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Peña E, Mas-Bermejo P, Lecube A, Ciudin A, Arenas C, Simó R, Rigla M, Caixàs A, Rosa A. Use of polygenic risk scores to assess weight loss after bariatric surgery: a 5-year follow-up study. J Gastrointest Surg 2024:S1091-255X(24)00485-2. [PMID: 38821212 DOI: 10.1016/j.gassur.2024.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/19/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Bariatric surgery (BS) is currently the most effective long-term treatment of severe obesity. However, the interindividual variability observed in surgical outcomes suggests a moderating effect of several factors, including individual genetic background. This study aimed to investigate the contribution of the genetic architecture of body mass index (BMI) to the variability in weight loss outcomes after BS. METHODS A total of 106 patients with severe obesity who underwent Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy were followed up for 5 years. Changes in BMI (BMIchange) and percentage of total weight loss (%TWL) were evaluated during the postoperative period. Polygenic risk scores (PRSs), including 50 genetic variants, were calculated for each participant to determine their genetic risk of high BMI based on a previous genome-wide association study. Generalized estimating equation models were used to study the role of the individual's polygenic score and other factors on BMIchange and %TWL in the long term after surgery. RESULTS This study found an effect of the polygenic score on %TWL and BMIchange, in which patients with lower scores had better outcomes after surgery than those with higher scores. Furthermore, when analyzing only patients who underwent RYGB, the results were replicated, showing greater weight loss after surgery for patients with lower polygenic scores. DISCUSSION Our results indicate that genetic background assessed with PRSs, along with other individual factors, such as biological sex, age, and preoperative BMI, has an effect on BS outcomes and could represent a useful tool for estimating surgical outcomes in advance.
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Affiliation(s)
- Elionora Peña
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Secció de Zoologia i Antropologia Biòlogica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Patricia Mas-Bermejo
- Secció de Zoologia i Antropologia Biòlogica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
| | - Albert Lecube
- Department of Endocrinology and Nutrition, Arnau de Vilanova University Hospital, Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, Spain
| | - Andreea Ciudin
- Diabetes and Metabolism Research Unit, Department of Endocrinology and Nutrition, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción Arenas
- Statistics Section of the Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Rafael Simó
- Diabetes and Metabolism Research Unit, Department of Endocrinology and Nutrition, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain
| | - Mercedes Rigla
- Department of Endocrinology and Nutrition, Institut d'Investigació i Innovació, Parc Taulí Hospital Universitari, Sabadell, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Assumpta Caixàs
- Department of Endocrinology and Nutrition, Institut d'Investigació i Innovació, Parc Taulí Hospital Universitari, Sabadell, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Araceli Rosa
- Secció de Zoologia i Antropologia Biòlogica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica En Red de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain.
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2
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Nishikori S, Fujita S. Association of fat-to-muscle mass ratio with physical activity and dietary protein, carbohydrate, sodium, and fiber intake in a cross-sectional study. Sci Rep 2024; 14:10631. [PMID: 38724633 PMCID: PMC11082163 DOI: 10.1038/s41598-024-61289-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
Higher fat-to-muscle mass ratio (FMR) is reported to be a risk factor for various diseases, including type 2 diabetes and cardiovascular diseases, and mortality. Although this association suggests that reducing FMR may help to prevent certain diseases and mortality, the relationship between FMR and lifestyle factors is unclear. Therefore, we performed a cross-sectional study with the aim to elucidate this relationship. This cross-sectional study included 1518 healthy Japanese adults aged 30 to 64 years. We measured FMR in the whole body, arms, legs, and trunk and assessed various lifestyle factors. Then, we performed forced entry multiple regression analyses for FMR with the following variables: sex, age, physical activity, dietary intake, sleep quality, cigarette smoking, stress levels, and body mass index. As a result, whole-body and regional FMRs were correlated with female sex (β = 0.71); age (β = 0.06); physical activity (β = - 0.07); dietary intake of protein (β = - 0.12), carbohydrate (β = 0.04), sodium (β = 0.13), and fiber (β = - 0.16); and body mass index (β = 0.70). The results suggest that in the Japanese middle-aged population, low FMR is associated with certain lifestyle factors, i.e. higher physical activity and a diet with higher protein and fiber and lower carbohydrate and sodium, independent of age, sex, and body mass index.
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Affiliation(s)
- Shu Nishikori
- Faculty of Sport and Health Science, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Japan
- Frontier Research Center, POLA Chemical Industries, Inc., 560 Kashio-cho, Totsuka-ku, Yokohama, Japan
| | - Satoshi Fujita
- Faculty of Sport and Health Science, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Japan.
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3
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Mauvais-Jarvis F. Sex differences in energy metabolism: natural selection, mechanisms and consequences. Nat Rev Nephrol 2024; 20:56-69. [PMID: 37923858 DOI: 10.1038/s41581-023-00781-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/06/2023]
Abstract
Metabolic homeostasis operates differently in men and women. This sex asymmetry is the result of evolutionary adaptations that enable women to resist loss of energy stores and protein mass while remaining fertile in times of energy deficit. During starvation or prolonged exercise, women rely on oxidation of lipids, which are a more efficient energy source than carbohydrates, to preserve glucose for neuronal and placental function and spare proteins necessary for organ function. Carbohydrate reliance in men could be an evolutionary adaptation related to defence and hunting, as glucose, unlike lipids, can be used as a fuel for anaerobic high-exertion muscle activity. The larger subcutaneous adipose tissue depots in healthy women than in healthy men provide a mechanism for lipid storage. As female mitochondria have higher functional capacity and greater resistance to oxidative damage than male mitochondria, uniparental inheritance of female mitochondria may reduce the transmission of metabolic disorders. However, in women, starvation resistance and propensity to obesity have evolved in tandem, and the current prevalence of obesity is greater in women than in men. The combination of genetic sex, programming by developmental testosterone in males, and pubertal sex hormones defines sex-specific biological systems in adults that produce phenotypic sex differences in energy homeostasis, metabolic disease and drug responses.
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Affiliation(s)
- Franck Mauvais-Jarvis
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine and Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA.
- Endocrine service, Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA.
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Abstract
Obesity is a common complex trait that elevates the risk for various diseases, including type 2 diabetes and cardiovascular disease. A combination of environmental and genetic factors influences the pathogenesis of obesity. Advances in genomic technologies have driven the identification of multiple genetic loci associated with this disease, ranging from studying severe onset cases to investigating common multifactorial polygenic forms. Additionally, findings from epigenetic analyses of modifications to the genome that do not involve changes to the underlying DNA sequence have emerged as key signatures in the development of obesity. Such modifications can mediate the effects of environmental factors, including diet and lifestyle, on gene expression and clinical presentation. This review outlines what is known about the genetic and epigenetic contributors to obesity susceptibility, along with the albeit limited therapeutic options currently available. Furthermore, we delineate the potential mechanisms of actions through which epigenetic changes can mediate environmental influences and the related opportunities they present for future interventions in the management of obesity.
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Affiliation(s)
- Khanh Trang
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Division of Diabetes and Endocrinology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104 USA
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5
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Carland C, Png G, Malarstig A, Kho PF, Gustafsson S, Michaelsson K, Lind L, Tsafantakis E, Karaleftheri M, Dedoussis G, Ramisch A, Macdonald-Dunlop E, Klaric L, Joshi PK, Chen Y, Björck HM, Eriksson P, Carrasco-Zanini J, Wheeler E, Suhre K, Gilly A, Zeggini E, Viñuela A, Dermitzakis ET, Wilson JF, Langenberg C, Thareja G, Halama A, Schmidt F, Zanetti D, Assimes T. Proteomic analysis of 92 circulating proteins and their effects in cardiometabolic diseases. Clin Proteomics 2023; 20:31. [PMID: 37550624 PMCID: PMC10405520 DOI: 10.1186/s12014-023-09421-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/17/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Human plasma contains a wide variety of circulating proteins. These proteins can be important clinical biomarkers in disease and also possible drug targets. Large scale genomics studies of circulating proteins can identify genetic variants that lead to relative protein abundance. METHODS We conducted a meta-analysis on genome-wide association studies of autosomal chromosomes in 22,997 individuals of primarily European ancestry across 12 cohorts to identify protein quantitative trait loci (pQTL) for 92 cardiometabolic associated plasma proteins. RESULTS We identified 503 (337 cis and 166 trans) conditionally independent pQTLs, including several novel variants not reported in the literature. We conducted a sex-stratified analysis and found that 118 (23.5%) of pQTLs demonstrated heterogeneity between sexes. The direction of effect was preserved but there were differences in effect size and significance. Additionally, we annotate trans-pQTLs with nearest genes and report plausible biological relationships. Using Mendelian randomization, we identified causal associations for 18 proteins across 19 phenotypes, of which 10 have additional genetic colocalization evidence. We highlight proteins associated with a constellation of cardiometabolic traits including angiopoietin-related protein 7 (ANGPTL7) and Semaphorin 3F (SEMA3F). CONCLUSION Through large-scale analysis of protein quantitative trait loci, we provide a comprehensive overview of common variants associated with plasma proteins. We highlight possible biological relationships which may serve as a basis for further investigation into possible causal roles in cardiometabolic diseases.
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Affiliation(s)
- Corinne Carland
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Grace Png
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Anders Malarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
| | - Pik Fang Kho
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford Cardiovascular Institute, Palo Alto, CA, USA
| | - Stefan Gustafsson
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Karl Michaelsson
- Department of Surgical Sciences, Medical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
| | | | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Anna Ramisch
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Erin Macdonald-Dunlop
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Yan Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Hanna M Björck
- Cardiovascular Medicine, Medicine, Karolinska Institute, Stockholm, Sweden
| | - Per Eriksson
- Cardiovascular Medicine, Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Eleanor Wheeler
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Karsten Suhre
- Bioinformatics Core, Cornell Medicine - Qatar Research, Doha, Qatar
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich, Germany
| | - Ana Viñuela
- Biosciences Institute, Faculty of Medical Sciences, University of Newcastle, Newcastle, UK
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Gaurav Thareja
- Bioinformatics Core, Cornell Medicine - Qatar Research, Doha, Qatar
| | - Anna Halama
- Bioinformatics Core, Cornell Medicine - Qatar Research, Doha, Qatar
| | - Frank Schmidt
- Proteomics Core, Research, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Daniela Zanetti
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford Cardiovascular Institute, Palo Alto, CA, USA
| | - Themistocles Assimes
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford Cardiovascular Institute, Palo Alto, CA, USA.
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Rouskas K, Katsareli EA, Amerikanou C, Dimopoulos AC, Glentis S, Kalantzi A, Skoulakis A, Panousis N, Ongen H, Bielser D, Planchon A, Romano L, Harokopos V, Reczko M, Moulos P, Griniatsos I, Diamantis T, Dermitzakis ET, Ragoussis J, Dedoussis G, Dimas AS. Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population. BMC Genomics 2023; 24:442. [PMID: 37543566 PMCID: PMC10403965 DOI: 10.1186/s12864-023-09532-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Expression quantitative trait loci (eQTL) studies provide insights into regulatory mechanisms underlying disease risk. Expanding studies of gene regulation to underexplored populations and to medically relevant tissues offers potential to reveal yet unknown regulatory variants and to better understand disease mechanisms. Here, we performed eQTL mapping in subcutaneous (S) and visceral (V) adipose tissue from 106 Greek individuals (Greek Metabolic study, GM) and compared our findings to those from the Genotype-Tissue Expression (GTEx) resource. RESULTS We identified 1,930 and 1,515 eGenes in S and V respectively, over 13% of which are not observed in GTEx adipose tissue, and that do not arise due to different ancestry. We report additional context-specific regulatory effects in genes of clinical interest (e.g. oncogene ST7) and in genes regulating responses to environmental stimuli (e.g. MIR21, SNX33). We suggest that a fraction of the reported differences across populations is due to environmental effects on gene expression, driving context-specific eQTLs, and suggest that environmental effects can determine the penetrance of disease variants thus shaping disease risk. We report that over half of GM eQTLs colocalize with GWAS SNPs and of these colocalizations 41% are not detected in GTEx. We also highlight the clinical relevance of S adipose tissue by revealing that inflammatory processes are upregulated in individuals with obesity, not only in V, but also in S tissue. CONCLUSIONS By focusing on an understudied population, our results provide further candidate genes for investigation regarding their role in adipose tissue biology and their contribution to disease risk and pathogenesis.
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Affiliation(s)
- Konstantinos Rouskas
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thessaloniki, Greece
| | - Efthymia A Katsareli
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Charalampia Amerikanou
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Alexandros C Dimopoulos
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Hellenic Naval Academy, Hatzikyriakou Avenue, Pireaus, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Pediatric Hematology/Oncology Unit (POHemU), First Department of Pediatrics, University of Athens, Aghia Sophia Children's Hospital, Athens, Greece
| | - Alexandra Kalantzi
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Anargyros Skoulakis
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | | | - Halit Ongen
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Deborah Bielser
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Alexandra Planchon
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Luciana Romano
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Vaggelis Harokopos
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Martin Reczko
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Griniatsos
- First Department of Surgery, National and Kapodistrian University of Athens, Medical School, Laiko Hospital, Athens, Greece
| | - Theodoros Diamantis
- First Department of Surgery, National and Kapodistrian University of Athens, Medical School, Laiko Hospital, Athens, Greece
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- Department of Bioengineering, McGill University, Montréal, QC, Canada
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Antigone S Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece.
