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Affiliation(s)
| | - E Ingelsson
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
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84
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Storz C, Heber SD, Rospleszcz S, Machann J, Sellner S, Nikolaou K, Lorbeer R, Gatidis S, Elser S, Peters A, Schlett CL, Bamberg F. The role of visceral and subcutaneous adipose tissue measurements and their ratio by magnetic resonance imaging in subjects with prediabetes, diabetes and healthy controls from a general population without cardiovascular disease. Br J Radiol 2018; 91:20170808. [PMID: 29388794 DOI: 10.1259/bjr.20170808] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVE To study the relationship of area- and volumetric-based visceral and subcutaneous adipose tissue (VAT and SAT) by MRI and their ratio in subjects with impaired glucose metabolism from the general population. METHODS Subjects from a population-based cohort with established prediabetes, diabetes and healthy controls without prior cardiovascular diseases underwent 3 T MRI. VAT and SAT were assessed as total volume and area on a single slice, and their ratio (VAT/SAT) was calculated. Clinical covariates and cardiovascular risk factors, such as hypertension and glycemic state were assessed in standardized fashion. Univariate and adjusted analyses were conducted. RESULTS Among 384 subjects (age: 56.2 ± 9.2 years, 58.1% male) with complete MRI data available, volumetric and single-slice VAT, SAT and VAT/SAT ratio were strongly correlated (all >r = 0.89). Similarly, VAT/SATvolume ratio was strongly correlated with VATvolume but not with SAT (r = 0.72 and r = -0.21, respectively). Significant higher levels of VAT, SAT and VAT/SAT ratio were found in subjects with impaired glucose metabolism (all p ≤ 0.01). After adjustment for potential cardiovascular confounders, VATvolume and VAT/SATvolume ratio remained significantly higher in subjects with impaired glucose metabolism (VATvolume = 6.9 ± 2.5 l and 3.4 ± 2.3 l; VAT/SATvolume ratio = 0.82 ± 0.34 l and 0.49 ± 0.29 l in patients with diabetes and controls, respectively, all p < 0.02), whereas the association for SATvolume attenuated. Additionally, there was a decreasing effect of glycemic status on VAT/SATvolume ratio with increasing body mass index and waist circumference (p < 0.05). CONCLUSIONS VATvolume and VAT/SATvolume ratio are associated with impaired glucose metabolism, independent of cardiovascular risk factors or MRI-based quantification technique, with a decreasing effect of VAT/SATvolume ratio in obese subjects. Advances in knowledge: Quantification of VATvolume and VAT/SATvolume ratio by MRI represents a reproducable biomarker associated with cardiometabolic risk factors in subjects with impaired glucose metabolism, while the association of VAT/SATvolume ratio with glycemic state is attenuated in obese subjects.
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Affiliation(s)
- Corinna Storz
- 1 Department of Diagnostic and Interventional Radiology, University Hospital Tuebingen , Tuebingen , Germany
| | - Sophia D Heber
- 1 Department of Diagnostic and Interventional Radiology, University Hospital Tuebingen , Tuebingen , Germany.,2 Department of Radiology, CTMH Doctors Hospital , George Town, Grand Cayman , Cayman Islands
| | - Susanne Rospleszcz
- 3 Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health , Neuherberg , Germany
| | - Jürgen Machann
- 4 Department of Diagnostic and Interventional Radiology, Section on Experimental Radiology, University Hospital Tuebingen , Tuebingen , Germany.,5 Institute for Diabetes Research and Metabolic Diseases, Helmholtz Center Munich at the University of Tuebingen , Tuebingen , Germany.,6 German Center for Diabetes Research (DZD) , Tuebingen , Germany
| | - Sabine Sellner
- 7 Department of Radiology, Ludwig-Maximilian-University Hospital , Munich , Germany
| | - Konstantin Nikolaou
- 1 Department of Diagnostic and Interventional Radiology, University Hospital Tuebingen , Tuebingen , Germany
| | - Roberto Lorbeer
- 7 Department of Radiology, Ludwig-Maximilian-University Hospital , Munich , Germany
| | - Sergios Gatidis
- 1 Department of Diagnostic and Interventional Radiology, University Hospital Tuebingen , Tuebingen , Germany
| | - Stefanie Elser
- 1 Department of Diagnostic and Interventional Radiology, University Hospital Tuebingen , Tuebingen , Germany
| | - Annette Peters
- 3 Institute of Epidemiology II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health , Neuherberg , Germany.,8 German Center for Cardiovascular Disease Research (DZHK e.V.) , Munich , Germany.,9 Institute for Cardiovascular Prevention, Ludwig-Maximilian-University-Hospital , Munich , Germany
| | - Christopher L Schlett
- 10 Department of Radiology, Diagnostic and Interventional Radiology, University of Heidelberg , Heidelberg , Germany
| | - Fabian Bamberg
- 1 Department of Diagnostic and Interventional Radiology, University Hospital Tuebingen , Tuebingen , Germany.,9 Institute for Cardiovascular Prevention, Ludwig-Maximilian-University-Hospital , Munich , Germany
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85
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Kim YJ, Osborn DP, Lee JY, Araki M, Araki K, Mohun T, Känsäkoski J, Brandstack N, Kim HT, Miralles F, Kim CH, Brown NA, Kim HG, Martinez-Barbera JP, Ataliotis P, Raivio T, Layman LC, Kim SH. WDR11-mediated Hedgehog signalling defects underlie a new ciliopathy related to Kallmann syndrome. EMBO Rep 2018; 19:269-289. [PMID: 29263200 PMCID: PMC5797970 DOI: 10.15252/embr.201744632] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/14/2017] [Accepted: 11/17/2017] [Indexed: 12/27/2022] Open
Abstract
WDR11 has been implicated in congenital hypogonadotropic hypogonadism (CHH) and Kallmann syndrome (KS), human developmental genetic disorders defined by delayed puberty and infertility. However, WDR11's role in development is poorly understood. Here, we report that WDR11 modulates the Hedgehog (Hh) signalling pathway and is essential for ciliogenesis. Disruption of WDR11 expression in mouse and zebrafish results in phenotypic characteristics associated with defective Hh signalling, accompanied by dysgenesis of ciliated tissues. Wdr11-null mice also exhibit early-onset obesity. We find that WDR11 shuttles from the cilium to the nucleus in response to Hh signalling. WDR11 regulates the proteolytic processing of GLI3 and cooperates with the transcription factor EMX1 in the induction of downstream Hh pathway gene expression and gonadotrophin-releasing hormone production. The CHH/KS-associated human mutations result in loss of function of WDR11. Treatment with the Hh agonist purmorphamine partially rescues the WDR11 haploinsufficiency phenotypes. Our study reveals a novel class of ciliopathy caused by WDR11 mutations and suggests that CHH/KS may be a part of the human ciliopathy spectrum.
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Affiliation(s)
- Yeon-Joo Kim
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Daniel Ps Osborn
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Ji-Young Lee
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Masatake Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | | | | | | | - Hyun-Taek Kim
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Francesc Miralles
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, Korea
| | - Nigel A Brown
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Hyung-Goo Kim
- Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Juan Pedro Martinez-Barbera
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Paris Ataliotis
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Taneli Raivio
- Helsinki University Central Hospital, Helsinki, Finland
| | | | - Soo-Hyun Kim
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
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86
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Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes. Nat Commun 2018; 9:321. [PMID: 29358691 PMCID: PMC5778074 DOI: 10.1038/s41467-017-02380-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 11/24/2017] [Indexed: 12/20/2022] Open
Abstract
The reanalysis of existing GWAS data represents a powerful and cost-effective opportunity to gain insights into the genetics of complex diseases. By reanalyzing publicly available type 2 diabetes (T2D) genome-wide association studies (GWAS) data for 70,127 subjects, we identify seven novel associated regions, five driven by common variants (LYPLAL1, NEUROG3, CAMKK2, ABO, and GIP genes), one by a low-frequency (EHMT2), and one driven by a rare variant in chromosome Xq23, rs146662075, associated with a twofold increased risk for T2D in males. rs146662075 is located within an active enhancer associated with the expression of Angiotensin II Receptor type 2 gene (AGTR2), a modulator of insulin sensitivity, and exhibits allelic specific activity in muscle cells. Beyond providing insights into the genetics and pathophysiology of T2D, these results also underscore the value of reanalyzing publicly available data using novel genetic resources and analytical approaches. Genome-wide association studies have uncovered several loci associated with diabetes risk. Here, the authors reanalyse public type 2 diabetes GWAS data to fine map 50 known loci and identify seven new ones, including one near ATGR2 on the X-chromosome that doubles the risk of diabetes in men.