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7
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Glunk V, Laber S, Sinnott-Armstrong N, Sobreira DR, Strobel SM, Batista TM, Kubitz P, Moud BN, Ebert H, Huang Y, Brandl B, Garbo G, Honecker J, Stirling DR, Abdennur N, Calabuig-Navarro V, Skurk T, Ocvirk S, Stemmer K, Cimini BA, Carpenter AE, Dankel SN, Lindgren CM, Hauner H, Nobrega MA, Claussnitzer M. A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes. Nat Metab 2023; 5:861-879. [PMID: 37253881 DOI: 10.1038/s42255-023-00807-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/12/2023] [Indexed: 06/01/2023]
Abstract
Recent large-scale genomic association studies found evidence for a genetic link between increased risk of type 2 diabetes and decreased risk for adiposity-related traits, reminiscent of metabolically obese normal weight (MONW) association signatures. However, the target genes and cellular mechanisms driving such MONW associations remain to be identified. Here, we systematically identify the cellular programmes of one of the top-scoring MONW risk loci, the 2q24.3 risk locus, in subcutaneous adipocytes. We identify a causal genetic variant, rs6712203, an intronic single-nucleotide polymorphism in the COBLL1 gene, which changes the conserved transcription factor motif of POU domain, class 2, transcription factor 2, and leads to differential COBLL1 gene expression by altering the enhancer activity at the locus in subcutaneous adipocytes. We then establish the cellular programme under the genetic control of the 2q24.3 MONW risk locus and the effector gene COBLL1, which is characterized by impaired actin cytoskeleton remodelling in differentiating subcutaneous adipocytes and subsequent failure of these cells to accumulate lipids and develop into metabolically active and insulin-sensitive adipocytes. Finally, we show that perturbations of the effector gene Cobll1 in a mouse model result in organismal phenotypes matching the MONW association signature, including decreased subcutaneous body fat mass and body weight along with impaired glucose tolerance. Taken together, our results provide a mechanistic link between the genetic risk for insulin resistance and low adiposity, providing a potential therapeutic hypothesis and a framework for future identification of causal relationships between genome associations and cellular programmes in other disorders.
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Affiliation(s)
- Viktoria Glunk
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Samantha Laber
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
| | - Nasa Sinnott-Armstrong
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Herbold Computational Biology Program, Publich Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Debora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Sophie M Strobel
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
| | - Thiago M Batista
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Phil Kubitz
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bahareh Nemati Moud
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Hannah Ebert
- Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Yi Huang
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Beate Brandl
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Garrett Garbo
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
| | - Julius Honecker
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - David R Stirling
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Virtu Calabuig-Navarro
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Institute of Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Thomas Skurk
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Soeren Ocvirk
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Intestinal Microbiology Research Group, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Kerstin Stemmer
- Molecular Cell Biology, Institute for Theoretical Medicine, University of Augsburg, Augsburg, Germany
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Beth A Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Simon N Dankel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Cecilia M Lindgren
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Hans Hauner
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
- ZIEL Institute for Food & Health, Else Kröner-Fresenius-Center for Nutritional Medicine, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Marcelo A Nobrega
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Medical and Population Genetics Program & Type 2 Diabetes Systems Genomics Initiative, Cambridge, MA, USA.
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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Karageorgiou V, Tyrrell J, Mckinley TJ, Bowden J. Weak and pleiotropy robust sex-stratified Mendelian randomization in the one sample and two sample settings. Genet Epidemiol 2023; 47:135-151. [PMID: 36682072 DOI: 10.1002/gepi.22512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 09/06/2022] [Accepted: 11/28/2022] [Indexed: 01/23/2023]
Abstract
BACKGROUND Mendelian randomization (MR) leverages genetic data as an instrumental variable to provide estimates for the causal effect of an exposure X on a health outcome Y that is robust to confounding. Unfortunately, horizontal pleiotropy-the direct association of a genetic variant with multiple phenotypes-is highly prevalent and can easily render a genetic variant an invalid instrument. METHODS Building on existing work, we propose a simple method for leveraging sex-specific genetic associations to perform weak and pleiotropy-robust MR analysis. This is achieved by constructing an MR estimator in which pleiotropy is perfectly removed by cancellation, while placing it within the powerful machinery of the robust adjusted profile score (MR-RAPS) method. Pleiotropy cancellation has the attractive property that it removes heterogeneity and therefore justifies a statistically efficient fixed effects model. We extend the method from the typical two-sample summary-data MR setting to the one-sample setting by adapting the technique of Collider-Correction. Simulation studies and applied examples are used to assess how the sex-stratified MR-RAPS estimator performs against other common approaches. RESULTS The sex-stratified MR-RAPS method is shown to be robust to pleiotropy even in cases where all genetic variants violated the standard Instrument Strength Independent of Direct Effect assumption. In some cases where the strength of the pleiotropic effect additionally varied by sex (and so perfect cancellation was not achieved), over-dispersed MR-RAPS implementations can still consistently estimate the true causal effect. In applied analyses, we investigate the causal effect of waist-hip ratio (WHR), an important marker of central obesity, on a range of downstream traits. While the conventional approaches suggested paradoxical links between WHR and height and body mass index, the sex-stratified approach obtained a more realistic null effect. Nonzero effects were also detected for systolic and diastolic blood pressure as well as high-density and low-density lipoprotein cholesterol. DISCUSSION We provide a simple but attractive method for weak and pleiotropy robust causal estimation of sexually dimorphic traits on downstream outcomes, by combining several existing approaches in a novel fashion.
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Affiliation(s)
- Vasilios Karageorgiou
- Exeter Diabetes Group (ExCEED), College of Medicine and Health, University of Exeter, Exeter, UK
| | - Jess Tyrrell
- Exeter Diabetes Group (ExCEED), College of Medicine and Health, University of Exeter, Exeter, UK
| | - Trevelyan J Mckinley
- Exeter Diabetes Group (ExCEED), College of Medicine and Health, University of Exeter, Exeter, UK
| | - Jack Bowden
- Exeter Diabetes Group (ExCEED), College of Medicine and Health, University of Exeter, Exeter, UK
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9
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Streicher SA, Lim U, Park SL, Li Y, Sheng X, Hom V, Xia L, Pooler L, Shepherd J, Loo LWM, Ernst T, Buchthal S, Franke AA, Tiirikainen M, Wilkens LR, Haiman CA, Stram DO, Cheng I, Le Marchand L. Genome-wide association study of abdominal MRI-measured visceral fat: The multiethnic cohort adiposity phenotype study. PLoS One 2023; 18:e0279932. [PMID: 36607984 PMCID: PMC9821421 DOI: 10.1371/journal.pone.0279932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/16/2022] [Indexed: 01/07/2023] Open
Abstract
Few studies have explored the genetic underpinnings of intra-abdominal visceral fat deposition, which varies substantially by sex and race/ethnicity. Among 1,787 participants in the Multiethnic Cohort (MEC)-Adiposity Phenotype Study (MEC-APS), we conducted a genome-wide association study (GWAS) of the percent visceral adiposity tissue (VAT) area out of the overall abdominal area, averaged across L1-L5 (%VAT), measured by abdominal magnetic resonance imaging (MRI). A genome-wide significant signal was found on chromosome 2q14.3 in the sex-combined GWAS (lead variant rs79837492: Beta per effect allele = -4.76; P = 2.62 × 10-8) and in the male-only GWAS (lead variant rs2968545: (Beta = -6.50; P = 1.09 × 10-9), and one suggestive variant was found at 13q12.11 in the female-only GWAS (rs79926925: Beta = 6.95; P = 8.15 × 10-8). The negatively associated variants were most common in European Americans (T allele of rs79837492; 5%) and African Americans (C allele of rs2968545; 5%) and not observed in Japanese Americans, whereas the positively associated variant was most common in Japanese Americans (C allele of rs79926925, 5%), which was all consistent with the racial/ethnic %VAT differences. In a validation step among UK Biobank participants (N = 23,699 of mainly British and Irish ancestry) with MRI-based VAT volume, both rs79837492 (Beta = -0.026, P = 0.019) and rs2968545 (Beta = -0.028, P = 0.010) were significantly associated in men only (n = 11,524). In the MEC-APS, the association between rs79926925 and plasma sex hormone binding globulin levels reached statistical significance in females, but not in males, with adjustment for total adiposity (Beta = -0.24; P = 0.028), on the log scale. Rs79837492 and rs2968545 are located in intron 5 of CNTNAP5, and rs79926925, in an intergenic region between GJB6 and CRYL1. These novel findings differing by sex and racial/ethnic group warrant replication in additional diverse studies with direct visceral fat measurements.
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Affiliation(s)
- Samantha A. Streicher
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America
| | - Unhee Lim
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America
| | - S. Lani Park
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America
| | - Yuqing Li
- Department of Epidemiology and Biostatistics, University of California–San Francisco, San Francisco, California, United States of America
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Victor Hom
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Lucy Xia
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Loreall Pooler
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - John Shepherd
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America
| | - Lenora W. M. Loo
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America
| | - Thomas Ernst
- University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Steven Buchthal
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America
| | - Adrian A. Franke
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America
| | - Maarit Tiirikainen
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America
| | - Lynne R. Wilkens
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Daniel O. Stram
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California–San Francisco, San Francisco, California, United States of America
| | - Loïc Le Marchand
- University of Hawaii Cancer Center, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America
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10
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Gholami M, Zoughi M, Hasanzad M, Larijani B, Amoli MM. Haplotypic variants of COVID-19 related genes are associated with blood pressure and metabolites levels. J Med Virol 2023; 95:e28355. [PMID: 36443248 PMCID: PMC9877746 DOI: 10.1002/jmv.28355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 07/27/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
The genetic association of coronavirus disease 2019 (COVID-19) with its complications has not been fully understood. This study aimed to identify variants and haplotypes of candidate genes implicated in COVID-19 related traits by combining the literature review and pathway analysis. To explore such genes, the protein-protein interactions and relevant pathways of COVID-19-associated genes were assessed. A number of variants on candidate genes were identified from Genome-wide association studies (GWASs) which were associated with COVID-19 related traits (p ˂ 10-6 ). Haplotypic blocks were assessed using haplotypic structures among the 1000 Genomes Project (r2 ≥ 0.8, D' ≥ 0.8). Further functional analyses were performed on the selected variants. The results demonstrated that a group of variants in ACE and AGT genes were significantly correlated with COVID-19 related traits. Three haplotypes were identified to be involved in the blood metabolites levels and the development of blood pressure. Functional analyses revealed that most GWAS index variants were expression quantitative trait loci and had transcription factor binding sites, exonic splicing enhancers or silencer activities. Furthermore, the proxy haplotype variants, rs4316, rs4353, rs4359, and three variants, namely rs2493133, rs2478543, and rs5051, were associated with blood metabolite and systolic blood pressure, respectively. These variants exerted more regulatory effects compared with other GWAS variants. The present study indicates that the genetic variants and candidate haplotypes of COVID-19 related genes are associated with blood pressure and blood metabolites. However, further observational studies are warranted to confirm these results.
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Affiliation(s)
- Morteza Gholami
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical SciencesTehranIran,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Marziyeh Zoughi
- Metabolomics and genomics research center endocrinology and metabolism molecular‐cellular sciences instituteTehran University of medical sciencesTehranIran
| | - Mandana Hasanzad
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Mahsa M. Amoli
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical SciencesTehranIran
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11
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Chen G, Zhou Y, Yu X, Wang J, Luo W, Pang M, Tong J. Genome-Wide Association Study Reveals SNPs and Candidate Genes Related to Growth and Body Shape in Bighead Carp (Hypophthalmichthys nobilis). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:1138-1147. [PMID: 36350467 DOI: 10.1007/s10126-022-10176-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Growth is an economically important trait in bighead carp and other aquaculture species that affects production efficiency. Interestingly, the head of the bighead carp has a high market value in China; therefore, it is important to study the genetic bases of both growth and body shape traits. A genome-wide association study was performed based on 2b-RAD sequencing of 776 individuals to identify SNPs associated with growth and body shape traits, including body weight, body length, body height, and deheaded body length. In total, 26 significant and 19 suggestive SNPs were identified, and more than half of these significant SNPs were clustered in LG16. Two LGs (LG16 and LG21) contained QTLs associated with body weight. Fourteen SNPs of LG16 and two LG21 SNPs were found to be associated with body length. For body height, 12 significantly associated SNPs were identified in LG16. Additionally, 12 SNPs of LG16 and 3 SNPs of LG21 were found to be associated with deheaded body length. Forty-three genes were significantly or suggestively associated with body shape/growth traits based on GWAS results, 18 of which were candidate genes for all BW, BL, BH, and DBL traits. One of these genes, fndc5b, was selected for further analyses. Association analysis revealed that one SNP (g.245 C > T) in the introns of fndc5b was significantly associated with growth-related traits in growth-extreme samples. The mRNA levels of fndc5b in the brains of the lightweight group were significantly higher than those of the heavy-weight group. This study helps to reveal the genetic structure of growth and body development in fish and provides candidate genes for future molecular marker-assisted selection for fast growth and better body conformation in bighead carp.