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87
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Abstract
Recently, genome-wide association studies (GWAS) have identified 11 loci associated with adipose-related traits across different populations. However, their functional roles still remain largely unknown. In this study, we aimed to explore the splicing regulation of these GWAS signals in a tissue-specific fashion. For adipose-related GWAS signals, we selected six adipose-related tissues (adipose subcutaneous, artery tibial, blood, heart left ventricle, muscle-skeletal, and thyroid) with the sample size greater than 80 for splicing quantitative trait loci (QTL) analysis using GTEx released datasets. We integrated GWAS summary statistics of nine adipose-related traits (an average of 2.6 million SNPs per GWAS), and splicing QTLs from 6 GTEx tissues with an average of 337,900 splicing QTL SNPs, and 684,859 junctions. Our filtering process generated an average of 86,549 SNPs and 162,841 exon-exon links (junctions) for each tissue. A total of seven exon-exon junctions in four genes (AKTIP, DTNBP1, FTO and UBE2E1) were found to be significantly associated with four SNPs that showed genome-wide significance with body fat distribution (rs17817288, rs7206790, rs11710420 and rs2237199). These splicing events might contribute to the causal effect on the regulation of ectopic-fat, which warrants further experimental validation.
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88
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Gao C, Langefeld CD, Ziegler JT, Taylor KD, Norris JM, Chen YDI, Hellwege JN, Guo X, Allison MA, Speliotes EK, Rotter JI, Bowden DW, Wagenknecht LE, Palmer ND. Genome-Wide Study of Subcutaneous and Visceral Adipose Tissue Reveals Novel Sex-Specific Adiposity Loci in Mexican Americans. Obesity (Silver Spring) 2018; 26:202-212. [PMID: 29178545 PMCID: PMC5740005 DOI: 10.1002/oby.22074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 01/02/2023]
Abstract
OBJECTIVE This study aimed to explore the genetic mechanisms of regional fat deposition, which is a strong risk factor for metabolic diseases beyond total adiposity. METHODS A genome-wide association study of 7,757,139 single-nucleotide polymorphisms (SNPs) in 983 Mexican Americans (nmale = 403; nfemale = 580) from the Insulin Resistance Atherosclerosis Family Study was performed. Association analyses were performed with and without sex stratification for subcutaneous adipose tissue, visceral adipose tissue (VAT), and visceral-subcutaneous ratio (VSR) obtained from computed tomography. RESULTS The strongest signal identified was SNP rs2185405 (minor allele frequencies [MAF] = 40%; PVAT = 1.98 × 10-8 ) with VAT. It is an intronic variant of the GLIS family zinc finger 3 gene (GLIS3). In addition, SNP rs12657394 (MAF = 19%) was associated with VAT in males (Pmale = 2.39×10-8 ; Pfemale = 2.5 × 10-3 ). It is located intronically in the serum response factor binding protein 1 gene (SRFBP1). On average, male carriers of the variant had 24.6 cm2 increased VAT compared with noncarriers. Subsequently, genome-wide SNP-sex interaction analysis was performed. SNP rs10913233 (MAF = 14%; Pint = 3.07 × 10-8 ) in PAPPA2 and rs10923724 (MAF = 38%; Pint = 2.89 × 10-8 ) upstream of TBX15 were strongly associated with the interaction effect for VSR. CONCLUSIONS Six loci were identified with genome-wide significant associations with fat deposition and interactive effects. These results provided genetic evidence for a differential basis of fat deposition between genders.
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Affiliation(s)
- Chuan Gao
- Molecular Genetics and Genomics Program; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Genomics and Personalized Medicine Research; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, NC
| | - Carl D. Langefeld
- Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biostatistical Sciences; Wake Forest School of Medicine, Winston-Salem, NC
| | - Julie T. Ziegler
- Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biostatistical Sciences; Wake Forest School of Medicine, Winston-Salem, NC
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences; Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health; University of Colorado, Aurora, CO
| | - Yii-Der I. Chen
- Institute for Translational Genomics and Population Sciences; Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Jacklyn N. Hellwege
- Center for Genomics and Personalized Medicine Research; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, NC
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences; Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Matthew A. Allison
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla CA
| | - Elizabeth K. Speliotes
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics; University of Michigan, Ann Arbor, MI
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences; Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
- Department of Pediatrics; Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry; Wake Forest School of Medicine, Winston-Salem, NC
| | - Lynne E. Wagenknecht
- Division of Public Health Sciences; Wake Forest School of Medicine, Winston-Salem, NC
| | - Nicholette D. Palmer