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Affiliation(s)
- Geng Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Junru Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Weiwei Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100039, China.
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12
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Xiao X, Tang C, Zhai X, Li S, Ma W, Liu K, Kokoro S, Sheerah HA, Zhu H, Cao J. Early-Adulthood Weight Change and Later Physical Activity in Relation to Cardiovascular and All-Cause Mortality: NHANES 1999-2014. Nutrients 2022; 14:nu14234974. [PMID: 36501003 PMCID: PMC9736862 DOI: 10.3390/nu14234974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/12/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022] Open
Abstract
Limited evidence investigated the combined influence of early-adulthood weight change and later physical activity on the risk of cardiovascular (CVD) and all-cause mortality. The aim of this study is to explore the associations of early-adulthood weight change and later physical activity with CVD and all-cause mortality. This is a cohort study of 23,193 US adults aged 40 to 85 years from the National Health and Nutrition Examination Survey (NHANES) 1999 to 2014. Cox proportional hazards regression was used to calculate hazard ratios (HRs) with 95% confidence intervals (CIs) of CVD and all-cause mortality associated with early-adulthood weight change and later physical activity. During a median follow-up of 9.2 years, there were 533 and 2734 cases of CVD and all-cause deaths. Compared with being physically inactive, the HRs of the CVD mortality of being physically active were 0.44 (0.26 to 0.73), 0.58 (0.19 to 1.82), 0.38 (0.17 to 0.86) and 0.46 (0.21 to 1.02) among individuals with stable normal, stable obese, non-obese to obese and maximum overweight early-adulthood weight change patterns. Using stable normal patterns that were physically active later as the reference, other early-adulthood weight change patterns did not show a significantly higher risk of CVD mortality when participants were physically active in later life; later physically inactive participants had a significantly increased risk of CVD mortality, with HRs of 2.17 (1.30 to 3.63), 5.32 (2.51 to 11.28), 2.59 (1.29 to 5.18) and 2.63 (1.32 to 5.26) in the stable normal, stable obese, non-obese to obese and maximum overweight groups, respectively. Similar results can be seen in the analyses for all-cause mortality. Our findings suggest that inadequate physical activity worsens the negative impact of unhealthy early-adulthood weight change patterns, which is worthy of being noted in the improvement of public health.
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Affiliation(s)
- Xinyu Xiao
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Chengyao Tang
- Biomedical Statistics, Department of Integrated Medicine, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita-shi 565-0871, Osaka, Japan
| | - Xiaobing Zhai
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SAR, China
| | - Shiyang Li
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Wenzhi Ma
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Keyang Liu
- Public Health, Department of Social Medicine, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita-shi 565-0871, Osaka, Japan
| | - Shirai Kokoro
- Public Health, Department of Social Medicine, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita-shi 565-0871, Osaka, Japan
| | | | - Huiping Zhu
- Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing 100069, China
- Correspondence: (J.C.); (H.Z.); Tel./Fax: +86-27-68759299 (J.C.)
| | - Jinhong Cao
- School of Public Health, Wuhan University, Wuhan 430071, China
- Correspondence: (J.C.); (H.Z.); Tel./Fax: +86-27-68759299 (J.C.)
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13
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Wang C, Duan M, Lin J, Wang G, Gao H, Yan M, Chen L, He J, Liu W, Yang F, Zhu S. LncRNA and mRNA expression profiles in brown adipose tissue of obesity-prone and obesity-resistant mice. iScience 2022; 25:104809. [PMID: 35992072 PMCID: PMC9382264 DOI: 10.1016/j.isci.2022.104809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/10/2022] [Accepted: 07/15/2022] [Indexed: 11/28/2022] Open
Abstract
Obesity-prone or obesity-resistant phenotypes can exist in individuals who consume the same diet type. Brown adipose tissue functions to dissipate energy in response to cold exposure or overfeeding. Long noncoding RNAs play important roles in a wide range of biological processes. However, systematic examination of lncRNAs in phenotypically divergent mice has not yet been reported. Here, the lncRNA expression profiles in BAT of HFD-induced C57BL/6J mice were investigated by high-throughput RNA sequencing. Genes that play roles in thermogenesis and related pathways were identified. We found lncRNA (Gm44502) may play a thermogenic role in obesity resistance by interacting with six mRNAs. Our results also indicated that seven differentially expressed lncRNAs (4930528G23Rik, Gm39490, Gm5627, Gm15551, Gm16083, Gm36860, Gm42002) may play roles in reducing heat production in obesity susceptibility by interacting with seven differentially expressed mRNAs. The screened lncRNAs may participate in the pathogenesis of weight regulation and provide insight into obesity therapy. First lncRNA profiles in BAT of OR and OP mice via bioinformatic analysis Gm44502 may play a thermogenic role by interacting with 6 mRNAs 7 DElncRNAs may reduce thermogenesis by interacting with 7 DEmRNAs Validation of expression changes of candidate genes in BAT by in vivo or in vitro
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Affiliation(s)
- Congcong Wang
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Meng Duan
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Jinhua Lin
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Guowei Wang
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - He Gao
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Mengsha Yan
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Lin Chen
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Jialing He
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
| | - Wei Liu
- Department of Biochemistry, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Fei Yang
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
- Corresponding author
| | - Shankuan Zhu
- Chronic Disease Research Institute, The Children’s Hospital, and National Clinical Research Center for Child Health, School of Public Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Nutrition and Food Hygiene, School of Public Health, School of Medicine, Zhejiang University, 866 Yu-hang-tang Road, Hangzhou, Zhejiang 310058, China
- Corresponding author
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14
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SARZYNSKI MARKA, RICE TREVAK, DESPRÉS JEANPIERRE, PÉRUSSE LOUIS, TREMBLAY ANGELO, STANFORTH PHILIPR, TCHERNOF ANDRÉ, BARBER JACOBL, FALCIANI FRANCESCO, CLISH CLARY, ROBBINS JEREMYM, GHOSH SUJOY, GERSZTEN ROBERTE, LEON ARTHURS, SKINNER JAMESS, RAO DC, BOUCHARD CLAUDE. The HERITAGE Family Study: A Review of the Effects of Exercise Training on Cardiometabolic Health, with Insights into Molecular Transducers. Med Sci Sports Exerc 2022; 54:S1-S43. [PMID: 35611651 PMCID: PMC9012529 DOI: 10.1249/mss.0000000000002859] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of the HERITAGE Family Study was to investigate individual differences in response to a standardized endurance exercise program, the role of familial aggregation, and the genetics of response levels of cardiorespiratory fitness and cardiovascular disease and diabetes risk factors. Here we summarize the findings and their potential implications for cardiometabolic health and cardiorespiratory fitness. It begins with overviews of background and planning, recruitment, testing and exercise program protocol, quality control measures, and other relevant organizational issues. A summary of findings is then provided on cardiorespiratory fitness, exercise hemodynamics, insulin and glucose metabolism, lipid and lipoprotein profiles, adiposity and abdominal visceral fat, blood levels of steroids and other hormones, markers of oxidative stress, skeletal muscle morphology and metabolic indicators, and resting metabolic rate. These summaries document the extent of the individual differences in response to a standardized and fully monitored endurance exercise program and document the importance of familial aggregation and heritability level for exercise response traits. Findings from genomic markers, muscle gene expression studies, and proteomic and metabolomics explorations are reviewed, along with lessons learned from a bioinformatics-driven analysis pipeline. The new opportunities being pursued in integrative -omics and physiology have extended considerably the expected life of HERITAGE and are being discussed in relation to the original conceptual model of the study.
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Affiliation(s)
- MARK A. SARZYNSKI
- Department of Exercise Science, Arnold School of Public Health, University of South Carolina, Columbia, SC
| | - TREVA K. RICE
- Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - JEAN-PIERRE DESPRÉS
- Department of Kinesiology, Faculty of Medicine, Laval University, Quebec, QC, CANADA
- Quebec Heart and Lung Institute Research Center, Laval University, Québec, QC, CANADA
| | - LOUIS PÉRUSSE
- Department of Kinesiology, Faculty of Medicine, Laval University, Quebec, QC, CANADA
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec, QC, CANADA
| | - ANGELO TREMBLAY
- Department of Kinesiology, Faculty of Medicine, Laval University, Quebec, QC, CANADA
- Institute of Nutrition and Functional Foods (INAF), Laval University, Quebec, QC, CANADA
| | - PHILIP R. STANFORTH
- Department of Kinesiology and Health Education, University of Texas at Austin, Austin, TX
| | - ANDRÉ TCHERNOF
- Quebec Heart and Lung Institute Research Center, Laval University, Québec, QC, CANADA
- School of Nutrition, Laval University, Quebec, QC, CANADA
| | - JACOB L. BARBER
- Department of Exercise Science, Arnold School of Public Health, University of South Carolina, Columbia, SC
| | - FRANCESCO FALCIANI
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UNITED KINGDOM
| | - CLARY CLISH
- Metabolomics Platform, Broad Institute and Harvard Medical School, Boston, MA
| | - JEREMY M. ROBBINS
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
- Cardiovascular Research Center, Beth Israel Deaconess Medical Center, Boston, MA
| | - SUJOY GHOSH
- Cardiovascular and Metabolic Disorders Program and Centre for Computational Biology, Duke-National University of Singapore Medical School, SINGAPORE
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA
| | - ROBERT E. GERSZTEN
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
- Cardiovascular Research Center, Beth Israel Deaconess Medical Center, Boston, MA
| | - ARTHUR S. LEON
- School of Kinesiology, University of Minnesota, Minneapolis, MN
| | | | - D. C. RAO
- Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - CLAUDE BOUCHARD
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA
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Cataloging the potential SNPs (single nucleotide polymorphisms) associated with quantitative traits, viz. BMI (body mass index), IQ (intelligence quotient) and BP (blood pressure): an updated review. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00266-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Single nucleotide polymorphism (SNP) variants are abundant, persistent and widely distributed across the genome and are frequently linked to the development of genetic diseases. Identifying SNPs that underpin complex diseases can aid scientists in the discovery of disease-related genes by allowing for early detection, effective medication and eventually disease prevention.
Main body
Various SNP or polymorphism-based studies were used to categorize different SNPs potentially related to three quantitative traits: body mass index (BMI), intelligence quotient (IQ) and blood pressure, and then uncovered common SNPs for these three traits. We employed SNPedia, RefSNP Report, GWAS Catalog, Gene Cards (Data Bases), PubMed and Google Scholar search engines to find relevant material on SNPs associated with three quantitative traits. As a result, we detected three common SNPs for all three quantitative traits in global populations: SNP rs6265 of the BDNF gene on chromosome 11p14.1, SNP rs131070325 of the SL39A8 gene on chromosome 4p24 and SNP rs4680 of the COMT gene on chromosome 22q11.21.
Conclusion
In our review, we focused on the prevalent SNPs and gene expression activities that influence these three quantitative traits. These SNPs have been used to detect and map complex, common illnesses in communities for homogeneity testing and pharmacogenetic studies. High blood pressure, diabetes and heart disease, as well as BMI, schizophrenia and IQ, can all be predicted using common SNPs. Finally, the results of our work can be used to find common SNPs and genes that regulate these three quantitative features across the genome.
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Wong HSC, Tsai SY, Chu HW, Lin MR, Lin GH, Tai YT, Shen CY, Chang WC. Genome-wide association study identifies genetic risk loci for adiposity in a Taiwanese population. PLoS Genet 2022; 18:e1009952. [PMID: 35051171 PMCID: PMC8853642 DOI: 10.1371/journal.pgen.1009952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 02/17/2022] [Accepted: 11/16/2021] [Indexed: 01/22/2023] Open
Abstract
Overweight and obese are risk factors for various diseases. In Taiwan, the combined prevalence of overweight and obesity has increased dramatically. Here, we conducted a genome-wide association study (GWAS) on four adiposity traits, including body-mass index (BMI), body fat percentage (BF%), waist circumference (WC), and waist-hip ratio (WHR), using the data for more than 21,000 subjects in Taiwan Biobank. Associations were evaluated between 6,546,460 single-nucleotide polymorphisms (SNPs) and adiposity traits, yielding 13 genome-wide significant (GWS) adiposity-associated trait-loci pairs. A known gene, FTO, as well as two BF%-associated loci (GNPDA2-GABRG1 [4p12] and RNU6-2-PIAS1 [15q23]) were identified as pleiotropic effects. Moreover, RALGAPA1 was found as a specific genetic predisposing factor to high BMI in a Taiwanese population. Compared to other populations, a slightly lower heritability of the four adiposity traits was found in our cohort. Surprisingly, we uncovered the importance of neural pathways that might influence BF%, WC and WHR in the Taiwanese (East Asian) population. Additionally, a moderate genetic correlation between the WHR and BMI (γg = 0.52; p = 2.37×10−9) was detected, suggesting different genetic determinants exist for abdominal adiposity and overall adiposity. In conclusion, the obesity-related genetic loci identified here provide new insights into the genetic underpinnings of adiposity in the Taiwanese population.
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Affiliation(s)
- Henry Sung-Ching Wong
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Szu-Yi Tsai
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Min-Rou Lin
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Gan-Hong Lin
- Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yu-Ting Tai
- Department of Anesthesiology, Taipei Municipal Wanfang Hospital, Taipei, Taiwan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
- College of Public Health, China Medical University, Taichung, Taiwan
- * E-mail: (C-YS); (W-CC)
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- * E-mail: (C-YS); (W-CC)
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Sex differences in white adipose tissue expansion: emerging molecular mechanisms. Clin Sci (Lond) 2021; 135:2691-2708. [PMID: 34908104 DOI: 10.1042/cs20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/15/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022]
Abstract
The escalating prevalence of individuals becoming overweight and obese is a rapidly rising global health problem, placing an enormous burden on health and economic systems worldwide. Whilst obesity has well described lifestyle drivers, there is also a significant and poorly understood component that is regulated by genetics. Furthermore, there is clear evidence for sexual dimorphism in obesity, where overall risk, degree, subtype and potential complications arising from obesity all differ between males and females. The molecular mechanisms that dictate these sex differences remain mostly uncharacterised. Many studies have demonstrated that this dimorphism is unable to be solely explained by changes in hormones and their nuclear receptors alone, and instead manifests from coordinated and highly regulated gene networks, both during development and throughout life. As we acquire more knowledge in this area from approaches such as large-scale genomic association studies, the more we appreciate the true complexity and heterogeneity of obesity. Nevertheless, over the past two decades, researchers have made enormous progress in this field, and some consistent and robust mechanisms continue to be established. In this review, we will discuss some of the proposed mechanisms underlying sexual dimorphism in obesity, and discuss some of the key regulators that influence this phenomenon.
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Jacob R, Bertrand C, Llewellyn C, Couture C, Labonté MÈ, Tremblay A, Bouchard C, Drapeau V, Pérusse L. Dietary Mediators of the Genetic Susceptibility to Obesity-Results from the Quebec Family Study. J Nutr 2021; 152:49-58. [PMID: 34610139 PMCID: PMC8754573 DOI: 10.1093/jn/nxab356] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/07/2021] [Accepted: 09/23/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Recent studies showed that eating behaviors such as disinhibition, emotional and external eating, and snacking mediate genetic susceptibility to obesity. It remains unknown if diet quality and intake of specific food groups also mediate the genetic susceptibility to obesity. OBJECTIVE This study aimed to assess if diet quality and intakes of specific food groups mediate the association between a polygenic risk score (PRS) for BMI and BMI and waist circumference (WC). We hypothesized that poor diet quality, high intakes of energy-dense food groups, and low intakes of nutrient-dense food groups mediate the genetic susceptibility to obesity. METHODS This cross-sectional study included 750 participants (56.3% women, aged 41.5 ± 14.9 y, BMI 27.8 ± 7.5 kg/m2) from the Quebec Family Study. A PRSBMI based on >500,000 genetic variants was calculated using LDpred2. Dietary intakes were assessed with a 3-d food record from which a diet quality score (i.e. Nutrient Rich Food Index 6.3) and food groups were derived. Mediation analyses were conducted using a regression-based and bootstrapping approach. RESULTS The PRSBMI explained 25.7% and 19.8% of the variance in BMI and WC, respectively. The association between PRSBMI and BMI was partly mediated by poor diet quality (β = 0.33 ± 0.12; 95% CI: 0.13, 0.60), high intakes of fat and high-fat foods (β = 0.46 ± 0.16; 95% CI: 0.19, 0.79) and sugar-sweetened beverages (β = 0.25 ± 0.14; 95% CI: 0.05, 0.60), and low intakes of vegetables (β = 0.15 ± 0.08; 95% CI: 0.03, 0.32), fruits (β = 0.37 ± 0.12; 95% CI: 0.17, 0.64), and dairy products (β = 0.17 ± 0.09; 95% CI: 0.02, 0.37). The same trends were observed for WC. CONCLUSIONS The genetic susceptibility to obesity was partly mediated by poor diet quality and intakes of specific food groups. These results suggest that improvement in diet quality may reduce obesity risk among individuals with high genetic susceptibility and emphasize the need to intervene on diet quality among these individuals.
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Affiliation(s)
- Raphaëlle Jacob
- Centre Nutrition, santé et société (NUTRISS), Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, Canada,School of Nutrition, Université Laval, Quebec, Canada,Quebec Heart and Lung Institute Research Center, Université Laval, Quebec, Canada
| | - Catherine Bertrand
- Centre Nutrition, santé et société (NUTRISS), Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, Canada,Department of Kinesiology, Faculty of Medicine, Université Laval, Quebec, Canada
| | - Clare Llewellyn
- Department of Behavioural Science and Health, University College London, London, United Kingdom
| | - Christian Couture
- Quebec Heart and Lung Institute Research Center, Université Laval, Quebec, Canada,Department of Kinesiology, Faculty of Medicine, Université Laval, Quebec, Canada
| | - Marie-Ève Labonté
- Centre Nutrition, santé et société (NUTRISS), Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, Canada,School of Nutrition, Université Laval, Quebec, Canada
| | - Angelo Tremblay
- Centre Nutrition, santé et société (NUTRISS), Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, Canada,Quebec Heart and Lung Institute Research Center, Université Laval, Quebec, Canada,Department of Kinesiology, Faculty of Medicine, Université Laval, Quebec, Canada
| | | | - Vicky Drapeau
- Centre Nutrition, santé et société (NUTRISS), Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, Canada,Quebec Heart and Lung Institute Research Center, Université Laval, Quebec, Canada,Department of Physical Education, Faculty of Education, Université Laval, Quebec, Canada
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Velazquez-Roman J, Angulo-Zamudio UA, León-Sicairos N, Medina-Serrano J, DeLira-Bustillos N, Villamil-Ramírez H, Canizales-Quinteros S, Macías-Kauffer L, Campos-Romero A, Alcántar-Fernández J, Canizalez-Roman A. Association of FTO, ABCA1, ADRB3, and PPARG variants with obesity, type 2 diabetes, and metabolic syndrome in a Northwest Mexican adult population. J Diabetes Complications 2021; 35:108025. [PMID: 34420811 DOI: 10.1016/j.jdiacomp.2021.108025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/10/2021] [Accepted: 08/14/2021] [Indexed: 11/28/2022]
Abstract
AIM To identify associations among allelic variants of the genes FTO, ABCA1, ADRB3, and PPARG with anthropometric and biochemical traits, metabolic diseases (obesity, T2D or metabolic syndrome) in an adult population from Northwest Mexico. METHODS Blood samples were collected from 846 subjects including 266 normal weight subjects, 285 with obesity, and 295 with T2D. Of the 846 persons in the study, 365 presented metabolic syndrome diagnostic criteria. Anthropometric and biochemical traits were recorded and 4 single nucleotide polymorphisms (SNPs): FTO rs9939609 A-allele, ABCA1 rs9282541 A-allele, ADRB3 rs4994 G-allele, and PPARG rs1801282 G-allele were genotyped by real-time PCR. RESULTS FTO rs9939609 A-allele was significantly associated with obesity (p: 8.3 × 10-4), and metabolic syndrome (p: 0.001), but no individual SNPs were significantly associated with T2D. Finally, the cumulative risk of the four SNPs was significantly associated with obesity (p: 1.95 × 10-4). CONCLUSION Associations in FTO, ABCA, ADRB3, and PPARG SNPs presented in this study with obesity and metabolic syndrome could represent a risk for developing metabolic diseases in Northwest Mexican adult subjects.
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Affiliation(s)
- Jorge Velazquez-Roman
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico
| | - Uriel A Angulo-Zamudio
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico
| | - Nidia León-Sicairos
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico; Pediatric Hospital of Sinaloa, 80200 Culiacan, Sinaloa, Mexico
| | - Julio Medina-Serrano
- Programa de Maestría en Ciencias en Biomedicina Molecular, UAS, 80246 Culiacan, Sinaloa, Mexico; Coordinación de Planeación y Enlace Institucional, Órgano de Operación Administrativa Desconcentrada (OOAD) de Sinaloa, Instituto Mexicano del Seguro Social (IMSS), Culiacan Sinaloa, Mexico
| | - Nora DeLira-Bustillos
- Programa de Maestría en Ciencias en Biomedicina Molecular, UAS, 80246 Culiacan, Sinaloa, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/INMEGEN, Mexico City, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/INMEGEN, Mexico City, Mexico
| | - Luis Macías-Kauffer
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/INMEGEN, Mexico City, Mexico
| | | | | | - Adrian Canizalez-Roman
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico; The Women's Hospital, Secretariat of Health, 80020 Culiacan, Sinaloa, Mexico.
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20
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Bouchard C. Genetics of Obesity: What We Have Learned Over Decades of Research. Obesity (Silver Spring) 2021; 29:802-820. [PMID: 33899337 DOI: 10.1002/oby.23116] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/14/2022]
Abstract
There is a genetic component to human obesity that accounts for 40% to 50% of the variability in body weight status but that is lower among normal weight individuals (about 30%) and substantially higher in the subpopulation of individuals with obesity and severe obesity (about 60%-80%). The appreciation that heritability varies across classes of BMI represents an important advance. After controlling for BMI, ectopic fat and fat distribution traits are characterized by heritability levels ranging from 30% to 55%. Defects in at least 15 genes are the cause of monogenic obesity cases, resulting mostly from deficiencies in the leptin-melanocortin signaling pathway. Approximately two-thirds of the BMI heritability can be imputed to common DNA variants, whereas low-frequency and rare variants explain the remaining fraction. Diminishing allele effect size is observed as the number of obesity-associated variants expands, with most BMI-increasing or -decreasing alleles contributing only a few grams or less to body weight. Obesity-promoting alleles exert minimal effects in normal weight individuals but have larger effects in individuals with a proneness to obesity, suggesting a higher penetrance; however, it is not known whether these larger effect sizes precede obesity or are caused by an obese state. The obesity genetic risk is conditioned by thousands of DNA variants that make genetically based obesity prevention and treatment a major challenge.
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Affiliation(s)
- Claude Bouchard
- Pennington Biomedical Research Center, Baton Rouge, Louisiana, USA
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21
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Huang Y, Li Y, Wang X, Yu J, Cai Y, Zheng Z, Li R, Zhang S, Chen N, Asadollahpour Nanaei H, Hanif Q, Chen Q, Fu W, Li C, Cao X, Zhou G, Liu S, He S, Li W, Chen Y, Chen H, Lei C, Liu M, Jiang Y. An atlas of CNV maps in cattle, goat and sheep. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1747-1764. [PMID: 33486588 DOI: 10.1007/s11427-020-1850-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/16/2020] [Indexed: 11/26/2022]
Abstract
Copy number variation (CNV) is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans, animals and plants. However, the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown. Here, we generated CNV region (CNVR) datasets which were diverged or shared among cattle, goat, and sheep, including 886 individuals from 171 diverse populations. Using 9 environmental factors for genome-wide association study (GWAS), we identified a series of candidate CNVRs, including genes relating to immunity, tick resistance, multi-drug resistance, and muscle development. The number of CNVRs shared between species is significantly higher than expected (P<0.00001), and these CNVRs may be more persist than the single nucleotide polymorphisms (SNPs) shared between species. We also identified genomic regions under long-term balancing selection and uncovered the potential diversity of the selected CNVRs close to the important functional genes. This study provides the evidence that balancing selection might be more common in mammals than previously considered, and might play an important role in the daily activities of these ruminant species.
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Affiliation(s)
- Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yunjia Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xihong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jiantao Yu
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Yudong Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shunjin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | | | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, 577, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, 45650, Islamabad, Pakistan
| | - Qiuming Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Weiwei Fu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiukai Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shudong Liu
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Sangang He
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Biotechnology Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, 830026, China
| | - Wenrong Li
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Biotechnology Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, 830026, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Mingjun Liu
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Biotechnology Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, 830026, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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Genome-wide association study of brain amyloid deposition as measured by Pittsburgh Compound-B (PiB)-PET imaging. Mol Psychiatry 2021; 26:309-321. [PMID: 30361487 PMCID: PMC6219464 DOI: 10.1038/s41380-018-0246-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 07/31/2018] [Indexed: 12/25/2022]
Abstract
Deposition of amyloid plaques in the brain is one of the two main pathological hallmarks of Alzheimer's disease (AD). Amyloid positron emission tomography (PET) is a neuroimaging tool that selectively detects in vivo amyloid deposition in the brain and is a reliable endophenotype for AD that complements cerebrospinal fluid biomarkers with regional information. We measured in vivo amyloid deposition in the brains of ~1000 subjects from three collaborative AD centers and ADNI using 11C-labeled Pittsburgh Compound-B (PiB)-PET imaging followed by meta-analysis of genome-wide association studies, first to our knowledge for PiB-PET, to identify novel genetic loci for this endophenotype. The APOE region showed the most significant association where several SNPs surpassed the genome-wide significant threshold, with APOE*4 being most significant (P-meta = 9.09E-30; β = 0.18). Interestingly, after conditioning on APOE*4, 14 SNPs remained significant at P < 0.05 in the APOE region that were not in linkage disequilibrium with APOE*4. Outside the APOE region, the meta-analysis revealed 15 non-APOE loci with P < 1E-05 on nine chromosomes, with two most significant SNPs on chromosomes 8 (P-meta = 4.87E-07) and 3 (P-meta = 9.69E-07). Functional analyses of these SNPs indicate their potential relevance with AD pathogenesis. Top 15 non-APOE SNPs along with APOE*4 explained 25-35% of the amyloid variance in different datasets, of which 14-17% was explained by APOE*4 alone. In conclusion, we have identified novel signals in APOE and non-APOE regions that affect amyloid deposition in the brain. Our data also highlights the presence of yet to be discovered variants that may be responsible for the unexplained genetic variance of amyloid deposition.