- Center for Genomics and Personalized Medicine Research; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Public Health Genomics; Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research; Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry; Wake Forest School of Medicine, Winston-Salem, NC
- Correspondence to Nicholette D. Palmer, PhD, Department of Biochemistry, 1 Medical Center Blvd, Winston-Salem, NC 27040, Phone: 336-713-7534,
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89
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Cha EDK, Veturi Y, Agarwal C, Patel A, Arbabshirani MR, Pendergrass SA. Using Adipose Measures from Health Care Provider-Based Imaging Data for Discovery. J Obes 2018; 2018:3253096. [PMID: 30363675 PMCID: PMC6180992 DOI: 10.1155/2018/3253096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/18/2018] [Indexed: 12/13/2022] Open
Abstract
The location and type of adipose tissue is an important factor in metabolic syndrome. A database of picture archiving and communication system (PACS) derived abdominal computerized tomography (CT) images from a large health care provider, Geisinger, was used for large-scale research of the relationship of volume of subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) with obesity-related diseases and clinical laboratory measures. Using a "greedy snake" algorithm and 2,545 CT images from the Geisinger PACS, we measured levels of VAT, SAT, total adipose tissue (TAT), and adipose ratio volumes. Sex-combined and sex-stratified association testing was done between adipose measures and 1,233 disease diagnoses and 37 clinical laboratory measures. A genome-wide association study (GWAS) for adipose measures was also performed. SAT was strongly associated with obesity and morbid obesity. VAT levels were strongly associated with type 2 diabetes-related diagnoses (p = 1.5 × 10-58), obstructive sleep apnea (p = 7.7 × 10-37), high-density lipoprotein (HDL) levels (p = 1.42 × 10-36), triglyceride levels (p = 1.44 × 10-43), and white blood cell (WBC) counts (p = 7.37 × 10-9). Sex-stratified tests revealed stronger associations among women, indicating the increased influence of VAT on obesity-related disease outcomes particularly among women. The GWAS identified some suggestive associations. This study supports the utility of pursuing future clinical and genetic discoveries with existing imaging data-derived adipose tissue measures deployed at a larger scale.
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Affiliation(s)
- Elliot D. K. Cha
- Biomedical and Translational Informatics Institute, Geisinger Research, Danville, PA, USA
| | - Yogasudha Veturi
- Biomedical and Translational Informatics Institute, Geisinger Research, Danville, PA, USA
| | - Chirag Agarwal
- Department of Imaging Science and Innovation, Geisinger Research, Danville, PA, USA
- Department of Electrical & Computer Engineering, University of Illinois at Chicago, Chicago, IL, USA
- Department of Radiology, Geisinger, Danville, PA, USA
| | - Aalpen Patel
- Department of Imaging Science and Innovation, Geisinger Research, Danville, PA, USA
- Department of Radiology, Geisinger, Danville, PA, USA
| | - Mohammad R. Arbabshirani
- Biomedical and Translational Informatics Institute, Geisinger Research, Danville, PA, USA
- Department of Imaging Science and Innovation, Geisinger Research, Danville, PA, USA
| | - Sarah A. Pendergrass
- Biomedical and Translational Informatics Institute, Geisinger Research, Danville, PA, USA
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90
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Watson RA, Gates AS, Wynn EH, Calvert FE, Girousse A, Lelliott CJ, Barroso I. Lyplal1 is dispensable for normal fat deposition in mice. Dis Model Mech 2017; 10:1481-1488. [PMID: 29084768 PMCID: PMC5769613 DOI: 10.1242/dmm.031864] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/17/2017] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies (GWAS) have detected association between variants in or near the Lysophospholipase-like 1 (LYPLAL1) locus and metabolic traits, including central obesity, fatty liver and waist-to-hip ratio. LYPLAL1 is also known to be upregulated in the adipose tissue of obese patients. However, the physiological role of LYPLAL1 is not understood. To investigate the function of Lyplal1 in vivo we investigated the phenotype of the Lyplal1tm1a(KOMP)Wtsi homozygous mouse. Body composition was unaltered in Lyplal1 knockout mice as assessed by dual-energy X-ray absorptiometry (DEXA) scanning, both on normal chow and on a high-fat diet. Adipose tissue distribution between visceral and subcutaneous fat depots was unaltered, with no change in adipocyte cell size. The response to both insulin and glucose dosing was normal in Lyplal1tm1a(KOMP)Wtsi homozygous mice, with normal fasting blood glucose concentrations. RNAseq analysis of liver, muscle and adipose tissue confirmed that Lyplal1 expression was ablated with minimal additional changes in gene expression. These results suggest that Lyplal1 is dispensable for normal mouse metabolic physiology and that despite having been maintained through evolution Lyplal1 is not an essential gene, suggesting possible functional redundancy. Further studies will be required to clarify its physiological role.