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Increased Plasma Levels of Adenylate Cyclase 8 and cAMP Are Associated with Obesity and Type 2 Diabetes: Results from a Cross-Sectional Study. BIOLOGY 2020; 9:biology9090244. [PMID: 32847122 PMCID: PMC7563501 DOI: 10.3390/biology9090244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/23/2022]
Abstract
Adenylate cyclases (ADCYs) catalyze the conversion of ATP to cAMP, an important co-factor in energy homeostasis. Giving ADCYs role in obesity, diabetes and inflammation, we questioned whether calcium-stimulated ADCY isoforms may be variably detectable in human plasma. We report the results of a cross-sectional study assessing circulating levels of functional ADCY1, -3 and -8 in patients with T2D vs. non-diabetic (ND) controls in association with obesity. ADCY1 levels exhibited no significant change between ND and T2D groups. ADCY3 levels were lower in obese individuals, albeit not statistically significantly. In contrast, ADCY8 plasma levels were significantly higher in obese and T2D patients compared to controls (p = 0.001) and patients with T2D only (p = 0.039). ADCY8 levels correlated positively with body mass index and Hb1Ac levels. Parallel to the increased ADCY8 levels, significantly higher cAMP levels were observed in patients with T2D compared with ND controls, and further elevated in obese individuals, irrespective of T2D status. Additionally, cAMP levels positively correlated with fasting plasma glucose levels. In conclusion, the current cross-sectional study demonstrated elevated levels of circulating plasma ADCY8 and cAMP in obesity and T2D.
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Identification of strong candidate genes for backfat and intramuscular fatty acid composition in three crosses based on the Iberian pig. Sci Rep 2020; 10:13962. [PMID: 32811870 PMCID: PMC7435270 DOI: 10.1038/s41598-020-70894-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 08/02/2020] [Indexed: 12/11/2022] Open
Abstract
Meat quality has an important genetic component and can be modified by the fatty acid (FA) composition and the amount of fat contained in adipose tissue and muscle. The present study aimed to find genomic regions associated with the FA composition in backfat and muscle (longissimus dorsi) in 439 pigs with three different genetic backgrounds but having the Iberian breed in common. Genome-wide association studies (GWAS) were performed between 38,424 single-nucleotide polymorphisms (SNPs) covering the pig genome and 60 phenotypic traits related to backfat and muscle FA composition. Nine significant associated regions were found in backfat on the Sus scrofa chromosomes (SSC): SSC1, SSC2, SSC4, SSC6, SSC8, SSC10, SSC12, and SSC16. For the intramuscular fat, six significant associated regions were identified on SSC4, SSC13, SSC14, and SSC17. A total of 52 candidate genes were proposed to explain the variation in backfat and muscle FA composition traits. GWAS were also reanalysed including SNPs on five candidate genes (ELOVL6, ELOVL7, FADS2, FASN, and SCD). Regions and molecular markers described in our study may be useful for meat quality selection of commercial pig breeds, although several polymorphisms were breed-specific, and further analysis would be needed to evaluate possible causal mutations.
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Banerjee P, Carmelo VAO, Kadarmideen HN. Integrative Analysis of Metabolomic and Transcriptomic Profiles Uncovers Biological Pathways of Feed Efficiency in Pigs. Metabolites 2020; 10:E275. [PMID: 32640603 PMCID: PMC7408121 DOI: 10.3390/metabo10070275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 12/12/2022] Open
Abstract
Feed efficiency (FE) is an economically important trait. Thus, reliable predictors would help to reduce the production cost and provide sustainability to the pig industry. We carried out metabolome-transcriptome integration analysis on 40 purebred Duroc and Landrace uncastrated male pigs to identify potential gene-metabolite interactions and explore the molecular mechanisms underlying FE. To this end, we applied untargeted metabolomics and RNA-seq approaches to the same animals. After data quality control, we used a linear model approach to integrate the data and find significant differently correlated gene-metabolite pairs separately for the breeds (Duroc and Landrace) and FE groups (low and high FE) followed by a pathway over-representation analysis. We identified 21 and 12 significant gene-metabolite pairs for each group. The valine-leucine-isoleucine biosynthesis/degradation and arginine-proline metabolism pathways were associated with unique metabolites. The unique genes obtained from significant metabolite-gene pairs were associated with sphingolipid catabolism, multicellular organismal process, cGMP, and purine metabolic processes. While some of the genes and metabolites identified were known for their association with FE, others are novel and provide new avenues for further research. Further validation of genes, metabolites, and gene-metabolite interactions in larger cohorts will elucidate the regulatory mechanisms and pathways underlying FE.
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Affiliation(s)
| | | | - Haja N. Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (P.B.); (V.A.O.C.)
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Duarte IDAE, Milenkovic D, Borges TKDS, Rosa AJDM, Morand C, de Oliveira LDL, Costa AM. Acute Effects of the Consumption of Passiflora setacea Juice on Metabolic Risk Factors and Gene Expression Profile in Humans. Nutrients 2020; 12:nu12041104. [PMID: 32316129 PMCID: PMC7231153 DOI: 10.3390/nu12041104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Passiflora setacea (PS) is a passionfruit variety of the Brazilian savannah and is a rich source of plant food bioactives with potential anti-inflammatory activity. This study aimed to investigate the effect of an acute intake of PS juice upon inflammation, metabolic parameters, and gene expression on circulating immune cells in humans. Methods: Overweight male volunteers (n = 12) were enrolled in two double-blind placebo-controlled studies. Blood samples were collected from fasting volunteers 3 h after the consumption of 250 mL of PS juice or placebo (PB). Metabolic parameters (insulin, glucose, total cholesterol, high-density lipoprotein (LDL), high-density lipoprotein (HDL), and total triglycerides) and circulating cytokines were evaluated (study 1). Peripheral blood mononuclear cell (PBMC) from the same subjects were isolated and RNA was extracted for transcriptomic analyses using microarrays (study 2). Results: Insulin and homeostatic model assessment for insulin resistance (HOMA-IR) levels decreased statistically after the PS juice intake, whereas HDL level increased significantly. Interleukin (IL)-17A level increased after placebo consumption, whereas its level remained unchanged after PS juice consumption. Nutrigenomic analyses revealed 1327 differentially expressed genes after PS consumption, with modulated genes involved in processes such as inflammation, cell adhesion, or cytokine–cytokine receptor. Conclusion: Taken together, these clinical results support the hypothesis that PS consumption may help the prevention of cardiometabolic diseases.
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Affiliation(s)
- Isabella de Araújo Esteves Duarte
- Postgraduate Program in Human Nutrition, College of Health Sciences, Campus Universitário Darcy Ribeiro, Universidade de Brasília, Brasília DF 70.910-900, Brazil;
- Correspondence: ; Tel.: +55-61-99996-8004
| | - Dragan Milenkovic
- Unité de Nutrition Humaine, Université Clermont Auvergne, INRAE, UNH, F-63000 Clermont-Ferrand, France; (D.M.); (C.M.)
- Department of Internal Medicine, Division of Cardiovascular Medicine, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | | | | | - Christine Morand
- Unité de Nutrition Humaine, Université Clermont Auvergne, INRAE, UNH, F-63000 Clermont-Ferrand, France; (D.M.); (C.M.)
| | - Livia de Lacerda de Oliveira
- Postgraduate Program in Human Nutrition, College of Health Sciences, Campus Universitário Darcy Ribeiro, Universidade de Brasília, Brasília DF 70.910-900, Brazil;
| | - Ana Maria Costa
- Laboratory of Food Science, Embrapa Cerrados, Planaltina DF 73.310-970, Brazil; (A.J.d.M.R.); (A.M.C.)
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Yang P, Zhang Z, Xu J, Qu K, Lyv S, Wang X, Cai C, Li Z, Wang E, Xie J, Ru B, Xu Z, Lei C, Chen H, Huang B, Huang Y. The Association of the Copy Number Variation of the MLLT10 Gene with Growth Traits of Chinese Cattle. Animals (Basel) 2020; 10:ani10020250. [PMID: 32033330 PMCID: PMC7070264 DOI: 10.3390/ani10020250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/10/2020] [Accepted: 02/01/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Copy number variation is a common genetic polymorphism, mainly represented by submicroscopic levels of deletion and duplication, caused by rearrangement of the genome. It is well-known that the copy number variation of a gene is associated with growth traits of livestock. In this study, we detected the correlation between the copy number variation of the the MLLT10 gene and the growth traits of Chinese yellow cattle. We found that the copy number variation of the MLLT10 gene has a significant influence on hip width, rump length, hucklebone width, and cannon bone circumference of some Chinese yellow cattle breeds. The results provide preliminary suggestions for Chinese yellow cattle breeding and new insights about the future of copy number variation (CNV) as a new promising molecular marker in animal breeding. Abstract Copy number variation is a part of genomic structural variation and has caused widespread concern. According to the results of high-throughput screening of the MLLT10 gene, we found that the copy number variation region of the MLLT10 gene was correlated with bovine growth traits. We aimed to detect the MLLT10 gene copy number variation and provide materials for the Chinese yellow cattle breed. In this study, the SPSS software was used to analyze the correlation among the copy number type of six different cattle breeds (i.e., Qinchuan, Xianan, Jiaxian, Yanbian, Sinan, Yunling) and the corresponding growth traits. The results showed the following: In Qinchuan cattle, the copy number duplication type was greater than the deletion and normal types; in Xianan cattle, the copy number duplication and normal types were less as compared with the deletion type; and in Yunling cattle, the frequency of the duplication type was dominant among the three types of copy number variants. The correlation analysis result showed that there is a significant correlation between the copy number variation (CNV) of the MLLT10 gene and the growth traits of three cattle breeds. Furthermore, correlation analysis showed that MLLT10 CNV had positive effects on growth traits such as hip width, rump length, hucklebone width, and cannon bone circumference (p < 0.05). This study provides a basis for the molecular-assisted marker breeding of cattle and contributes to the breeding of cattle.
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Affiliation(s)
- Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 45002, China; (Z.Z.); (S.L.); (E.W.)
| | - Jiawei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Kaixing Qu
- Yunnan Academy of Grassland Animal Science, Kunming 650212, China;
| | - Shijie Lyv
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 45002, China; (Z.Z.); (S.L.); (E.W.)
| | - Xianwei Wang
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Cuicui Cai
- Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 756000, China; (C.C.); (J.X.)
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 45002, China; (Z.Z.); (S.L.); (E.W.)
| | - Jianliang Xie
- Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 756000, China; (C.C.); (J.X.)
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Zejun Xu
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China; (X.W.); (Z.L.); (B.R.); (Z.X.)
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
| | - Bizhi Huang
- Yunnan Academy of Grassland Animal Science, Kunming 650212, China;
- Correspondence: (B.H.); (Y.H.)
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.Y.); (J.X.); (C.L.); (H.C.)
- Correspondence: (B.H.); (Y.H.)
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28
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Huerta-Chagoya A, Moreno-Macías H, Sevilla-González M, Rodríguez-Guillén R, Ordóñez-Sánchez ML, Gómez-Velasco D, Muñóz-Hernández L, Segura-Kato Y, Arellano-Campos O, Cruz-Bautista I, Aguilar-Salinas CA, Tusié-Luna T. Contribution of Known Genetic Risk Variants to Dyslipidemias and Type 2 Diabetes in Mexico: A Population-Based Nationwide Study. Genes (Basel) 2020; 11:genes11010114. [PMID: 31968565 PMCID: PMC7016795 DOI: 10.3390/genes11010114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/13/2022] Open
Abstract
Dyslipidemias are common risk factors for the development of chronic disorders including type 2 diabetes (T2D). Over 100 associated loci have been identified but few reports have evaluated the population attributable fraction captured by them in population-based nationwide surveys. Therefore, we determined the population contribution of a set of known genetic risk variants to the development of dyslipidemias and T2D in Mexico. This study included 1665 participants from a Mexican National Health Survey carried out in the year 2000. It is a probabilistic complex sample survey of households, which comprises representative data at a national level. 103 previously reported SNPs associated with different dyslipidemias or T2D were genotyped and used to compute polygenic risk scores. We found that the previously known variants associated with dyslipidemias explain at most 7% of the total risk variance of lipid levels. In contrast, the known genetic risk component for T2D explained a negligible amount of variance (0.1%). Notably, variants derived from the Native-American ancestry have the strongest effect and contribute with a high proportion of the variance. These results support the need for additional studies aimed to identify specific genetic risk variants for Mexican population.