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Affiliation(s)
- Rachel A Watson
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Amy S Gates
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, Medical Genetics, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Elizabeth H Wynn
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Fiona E Calvert
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Amandine Girousse
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.,Université de Toulouse, Inserm U1031, CHU Rangueil, Batiment L1, BP 84225, 31 432 Toulouse, France
| | - Christopher J Lelliott
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Inês Barroso
- Human Genetics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK .,Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
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91
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Associations of adult genetic risk scores for adiposity with childhood abdominal, liver and pericardial fat assessed by magnetic resonance imaging. Int J Obes (Lond) 2017; 42:897-904. [PMID: 29437161 PMCID: PMC5985956 DOI: 10.1038/ijo.2017.302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 10/05/2017] [Accepted: 11/19/2017] [Indexed: 02/07/2023]
Abstract
Background Genome-wide association studies (GWAS) identified single nucleotide polymorphisms (SNPs) involved in adult fat distribution. Whether these SNPs also affect abdominal and organ-specific fat accumulation in children is unknown. Methods In a population-based prospective cohort study among 1 995 children (median age: 9.8 years, 95% range 9.4;10.8), We tested the associations of six genetic risk scores based on previously identified SNPs for childhood BMI, adult BMI, liver fat, WHR, pericardial fat mass, visceral- and subcutaneous adipose tissue ratio (VAT/SAT ratio), and four individual SAT and VAT associated SNPs, for association with SAT (N=1 746), VAT (N=1 742), VAT/SAT ratio (N=1 738), liver fat fraction (N=1 950), and pericardial fat mass (N=1 803) measured by Magnetic Resonance Imaging. Results Per additional risk allele in the childhood BMI genetic risk score, SAT increased 0.020 standard deviation scores (SDS), (95% confidence interval (CI) 0.009;0.031, p-value:3.28*10-4) and VAT increased 0.021 SDS, 95% CI:0.009;0.032, p-value:4.68*10-4). The adult BMI risk score was positively associated with SAT (0.022 SDS increase, CI:0.015;0.029, p-value:1.33*10-9), VAT (0.017 SDS increase, CI:0.010;0.025, p-value:7.00*10-6), and negatively with VAT/SAT ratio (-0.012 SDS decrease, CI:-0.019;-0.006, p-value:2.88*10-4). The liver fat risk score was associated with liver fat fraction (0.121 SDS, CI:0.086;0.157, p-value:2.65*10-11). Rs7185735 (SAT), was associated with SAT (0.151 SDS, CI:0.087;0.214, p-value:3.00*10-6) and VAT/SAT ratio (-0.126 SDS, CI:-0.186;-0.065, p-value:4.70*10-5). After stratification by sex the associations of the adult BMI risk score with SAT and VAT and of the liver fat risk score with liver fat fraction remained in both sexes. Associations of the childhood BMI risk score with SAT, and the adult BMI risk score with VAT/SAT ratio were present among boys only, whereas the association of the pericardial fat risk score with pericardial fat was present among girls only. Conclusion Genetic variants associated with BMI, body fat distribution, liver and pericardial fat already affect body fat distribution in childhood.
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Meyers JL, Zhang J, Wang JC, Su J, Kuo SI, Kapoor M, Wetherill L, Bertelsen S, Lai D, Salvatore JE, Kamarajan C, Chorlian D, Agrawal A, Almasy L, Bauer L, Bucholz KK, Chan G, Hesselbrock V, Koganti L, Kramer J, Kuperman S, Manz N, Pandey A, Seay M, Scott D, Taylor RE, Dick DM, Edenberg HJ, Goate A, Foroud T, Porjesz B. An endophenotype approach to the genetics of alcohol dependence: a genome wide association study of fast beta EEG in families of African ancestry. Mol Psychiatry 2017; 22:1767-1775. [PMID: 28070124 PMCID: PMC5503794 DOI: 10.1038/mp.2016.239] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/24/2016] [Accepted: 10/27/2016] [Indexed: 01/16/2023]
Abstract
Fast beta (20-28 Hz) electroencephalogram (EEG) oscillatory activity may be a useful endophenotype for studying the genetics of disorders characterized by neural hyperexcitability, including substance use disorders (SUDs). However, the genetic underpinnings of fast beta EEG have not previously been studied in a population of African-American ancestry (AA). In a sample of 2382 AA individuals from 482 families drawn from the Collaborative Study on the Genetics of Alcoholism (COGA), we performed a genome-wide association study (GWAS) on resting-state fast beta EEG power. To further characterize our genetic findings, we examined the functional and clinical/behavioral significance of GWAS variants. Ten correlated single-nucleotide polymorphisms (SNPs) (r2>0.9) located in an intergenic region on chromosome 3q26 were associated with fast beta EEG power at P<5 × 10-8. The most significantly associated SNP, rs11720469 (β: -0.124; P<4.5 × 10-9), is also an expression quantitative trait locus for BCHE (butyrylcholinesterase), expressed in thalamus tissue. Four of the genome-wide SNPs were also associated with Diagnostic and Statistical Manual of Mental Disorders Alcohol Dependence in COGA AA families, and two (rs13093097, rs7428372) were replicated in an independent AA sample (Gelernter et al.). Analyses in the AA adolescent/young adult (offspring from COGA families) subsample indicated association of rs11720469 with heavy episodic drinking (frequency of consuming 5+ drinks within 24 h). Converging findings presented in this study provide support for the role of genetic variants within 3q26 in neural and behavioral disinhibition. These novel genetic findings highlight the importance of including AA populations in genetics research on SUDs and the utility of the endophenotype approach in enhancing our understanding of mechanisms underlying addiction susceptibility.