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Affiliation(s)
- Alicia Huerta-Chagoya
- CONACYT, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 03940, Mexico;
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | | | - Magdalena Sevilla-González
- Clinical and Traslational Epidemiological Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Rosario Rodríguez-Guillén
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - María L. Ordóñez-Sánchez
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Donají Gómez-Velasco
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Liliana Muñóz-Hernández
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Yayoi Segura-Kato
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Olimpia Arellano-Campos
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Ivette Cruz-Bautista
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Carlos A. Aguilar-Salinas
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, Mexico 04510, Mexico
- Correspondence: ; Tel.: +52-55-5655-0011
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29
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Jung SY, Papp JC, Sobel EM, Zhang ZF. Post Genome-Wide Gene-Environment Interaction Study Using Random Survival Forest: Insulin Resistance, Lifestyle Factors, and Colorectal Cancer Risk. Cancer Prev Res (Phila) 2019; 12:877-890. [PMID: 31554631 PMCID: PMC6893139 DOI: 10.1158/1940-6207.capr-19-0278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/28/2019] [Accepted: 09/20/2019] [Indexed: 01/23/2023]
Abstract
Molecular and genetic pathways of insulin resistance (IR) connecting colorectal cancer and obesity factors in postmenopausal women remain inconclusive. We examined the IR pathways on both genetic and phenotypic perspectives at the genome-wide level. We further constructed colorectal cancer risk profiles with the most predictive IR SNPs and lifestyle factors. In our earlier genome-wide association gene-environmental interaction study, we used data from a large cohort of postmenopausal women in the Women's Health Initiative Database for Genotypes and Phenotypes Study and identified 58 SNPs in relation to IR phenotypes. In this study, we evaluated the identified IR SNPs and selected 34 lifestyles for their association with colorectal cancer risk in a total of 11,078 women (including 736 women with colorectal cancer) using a 2-stage multimodal random survival forest analysis. In overall and subgroup (defined via body mass index, exercise, and dietary-fat intake) analyses, we identified 2 SNPs (LINC00460 rs1725459 and MTRR rs722025) and lifetime cumulative exposure to estrogen (oral contraceptive use) and cigarette smoking as the most common and strongest predictive markers for colorectal cancer risk across the analyses. The combinations of genetic and lifestyle factors had much greater impact on colorectal cancer risk than any individual risk factors, and a possible synergism existed to increase colorectal cancer risk in a gene-behavior dose-dependent manner. Our findings may inform research on the role of IR in the etiology of colorectal cancer and contribute to more accurate prediction of colorectal cancer risk, suggesting potential intervention strategies for women with specific genotypes and lifestyles to reduce their colorectal cancer risk.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of California, Los Angeles, Los Angeles, California.
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Eric M Sobel
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
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30
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de Toro-Martín J, Guénard F, Bouchard C, Tremblay A, Pérusse L, Vohl MC. The Challenge of Stratifying Obesity: Attempts in the Quebec Family Study. Front Genet 2019; 10:994. [PMID: 31649740 PMCID: PMC6796792 DOI: 10.3389/fgene.2019.00994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 09/18/2019] [Indexed: 01/23/2023] Open
Abstract
Background and aims: Obesity is a major health problem worldwide. Given the heterogeneous obesity phenotype, an optimal obesity stratification would improve clinical management. Since obesity has a strong genetic component, we aimed to develop a polygenic risk score (PRS) to stratify obesity according to the genetic background of the individuals. Methods: A total of 231 single nucleotide polymorphisms (SNP) significantly associated to body mass index (BMI) from 21 genome-wide association studies were genotyped or imputed in 881 subjects from the Quebec Family Study (QFS). The population was randomly split into discovery (80%; n = 704) and validation (20%; n = 177) samples with similar obesity (BMI ≥ 30) prevalence (27.8% and 28.2%, respectively). Family-based associations with obesity were tested for every SNP in the discovery sample and a weighed and continuous PRS231 was constructed. Generalized linear mixed effects models were used to test the association of PRS231 with obesity in the QFS discovery sample and validated in the QFS replication sample. Furthermore, the Fatty Acid Sensor (FAS) Study (n = 141; 27.7% obesity prevalence) was used as an independent sample to replicate the results. Results: The linear trend test demonstrated a significant association of PRS231 with obesity in the QFS discovery sample (ORtrend = 1.19 [95% CI, 1.14-1.24]; P = 2.0x10-16). We also found that the obesity prevalence was significantly greater in the higher PRS231 quintiles compared to the lowest quintile. Significant and consistent results were obtained in the QFS validation sample for both the linear trend test (ORtrend = 1.16 [95% CI, 1.07-1.26]; P = 6.7x10-4), and obesity prevalence across quintiles. These results were partially replicated in the FAS sample (ORtrend = 1.12 [95% CI, 1.02-1.24]; P = 2.2x10-2). PRS231 explained 7.5%, 3.2%, and 1.2% of BMI variance in QFS discovery, QFS validation, and FAS samples, respectively. Conclusions: These results revealed that genetic background in the form of a 231 BMI-associated PRS has a significant impact on obesity, but a limited potential to accurately stratify it. Further studies are encouraged on larger populations.
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Affiliation(s)
- Juan de Toro-Martín
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, QC, Canada.,School of Nutrition, Université Laval, Quebec, QC, Canada
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, QC, Canada.,School of Nutrition, Université Laval, Quebec, QC, Canada
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, United States
| | - Angelo Tremblay
- Department of Kinesiology, Université Laval, Quebec, QC, Canada.,Quebec Heart and Lung Institute Research Center, Quebec, QC, Canada
| | - Louis Pérusse
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, QC, Canada.,Department of Kinesiology, Université Laval, Quebec, QC, Canada
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec, QC, Canada.,School of Nutrition, Université Laval, Quebec, QC, Canada
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31
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Huebschmann AG, Huxley RR, Kohrt WM, Zeitler P, Regensteiner JG, Reusch JEB. Sex differences in the burden of type 2 diabetes and cardiovascular risk across the life course. Diabetologia 2019; 62:1761-1772. [PMID: 31451872 PMCID: PMC7008947 DOI: 10.1007/s00125-019-4939-5] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 05/29/2019] [Indexed: 12/11/2022]
Abstract
By 2017 estimates, diabetes mellitus affects 425 million people globally; approximately 90-95% of these have type 2 diabetes. This narrative review highlights two domains of sex differences related to the burden of type 2 diabetes across the life span: sex differences in the prevalence and incidence of type 2 diabetes, and sex differences in the cardiovascular burden conferred by type 2 diabetes. In the presence of type 2 diabetes, the difference in the absolute rates of cardiovascular disease (CVD) between men and women lessens, albeit remaining higher in men. Large-scale observational studies suggest that type 2 diabetes confers 25-50% greater excess risk of incident CVD in women compared with men. Physiological and behavioural mechanisms that may underpin both the observed sex differences in the prevalence of type 2 diabetes and the associated cardiovascular burden are discussed in this review. Gender differences in social behavioural norms and disparities in provider-level treatment patterns are also highlighted, but not described in detail. We conclude by discussing research gaps in this area that are worthy of further investigation.
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Affiliation(s)
- Amy G Huebschmann
- Center for Women's Health Research, University of Colorado School of Medicine, MS C263, 12348 E. Montview Boulevard, Aurora, CO, 80045, USA
- Division of General Internal Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Rachel R Huxley
- College of Science, Health and Engineering, La Trobe University, Melbourne, VIC, Australia
- The George Institute for Global Health, University of New South Wales, Sydney, NSW, Australia
| | - Wendy M Kohrt
- Center for Women's Health Research, University of Colorado School of Medicine, MS C263, 12348 E. Montview Boulevard, Aurora, CO, 80045, USA
- Division of Geriatric Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, USA
| | - Philip Zeitler
- Division of Pediatric Endocrinology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Judith G Regensteiner
- Center for Women's Health Research, University of Colorado School of Medicine, MS C263, 12348 E. Montview Boulevard, Aurora, CO, 80045, USA
- Division of General Internal Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Division of Cardiology, University of Colorado School of Medicine (CU-SOM), Aurora, CO, USA
| | - Jane E B Reusch
- Center for Women's Health Research, University of Colorado School of Medicine, MS C263, 12348 E. Montview Boulevard, Aurora, CO, 80045, USA.
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, USA.
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado School of Medicine, Aurora, CO, USA.
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32
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Karlsson T, Rask-Andersen M, Pan G, Höglund J, Wadelius C, Ek WE, Johansson Å. Contribution of genetics to visceral adiposity and its relation to cardiovascular and metabolic disease. Nat Med 2019; 25:1390-1395. [DOI: 10.1038/s41591-019-0563-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/29/2019] [Indexed: 12/17/2022]
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Nordstoga AL, Zotcheva E, Svedahl ER, Nilsen TIL, Skarpsno ES. Long-term changes in body weight and physical activity in relation to all-cause and cardiovascular mortality: the HUNT study. Int J Behav Nutr Phys Act 2019; 16:45. [PMID: 31109336 PMCID: PMC6528195 DOI: 10.1186/s12966-019-0809-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/10/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most previous studies have relied on single measurements of body weight and physical activity and have not considered the interplay between long-term changes in body weight and physical activity in relation to mortality. The aim of the current study was therefore to examine the joint effect of changes in body weight and leisure-time physical activity over a period of ~ 10 years on all-cause and cardiovascular mortality. METHODS The study population comprised 34,257 individuals who participated in the first (1984-86) and second (1995-97) waves of the HUNT Study, and were followed up through the Norwegian Cause of Death Registry until December 31st, 2013. We used Cox regression to estimate hazard ratios (HR) with 95% confidence intervals (CI) of death associated with changes in body weight and leisure-time physical activity. RESULTS Compared to the reference group with stable weight who were long-term physically active, people who gained ≥5% of their weight had a HR for all-cause mortality of 1.54 (95% CI: 1.28-1.85) if they were long-term physically inactive; a HR of 1.23 (1.09-1.40) if they became physically active, and a HR of 1.00 (95% CI 0.94-1.06) if they were long-term physically active. The corresponding HRs for cardiovascular mortality were 1.57 (95% CI 1.17-2.12), 1.28 (95% CI 1.04-1.58) and 1.06 (95% CI 0.96-1.16), respectively. Long-term physical inactivity was associated with increased all-cause (HR 1.29; 95% CI 1.08-1.53) and cardiovascular (HR 1.37; 95% CI 1.05-1.79) mortality among those who were weight stable. CONCLUSIONS The risk of all-cause and cardiovascular mortality is particularly evident among people who gain weight while remaining inactive during a ~ 10 year period. However, participants who remained physically active had the lowest risk of premature mortality, regardless of maintenance or increase in weight. These findings suggest that there is an interplay between long-term changes in body weight and physical activity that should receive particular attention in the prevention of premature mortality.
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Affiliation(s)
- Anne Lovise Nordstoga
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Håkon Jarls gate, 11, 7030, Trondheim, Norway
| | - Ekaterina Zotcheva
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Håkon Jarls gate, 11, 7030, Trondheim, Norway.
| | - Ellen Rabben Svedahl
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Håkon Jarls gate, 11, 7030, Trondheim, Norway
| | - Tom I L Nilsen
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Håkon Jarls gate, 11, 7030, Trondheim, Norway.,Clinic of Anaesthesia and Intensive Care, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Eivind Schjelderup Skarpsno
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Håkon Jarls gate, 11, 7030, Trondheim, Norway.,Department of Neurology and Clinical Neurophysiology, St. Olavs Hospital, Trondheim, Norway
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Jung SY, Papp JC, Sobel EM, Yu H, Zhang ZF. Breast Cancer Risk and Insulin Resistance: Post Genome-Wide Gene-Environment Interaction Study Using a Random Survival Forest. Cancer Res 2019; 79:2784-2794. [PMID: 30936085 PMCID: PMC6522308 DOI: 10.1158/0008-5472.can-18-3688] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/13/2019] [Accepted: 03/25/2019] [Indexed: 01/17/2023]
Abstract
Obesity-insulin connections have been considered potential risk factors for postmenopausal breast cancer, and the association between insulin resistance (IR) genotypes and phenotypes can be modified by obesity-lifestyle factors, affecting breast cancer risk. In this study, we explored the role of IR in those pathways at the genome-wide level. We identified IR-genetic factors and selected lifestyles to generate risk profiles for postmenopausal breast cancer. Using large-scale cohort data from postmenopausal women in the Women's Health Initiative Database for Genotypes and Phenotypes Study, our previous genome-wide association gene-behavior interaction study identified 58 loci for associations with IR phenotypes (homeostatic model assessment-IR, hyperglycemia, and hyperinsulinemia). We evaluated those single-nucleotide polymorphisms (SNP) and additional 31 lifestyles in relation to breast cancer risk by conducting a two-stage multimodal random survival forest analysis. We identified the most predictive genetic and lifestyle variables in overall and subgroup analyses [stratified by body mass index (BMI), exercise, and dietary fat intake]. Two SNPs (LINC00460 rs17254590 and MKLN1 rs117911989), exogenous factors related to lifetime cumulative exposure to estrogen, BMI, and dietary alcohol consumption were the most common influential factors across the analyses. Individual SNPs did not have significant associations with breast cancer, but SNPs and lifestyles combined synergistically increased the risk of breast cancer in a gene-behavior, dose-dependent manner. These findings may contribute to more accurate predictions of breast cancer and suggest potential intervention strategies for women with specific genetic and lifestyle factors to reduce their breast cancer risk. SIGNIFICANCE: These findings identify insulin resistance SNPs in combination with lifestyle as synergistic factors for breast cancer risk, suggesting lifestyle changes can prevent breast cancer in women who carry the risk genotypes.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, Jonsson Comprehensive Cancer Center, School of Nursing, University of California, Los Angeles, Los Angeles, California.
| | - Jeanette C Papp
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Eric M Sobel
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Zuo-Feng Zhang
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
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Ahn J, Wu H, Lee K. Integrative Analysis Revealing Human Adipose-Specific Genes and Consolidating Obesity Loci. Sci Rep 2019; 9:3087. [PMID: 30816281 PMCID: PMC6395763 DOI: 10.1038/s41598-019-39582-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/21/2019] [Indexed: 12/11/2022] Open
Abstract
Identification of adipose-specific genes has contributed to an understanding of mechanisms underlying adipocyte development and obesity. Herein, our analyses of the recent Genotype-Tissue Expression (GTEx) database revealed 38 adipose-specific/enhanced protein coding genes, among which 3 genes were novel adipose-specific, and 414 highly differentially expressed genes (DEGs) between subcutaneous and omental adipose depots. By integrative analyses of genome-wide association studies (GWASs), 14 adipose-specific/enhanced genes and 60 DEGs were found to be associated with obesity-related traits and diseases, consolidating evidence for contribution of these genes to the regional fat distribution and obesity phenotypes. In addition, expression of HOXC cluster was up-regulated in subcutaneous adipose tissue, and the majority of the HOXB cluster was expressed highly in omental adipose tissue, indicating differential expression patterns of HOX clusters in adipose depots. Our findings on the distinct gene expression profiles in adipose tissue and their relation to obesity provide an important foundation for future functional biological studies and therapeutic targets in obesity and associated diseases.
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Affiliation(s)
- Jinsoo Ahn
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Huiguang Wu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA.,College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA.
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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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Vukovic R, Dos Santos TJ, Ybarra M, Atar M. Children With Metabolically Healthy Obesity: A Review. Front Endocrinol (Lausanne) 2019; 10:865. [PMID: 31920976 PMCID: PMC6914809 DOI: 10.3389/fendo.2019.00865] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023] Open
Abstract
Children with "metabolically healthy obesity" (MHO) are a distinct subgroup of youth with obesity, who are less prone to the clustering of cardiometabolic risk factors. Although this phenotype, frequently defined by the absence of metabolic syndrome components or insulin resistance, was first described during the early 1980s, a consensus-based definition of pediatric MHO was introduced only recently, in 2018. The purpose of this review was to concisely summarize current knowledge regarding the MHO phenomenon in youth. The prevalence of MHO in children varies from 3 to 87%, depending on the definition used and the parameters evaluated, as well as the ethnicity and the pubertal status of the sample. The most consistent predictors of MHO in youth include younger age, lower body mass index, lower waist circumference, and lower body fat measurements. Various hypotheses have been proposed to elucidate the underlying factors maintaining the favorable MHO phenotype. While preserved insulin sensitivity and lack of inflammation were previously considered to be the main etiological factors, the most recent findings have implicated adipokine levels, the number of inflammatory immune cells in the adipose tissue, and the reduction of visceral adiposity due to adipose tissue expandability. Physical activity and genetic factors also contribute to the MHO phenotype. Obesity constitutes a continuum-increased risk for cardiometabolic complications, which is less evident in children with MHO. However, some findings have highlighted the emergence of hepatic steatosis, increased carotid intima-media thickness and inflammatory biomarkers in the MHO group compared to peers without obesity. Screening should be directed at those more likely to develop clustering of cardiometabolic risk factors. Lifestyle modifications should include behavioral changes focusing on sleep duration, screen time, diet, physical activity, and tobacco smoke exposure. Weight loss has also been associated with the improvement of insulin sensitivity and inflammation. Further investigative efforts are needed in order to elucidate the mechanisms which protect against the clustering of cardiometabolic risk factors in pediatric obesity, to provide more efficient, targeted treatment approaches for children with obesity, and to identify the protective factors preserving the MHO profile, avoiding the crossover of MHO to the phenotype with metabolically unhealthy obesity.
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Affiliation(s)
- Rade Vukovic
- Department of Pediatric Endocrinology, Mother and Child Healthcare Institute of Serbia “Dr Vukan Cupic”, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
- *Correspondence: Rade Vukovic
| | | | - Marina Ybarra
- Research Center of Sainte Justine University Hospital, Université de Montréal, Montreal, QC, Canada
- Centre Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
| | - Muge Atar
- Department of Pediatric Endocrinology, School of Medicine, Demirel University, Isparta, Turkey
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Corella D, Coltell O, Portolés O, Sotos-Prieto M, Fernández-Carrión R, Ramirez-Sabio JB, Zanón-Moreno V, Mattei J, Sorlí JV, Ordovas JM. A Guide to Applying the Sex-Gender Perspective to Nutritional Genomics. Nutrients 2018; 11:E4. [PMID: 30577445 PMCID: PMC6357147 DOI: 10.3390/nu11010004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 02/07/2023] Open
Abstract
Precision nutrition aims to make dietary recommendations of a more personalized nature possible, to optimize the prevention or delay of a disease and to improve health. Therefore, the characteristics (including sex) of an individual have to be taken into account as well as a series of omics markers. The results of nutritional genomics studies are crucial to generate the evidence needed so that precision nutrition can be applied. Although sex is one of the fundamental variables for making recommendations, at present, the nutritional genomics studies undertaken have not analyzed, systematically and with a gender perspective, the heterogeneity/homogeneity in gene-diet interactions on the different phenotypes studied, thus there is little information available on this issue and needs to be improved. Here we argue for the need to incorporate the gender perspective in nutritional genomics studies, present the general context, analyze the differences between sex and gender, as well as the limitations to measuring them and to detecting specific sex-gene or sex-phenotype associations, both at the specific gene level or in genome-wide-association studies. We analyzed the main sex-specific gene-diet interactions published to date and their main limitations and present guidelines with recommendations to be followed when undertaking new nutritional genomics studies incorporating the gender perspective.
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Affiliation(s)
- Dolores Corella
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain.
| | - Oscar Coltell
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellón, Spain.
| | - Olga Portolés
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain.
| | - Mercedes Sotos-Prieto
- School of Applied Health Sciences and Wellness, Ohio University, Athens, OH 45701, USA.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Rebeca Fernández-Carrión
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain.
| | | | - Vicente Zanón-Moreno
- Ophthalmology Research Unit "Santiago Grisolia", Dr. Peset University Hospital, 46017 Valencia, Spain.
- Red Temática de Investigación Cooperativa OftaRed, Instituto de Salud Carlos III, 28029 Madrid, Spain.
| | - Josiemer Mattei
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - José V Sorlí
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain.
| | - Jose M Ordovas
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111 USA.
- Department of Cardiovascular Epidemiology and Population Genetics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain.
- IMDEA Alimentación, 28049 Madrid, Spain.
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Epigenome-wide methylation differences in a group of lean and obese women - A HUNT Study. Sci Rep 2018; 8:16330. [PMID: 30397228 PMCID: PMC6218540 DOI: 10.1038/s41598-018-34003-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/07/2018] [Indexed: 01/04/2023] Open
Abstract
Knowledge of epigenetically regulated biomarkers linked to obesity development is still scarce. Improving molecular understanding of the involved factors and pathways would improve obesity phenotype characterization and reveal potentially relevant targets for obesity intervention. The Illumina Infinium HumanMethylation450 BeadChip was used in a leucocyte epigenome-wide association study (EWAS) to quantify differential DNA methylation in 60 lean compared with 60 obese young women. Replication was done in monozygotic twins discordant for obesity. At adolescence and adulthood, the two weight groups differed significantly in obesity-related traits and metabolic risk factors. Differential hypomethylation was overrepresented in obese compared to lean women. In the adjusted model, the EWAS revealed 10 differentially methylated CpG sites linked to 8 gene loci – COX6A1P2/FGD2, SBNO2, TEX41, RPS6KA2, IGHE/IGHG1/IGHD, DMAP1, SOCS3, and SETBP1– and an enhancer locus at chromosome 2 (2p25.1). The sites linked to TEX41, IGHE/IGHG1/IGHD, DMAP1, and SETBP1 were novel findings, while COX6A1P/FGD2, SBNO2, RPS6KA2, and SOCS3 had been identified previously with concordant direction of effects. RPS6KA2, DMAP1, and SETBP1 were replicated in the BMI-discordant monozygotic twin cohort using the FDR of 5%.
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40
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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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41
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Das R, Upadhyai P. An Ancestry Informative Marker Set Which Recapitulates the Known Fine Structure of Populations in South Asia. Genome Biol Evol 2018; 10:2408-2416. [PMID: 30184103 PMCID: PMC6143162 DOI: 10.1093/gbe/evy182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2018] [Indexed: 12/16/2022] Open
Abstract
The inference of genomic ancestry using ancestry informative markers (AIMs) can be useful for a range of studies in evolutionary genetics, biomedical research, and forensic analyses. However, the determination of AIMs for highly admixed populations with complex ancestries has remained a formidable challenge. Given the immense genetic heterogeneity and unique population structure of the Indian subcontinent, here we sought to derive AIMs that would yield a cohesive and faithful understanding of South Asian genetic origins. To discern the most optimal strategy for extracting AIMs for South Asians we compared three commonly used AIMs-determining methods namely, Infocalc, FST, and Smart Principal Component Analysis with ADMIXTURE, using previously published whole genome data from the Indian subcontinent. Our findings suggest that the Infocalc approach is likely most suitable for delineation of South Asian AIMs. In particular, Infocalc-2,000 (N = 2,000) appeared as the most informative South Asian AIMs panel that recapitulated the finer structure within South Asian genomes with high degree of sensitivity and precision, whereas a negative control with an equivalent number of randomly selected markers when used to interrogate the South Asian populations, failed to do so. We discuss the utility of all approaches under evaluation for AIMs derivation and interpreting South Asian genomic ancestries. Notably, this is the first report of an AIMs panel for South Asian ancestry inference. Overall these findings may aid in developing cost-effective resources for large-scale demographic analyses and foster expansion of our knowledge of human origins and disease, in the South Asian context.
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Affiliation(s)
- Ranajit Das
- Manipal Centre for Natural Sciences (MCNS), Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
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42
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Jacob R, Drapeau V, Tremblay A, Provencher V, Bouchard C, Pérusse L. The role of eating behavior traits in mediating genetic susceptibility to obesity. Am J Clin Nutr 2018; 108:445-452. [PMID: 29982344 DOI: 10.1093/ajcn/nqy130] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/18/2018] [Indexed: 12/24/2022] Open
Abstract
Background Genome-wide association studies (GWASs) have identified several genes associated with obesity. The mechanisms through which these genes affect body weight are not fully characterized. Recent studies suggest that eating behavior (EB) traits could be involved, but only a few EB traits were investigated. Objective This study aimed to investigate whether genetic susceptibility to obesity is mediated by EB traits (cognitive restraint, disinhibition, hunger) and their subscales. We hypothesized that EB traits, and their subscales, partly mediate this association. Design Adult individuals (n = 768) who participated in the Quebec Family Study were included in this cross-sectional study. A genetic risk score (GRS) of obesity was calculated based on the 97 genetic variants recently identified in a GWAS meta-analysis of body mass index (BMI). EB traits and their subscales were assessed with the use of the Three-Factor Eating Questionnaire. Regression analyses with age and sex as covariates were used to investigate the associations between GRS, EB traits, BMI, and WC and whether the association between GRS and obesity is mediated by EB traits, which represents the indirect effect of GRS on obesity. Results The GRS of obesity was positively associated with BMI (β = 0.19 ± 0.04, P < 0.0001) and WC (β = 0.46 ± 0.10, P < 0.0001). Regression analyses also revealed that the association between GRS of obesity and BMI was partly mediated by disinhibition and susceptibility to hunger (βindirect = 0.09 ± 0.03, P = 0.0007, and βindirect = 0.04 ± 0.02, P = 0.02, respectively). Habitual and situational susceptibility to disinhibition (βindirect = 0.08 ± 0.03, P = 0.002 and βindirect = 0.05 ± 0.02, P = 0.003, respectively) as well as internal and external locus of hunger (βindirect = 0.03 ± 0.02, P = 0.03 for both) were also found to mediate the association between GRS of obesity and BMI. The same trends were observed with WC. Conclusions The results of this study indicate that the genetic susceptibility to obesity is partly mediated through undesirable EB traits, which suggests that they could be targeted in obesity treatment and prevention. This trial was registered at clinicaltrials.gov as NCT03355729.