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Affiliation(s)
- J L Meyers
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - J Zhang
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - J C Wang
- Department of Neuroscience, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Su
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA
| | - S I Kuo
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA
| | - M Kapoor
- Department of Neuroscience, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - L Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - S Bertelsen
- Department of Neuroscience, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - D Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - J E Salvatore
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - C Kamarajan
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - D Chorlian
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - A Agrawal
- Department of Psychiatry, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - L Almasy
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - L Bauer
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT, USA
| | - K K Bucholz
- Department of Psychiatry, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - G Chan
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT, USA
| | - V Hesselbrock
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, CT, USA
| | - L Koganti
- Department of Neuroscience, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Kramer
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - S Kuperman
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - N Manz
- Department of Physics, The College of Wooster, Wooster, OH, USA
| | - A Pandey
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - M Seay
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - D Scott
- Collaborative Alcohol Research Center, Howard University College of Medicine, Washington, DC, USA
| | - R E Taylor
- Collaborative Alcohol Research Center, Howard University College of Medicine, Washington, DC, USA
| | - D M Dick
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - H J Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - A Goate
- Department of Neuroscience, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - T Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - B Porjesz
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, NY, USA
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High fat diet consumption differentially affects adipose tissue inflammation and adipocyte size in obesity-prone and obesity-resistant rats. Int J Obes (Lond) 2017; 42:535-541. [PMID: 29151595 PMCID: PMC5876080 DOI: 10.1038/ijo.2017.280] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/29/2017] [Accepted: 10/29/2017] [Indexed: 12/18/2022]
Abstract
Background/Objectives Expanding visceral adiposity is associated with increased inflammation and increased risk for developing obesity-related comorbidities. The goal of this study was to examine high fat diet (HFD)-induced differences in adipocyte size and cytokine/chemokine expression in visceral and subcutaneous adipose depots in obesity-prone (OP) and obesity-resistant (OR) rats. Methods OP and OR rats were fed either a low fat diet (LFD, 10% kilocalories from fat) or HFD (60% kilocalories from fat) for 7 weeks. Adipocyte size and the presence of crown-like structures in epididymal and inguinal adipose tissue were determined. A multiplex cytokine/chemokine panel was used to assess the expression of inflammatory markers in epididymal and inguinal adipose tissues. Results A higher percentage of large adipocytes (> 5000 μm2) was detected in the epididymal and inguinal adipose tissues of OP rats and a higher percentage of small adipocytes (< 4000 μm2) was detected in the epididymal and inguinal adipose tissues of OR rats. More crown-like structures were identified in epididymal adipose tissue of OP rats fed a LFD, compared to OR rats. Consumption of a HFD increased the number of crown-like structures in OR, but not OP rats. Epididymal expression of pro-inflammatory cytokines (IL-1β, TNF-α) was higher in OP rats, compared to OR rats fed LFD. HFD consumption increased epididymal expression of GM-CSF, IL-1α, IL-1β, IL-6, MIP-2, and TNF-α in OP and OR rats. Inguinal expression of pro-inflammatory cytokines (IL-1α, IL-1β, TNF-α) was higher in OP rats, compared to OR rats. Conclusions Overall, these data suggest that a higher susceptibility to developing obesity is characterized by large adipocytes and increased visceral adipose inflammation. Interestingly, in OR rats, the detrimental effects of HFD consumption on visceral adipose inflammation are evident with only small increases in weight and adiposity, suggesting that HFD also increases the risk for obesity-related comorbidities in OR rats.
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94
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Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević P, Hajdinjak M, Vernot B, Skov L, Hsieh P, Peyrégne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu Q, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 2017; 358:655-658. [PMID: 28982794 PMCID: PMC6185897 DOI: 10.1126/science.aao1887] [Citation(s) in RCA: 317] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/27/2017] [Indexed: 12/30/2022]
Abstract
To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
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Affiliation(s)
- Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
| | - Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Steffi Grote
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fabrizio Mafessoni
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Pinghsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stéphane Peyrégne
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - David Reher
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Charlotte Hopfe
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Christoph Theunert
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Rebekah Rogers
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Pontus Skoglund
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Felix M Key
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Pavao Rudan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Željko Kućan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Ivan Gušić
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | | | | | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Reich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Aida M Andrés
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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Yener S, Baris M, Peker A, Demir O, Ozgen B, Secil M. Autonomous cortisol secretion in adrenal incidentalomas and increased visceral fat accumulation during follow-up. Clin Endocrinol (Oxf) 2017; 87:425-432. [PMID: 28656620 DOI: 10.1111/cen.13408] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Autonomous cortisol secretion of adrenal incidentalomas (AIs) is associated with poor cardiovascular outcome. Because centripetal obesity is a cardiovascular risk factor, we aimed to investigate whether autonomous cortisol secretion is associated with increased visceral fat accumulation. DESIGN Retrospective cohort study. PATIENTS Patients with AIs who attended for follow-up between January 2014 and December 2016 were evaluated. Autonomous cortisol secretion was diagnosed when 1 mg overnight dexamethasone (post-DST) cortisol was >50 nmol/L at baseline and follow-up. Follow-up duration was 34 (12-105) months. Thirty patients with nonfunctioning AIs and 44 patients with autonomous cortisol secretion were included. Adrenalectomy was performed in five patients. Six patients with Cushing's syndrome were also recruited. MEASUREMENTS Hormonal evaluation and assessment of total (T), visceral (V) and subcutaneous (S) fat area by computed tomography and calculation of V:S and V:T ratios at baseline and follow-up. RESULTS V, V:S and V:T increased (P<.001 for each comparison, Wilcoxon signed rank test for repeated measures) in patients with autonomous cortisol secretion while did not change significantly in patients with nonfunctioning adenomas. Linear regression models including post-DST cortisol, gender, concomitant treatments and follow-up duration showed that both baseline and follow-up DST significantly predicted Δ(V:S) and Δ(V:T) (P<.01 for all models). CONCLUSIONS In patients with AIs, a post-DST cortisol >50 nmol/L at both baseline and follow-up, was associated with a significant increase in visceral fat after a follow-up duration of ~3 years. This may be of importance to explain the link between autonomous cortisol secretion and poor cardiovascular outcome.
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Affiliation(s)
- Serkan Yener
- Department of Endocrinology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Mustafa Baris
- Department of Radiology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Ahmet Peker
- Department of Radiology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Omer Demir
- Department of Urology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Basak Ozgen
- Department of Endocrinology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Mustafa Secil
- Department of Radiology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
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Differential DNA Methylation in Monozygotic Twins Discordant for Female Sexual Functioning. J Sex Med 2017; 14:1357-1364. [DOI: 10.1016/j.jsxm.2017.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/29/2017] [Accepted: 09/01/2017] [Indexed: 01/13/2023]
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97
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Pulit SL, Laber S, Glastonbury CA, Lindgren CM. The genetic underpinnings of body fat distribution. Expert Rev Endocrinol Metab 2017; 12:417-427. [PMID: 30063432 DOI: 10.1080/17446651.2017.1390427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Obesity, defined as a body mass index (BMI) ≥ 30 kg/m2, has reached epidemic proportions; people who are overweight (BMI > 25 kg/m2) or obese now comprise more than 25% of the world's population. Obese individuals have a higher risk of comorbidity development including type 2 diabetes, cardiovascular disease, cancer, and fertility complications. Areas covered: The study of monogenic and syndromic forms of obesity have revealed a small number of genes key to metabolic perturbations. Further, obesity and body shape in the general population are highly heritable phenotypes. Study of obesity at the population level, through genome-wide association studies of BMI and waist-to-hip ratio (WHR), have revealed > 150 genomic loci that associate with these traits, and highlight the role of adipose tissue and the central nervous system in obesity-related traits. Studies in animal models and cell lines have helped further elucidate the potential biological mechanisms underlying obesity. In particular, these studies implicate adipogenesis and expansion of adipose tissue as key biological pathways in obesity and weight gain. Expert commentary: Further work, including a focus on integrating genetic and additional genomic data types, as well as modeling obesity-like features in vitro, will be crucial in translating genome-wide association signals to the causal mechanisms driving disease.
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Affiliation(s)
- Sara L Pulit
- a Big Data Institute , Li Ka Shing Centre for Health Information and Discovery, University of Oxford , Oxford , UK
- b Department of Genetics , University Medical Center Utrecht , Utrecht , The Netherlands
- f Program in Medical and Population Genetics , Broad Institute , Cambridge , Massachusetts , USA
| | - Samantha Laber
- a Big Data Institute , Li Ka Shing Centre for Health Information and Discovery, University of Oxford , Oxford , UK
- c MRC Harwell Institute , Mammalian Genetics Unit , Harwell , Oxford , UK
- d Department of Physiology , Anatomy and Genetics, University of Oxford , Oxford , U.K
| | - Craig A Glastonbury
- a Big Data Institute , Li Ka Shing Centre for Health Information and Discovery, University of Oxford , Oxford , UK
- e Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine , University of Oxford , Oxford , UK
| | - Cecilia M Lindgren
- a Big Data Institute , Li Ka Shing Centre for Health Information and Discovery, University of Oxford , Oxford , UK
- e Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine , University of Oxford , Oxford , UK
- f Program in Medical and Population Genetics , Broad Institute , Cambridge , Massachusetts , USA
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98
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Zeng H, Gifford DK. Predicting the impact of non-coding variants on DNA methylation. Nucleic Acids Res 2017; 45:e99. [PMID: 28334830 PMCID: PMC5499808 DOI: 10.1093/nar/gkx177] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/13/2017] [Indexed: 12/22/2022] Open
Abstract
DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variation. We introduce CpGenie, a sequence-based framework that learns a regulatory code of DNA methylation using a deep convolutional neural network and uses this network to predict the impact of sequence variation on proximal CpG site DNA methylation. CpGenie produces allele-specific DNA methylation prediction with single-nucleotide sensitivity that enables accurate prediction of methylation quantitative trait loci (meQTL). We demonstrate that CpGenie prioritizes validated GWAS SNPs, and contributes to the prediction of functional non-coding variants, including expression quantitative trait loci (eQTL) and disease-associated mutations. CpGenie is publicly available to assist in identifying and interpreting regulatory non-coding variants.
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Affiliation(s)
- Haoyang Zeng
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology Cambridge, MA 02142, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology Cambridge, MA 02142, USA
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99
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Singh J, Minster RL, Schupf N, Kraja A, Liu Y, Christensen K, Newman AB, Kammerer CM. Genomewide Association Scan of a Mortality Associated Endophenotype for a Long and Healthy Life in the Long Life Family Study. J Gerontol A Biol Sci Med Sci 2017; 72:1411-1416. [PMID: 28329217 DOI: 10.1093/gerona/glx011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Indexed: 01/21/2023] Open
Abstract
Background Identification of genes or fundamental biological pathways that regulate aging phenotypes and longevity could lead to possible interventions to increase healthy longevity. Methods Using data from the Long Life Family Study, we performed genomewide association analyses on an endophenotype construct, LF1, comprising a linear combination of traits across health domains. LF1 primarily reflected traits from the pulmonary and physical activity domains. Results We detected a significant association between LF1 and a locus on chromosome 10p15 (p-value = 4.65 × 10-8) and suggestive evidence (p-value < 5 × 10-6) for association on chromosomes 1, 2, 8, 12, 15, 18, and 22. Using data from the Health, Aging and Body Composition Study, we subsequently replicated the association for the 1p13 region near the NBPF6 locus (p-value = 3.65 × 10-4). Conclusions Our analyses indicate that loci influencing a healthy aging endophenotype construct predominantly comprised of pulmonary and physical function domains may be located on chromosome 1p13 near the NBPF6 locus. Further investigation of this possible locus and other suggestive loci may reveal novel biological pathways that influence healthy aging.
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Affiliation(s)
- Jatinder Singh
- Department of Human Genetics, University of Pittsburgh, Pennsylvania
| | - Ryan L Minster
- Department of Human Genetics, University of Pittsburgh, Pennsylvania
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, New York
| | - Aldi Kraja
- Division of Statistical Genomics, School of Medicine, Washington University in St. Louis, Missouri
| | - YongMei Liu
- Department of Epidemiology & Prevention, Wake Forest University Health Sciences, Winston-Salem, North Carolina
| | - Kaare Christensen
- The Danish Aging Research Center, University of Southern Denmark; Department of Clinical Biochemistry and Pharmacology and Department of Clinical Genetics, Odense University Hospital, Denmark
| | - Anne B Newman
- Department of Epidemiology, University of Pittsburgh, Pennsylvania
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100
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Dietary Fatty Acid Composition Modulates Obesity and Interacts with Obesity-Related Genes. Lipids 2017; 52:803-822. [DOI: 10.1007/s11745-017-4291-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/18/2017] [Indexed: 12/22/2022]
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