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Affiliation(s)
- Raphaëlle Jacob
- Institute of Nutrition and Functional Foods (INAF).,School of Nutrition.,Quebec Heart and Lung Institute Research Center
| | - Vicky Drapeau
- Institute of Nutrition and Functional Foods (INAF).,Quebec Heart and Lung Institute Research Center.,Department of Physical Education, Faculty of Educational Sciences
| | - Angelo Tremblay
- Institute of Nutrition and Functional Foods (INAF).,Quebec Heart and Lung Institute Research Center.,Department of Kinesiology, Faculty of Medicine, Laval University, Quebec, Canada
| | | | | | - Louis Pérusse
- Institute of Nutrition and Functional Foods (INAF).,Department of Kinesiology, Faculty of Medicine, Laval University, Quebec, Canada
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A Large Multiethnic Genome-Wide Association Study of Adult Body Mass Index Identifies Novel Loci. Genetics 2018; 210:499-515. [PMID: 30108127 DOI: 10.1534/genetics.118.301479] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/08/2018] [Indexed: 12/31/2022] Open
Abstract
Body mass index (BMI), a proxy measure for obesity, is determined by both environmental (including ethnicity, age, and sex) and genetic factors, with > 400 BMI-associated loci identified to date. However, the impact, interplay, and underlying biological mechanisms among BMI, environment, genetics, and ancestry are not completely understood. To further examine these relationships, we utilized 427,509 calendar year-averaged BMI measurements from 100,418 adults from the single large multiethnic Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. We observed substantial independent ancestry and nationality differences, including ancestry principal component interactions and nonlinear effects. To increase the list of BMI-associated variants before assessing other differences, we conducted a genome-wide association study (GWAS) in GERA, with replication in the Genetic Investigation of Anthropomorphic Traits (GIANT) consortium combined with the UK Biobank (UKB), followed by GWAS in GERA combined with GIANT, with replication in the UKB. We discovered 30 novel independent BMI loci (P < 5.0 × 10-8) that replicated. We then assessed the proportion of BMI variance explained by sex in the UKB using previously identified loci compared to previously and newly identified loci and found slight increases: from 3.0 to 3.3% for males and from 2.7 to 3.0% for females. Further, the variance explained by previously and newly identified variants decreased with increasing age in the GERA and UKB cohorts, echoed in the variance explained by the entire genome, which also showed gene-age interaction effects. Finally, we conducted a tissue expression QTL enrichment analysis, which revealed that GWAS BMI-associated variants were enriched in the cerebellum, consistent with prior work in humans and mice.
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Barba M, Di Pietro L, Massimi L, Geloso MC, Frassanito P, Caldarelli M, Michetti F, Della Longa S, Romitti PA, Di Rocco C, Arcovito A, Parolini O, Tamburrini G, Bernardini C, Boyadjiev SA, Lattanzi W. BBS9 gene in nonsyndromic craniosynostosis: Role of the primary cilium in the aberrant ossification of the suture osteogenic niche. Bone 2018; 112:58-70. [PMID: 29674126 PMCID: PMC5970090 DOI: 10.1016/j.bone.2018.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 12/26/2022]
Abstract
Nonsyndromic craniosynostosis (NCS) is the premature ossification of skull sutures, without associated clinical features. Mutations in several genes account for a small number of NCS patients; thus, the molecular etiopathogenesis of NCS remains largely unclear. Our study aimed at characterizing the molecular signaling implicated in the aberrant ossification of sutures in NCS patients. Comparative gene expression profiling of NCS patient sutures identified a fused suture-specific signature, including 17 genes involved in primary cilium signaling and assembly. Cells from fused sutures displayed a reduced potential to form primary cilia compared to cells from control patent sutures of the same patient. We identified specific upregulated splice variants of the Bardet Biedl syndrome-associated gene 9 (BBS9), which encodes a structural component of the ciliary BBSome complex. BBS9 expression increased during in vitro osteogenic differentiation of suture-derived mesenchymal cells of NCS patients. Also, Bbs9 expression increased during in vivo ossification of rat sutures. BBS9 functional knockdown affected the expression of primary cilia on patient suture cells and their osteogenic potential. Computational modeling of the upregulated protein isoforms (observed in patients) predicted that their binding affinity within the BBSome may be affected, providing a possible explanation for the aberrant suture ossification in NCS.
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Affiliation(s)
- Marta Barba
- Istituto di Anatomia Umana e Biologia Cellulare, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "Agostino Gemelli", 00168 Rome, Italy
| | - Lorena Di Pietro
- Istituto di Anatomia Umana e Biologia Cellulare, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Luca Massimi
- Fondazione Policlinico Universitario "Agostino Gemelli", 00168 Rome, Italy; Istituto di Neurochirurgia, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Maria Concetta Geloso
- Istituto di Anatomia Umana e Biologia Cellulare, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "Agostino Gemelli", 00168 Rome, Italy
| | - Paolo Frassanito
- Fondazione Policlinico Universitario "Agostino Gemelli", 00168 Rome, Italy
| | - Massimo Caldarelli
- Fondazione Policlinico Universitario "Agostino Gemelli", 00168 Rome, Italy; Istituto di Neurochirurgia, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Fabrizio Michetti
- Istituto di Anatomia Umana e Biologia Cellulare, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Stefano Della Longa
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, 52242, IA, USA
| | - Concezio Di Rocco
- Department of Neurosurgery, International Neuroscience Institute, 30625 Hannover, Germany
| | - Alessandro Arcovito
- Istituto di Neurochirurgia, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Ornella Parolini
- Istituto di Anatomia Umana e Biologia Cellulare, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "Agostino Gemelli", 00168 Rome, Italy; Centro di Ricerca E. Menni, Fondazione Poliambulanza-Istituto Ospedaliero, 25124 Brescia, Italy
| | - Gianpiero Tamburrini
- Fondazione Policlinico Universitario "Agostino Gemelli", 00168 Rome, Italy; Istituto di Neurochirurgia, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Camilla Bernardini
- Istituto di Anatomia Umana e Biologia Cellulare, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "Agostino Gemelli", 00168 Rome, Italy
| | - Simeon A Boyadjiev
- Section of Genomics, Department of Pediatrics, University of California, 95817 Sacramento, CA, USA
| | - Wanda Lattanzi
- Istituto di Anatomia Umana e Biologia Cellulare, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "Agostino Gemelli", 00168 Rome, Italy.
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Li W, Tang R, Ma F, Ouyang S, Liu Z, Wu J. Folic acid supplementation alters the DNA methylation profile and improves insulin resistance in high-fat-diet-fed mice. J Nutr Biochem 2018; 59:76-83. [PMID: 29986310 DOI: 10.1016/j.jnutbio.2018.05.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/20/2018] [Accepted: 05/31/2018] [Indexed: 12/11/2022]
Abstract
Folic acid (FA) supplementation may protect from obesity and insulin resistance, the effects and mechanism of FA on chronic high-fat-diet-induced obesity-related metabolic disorders are not well elucidated. We adopted a genome-wide approach to directly examine whether FA supplementation affects the DNA methylation profile of mouse adipose tissue and identify the functional consequences of these changes. Mice were fed a high-fat diet (HFD), normal diet (ND) or an HFD supplemented with folic acid (20 μg/ml in drinking water) for 10 weeks, epididymal fat was harvested, and genome-wide DNA methylation analyses were performed using methylated DNA immunoprecipitation sequencing (MeDIP-seq). Mice exposed to the HFD expanded their adipose mass, which was accompanied by a significant increase in circulating glucose and insulin levels. FA supplementation reduced the fat mass and serum glucose levels and improved insulin resistance in HFD-fed mice. MeDIP-seq revealed distribution of differentially methylated regions (DMRs) throughout the adipocyte genome, with more hypermethylated regions in HFD mice. Methylome profiling identified DMRs associated with 3787 annotated genes from HFD mice in response to FA supplementation. Pathway analyses showed novel DNA methylation changes in adipose genes associated with insulin secretion, pancreatic secretion and type 2 diabetes. The differential DNA methylation corresponded to changes in the adipose tissue gene expression of Adcy3 and Rapgef4 in mice exposed to a diet containing FA. FA supplementation improved insulin resistance, decreased the fat mass, and induced DNA methylation and gene expression changes in genes associated with obesity and insulin secretion in obese mice fed a HFD.
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Affiliation(s)
- Wei Li
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China; Department of Biochemistry & Immunology, Capital Institute of Pediatrics, No. 2, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Renqiao Tang
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China; Department of Biochemistry & Immunology, Capital Institute of Pediatrics, No. 2, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Feifei Ma
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China
| | - Shengrong Ouyang
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China
| | - Zhuo Liu
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China
| | - Jianxin Wu
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China; Department of Biochemistry & Immunology, Capital Institute of Pediatrics, No. 2, Yabao Road, Chaoyang District, Beijing 100020, China.
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Ruiz-Larrañaga O, Langa J, Rendo F, Manzano C, Iriondo M, Estonba A. Genomic selection signatures in sheep from the Western Pyrenees. Genet Sel Evol 2018; 50:9. [PMID: 29566643 PMCID: PMC5865298 DOI: 10.1186/s12711-018-0378-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/12/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The current large spectrum of sheep phenotypic diversity results from the combined product of sheep selection for different production traits such as wool, milk and meat, and its natural adaptation to new environments. In this study, we scanned the genome of 25 Sasi Ardi and 75 Latxa sheep from the Western Pyrenees for three types of regions under selection: (1) regions underlying local adaptation of Sasi Ardi semi-feral sheep, (2) regions related to a long traditional dairy selection pressure in Latxa sheep, and (3) regions experiencing the specific effect of the modern genetic improvement program established for the Latxa breed during the last three decades. RESULTS Thirty-two selected candidate regions including 147 annotated genes were detected by using three statistical parameters: pooled heterozygosity H, Tajima's D, and Wright's fixation index Fst. For Sasi Ardi sheep, chromosomes Ovis aries (OAR)4, 6, and 22 showed the strongest signals and harbored several candidate genes related to energy metabolism and morphology (BBS9, ELOVL3 and LDB1), immunity (NFKB2), and reproduction (H2AFZ). The major genomic difference between Sasi Ardi and Latxa sheep was on OAR6, which is known to affect milk production, with highly selected regions around the ABCG2, SPP1, LAP3, NCAPG, LCORL, and MEPE genes in Latxa sheep. The effect of the modern genetic improvement program on Latxa sheep was also evident on OAR15, on which several olfactory genes are located. We also detected several genes involved in reproduction such as ESR1 and ZNF366 that were affected by this selection program. CONCLUSIONS Natural and artificial selection have shaped the genome of both Sasi Ardi and Latxa sheep. Our results suggest that Sasi Ardi traits related to energy metabolism, morphological, reproductive, and immunological features have been under positive selection to adapt this semi-feral sheep to its particular environment. The highly selected Latxa sheep for dairy production showed clear signatures of selection in genomic regions related to milk production. Furthermore, our data indicate that the selection criteria applied in the modern genetic improvement program affect immunity and reproduction traits.
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Affiliation(s)
- Otsanda Ruiz-Larrañaga
- Genetics, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/EHU), Leioa, Spain.
| | - Jorge Langa
- Genetics, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Fernando Rendo
- Genetics, Sequencing and Genotyping Unit, Advanced Research Facilities (SGIker), University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Carmen Manzano
- Genetics, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Mikel Iriondo
- Genetics, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Andone Estonba
- Genetics, Physical Anthropology and Animal Physiology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
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47
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Mychaleckyj JC, Nayak U, Colgate ER, Zhang D, Carstensen T, Ahmed S, Ahmed T, Mentzer AJ, Alam M, Kirkpatrick BD, Haque R, Faruque ASG, Petri WA. Multiplex genomewide association analysis of breast milk fatty acid composition extends the phenotypic association and potential selection of FADS1 variants to arachidonic acid, a critical infant micronutrient. J Med Genet 2018. [PMID: 29514873 PMCID: PMC6047159 DOI: 10.1136/jmedgenet-2017-105134] [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] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Breast milk is the sole nutrition source during exclusive breastfeeding, and polyunsaturated fatty acids (FAs) are critical micronutrients in infant physical and cognitive development. There has been no prior genomewide association study of breast milk, hence our objective was to test for genetic association with breast milk FA composition. METHODS We measured the fractional composition of 26 individual FAs in breast milk samples from three cohorts totalling 1142 Bangladeshi mothers whose infants were genotyped on the Illumina MEGA chip and replicated on a custom Affymetrix 30K SNP array (n=616). Maternal genotypes were imputed using IMPUTE. RESULTS After running 33 separate FA fraction phenotypes, we found that SNPs known to be associated with serum FAs in the FADS1/2/3 region were also associated with breast milk FA composition (experiment-wise significance threshold 4.2×10-9). Hypothesis-neutral comparison of the 33 fractions showed that the most significant genetic association at the FADS1/2/3 locus was with fraction of arachidonic acid (AA) at SNP rs174556, with a very large per major allele effect size of 17% higher breast milk AA level. There was no evidence of independent association at FADS1/2/3 with any other FA or SNP after conditioning on AA and rs174556. We also found novel significant experiment-wise SNP associations with: polyunsaturated fatty acid (PUFA) 6/PUFA3 ratio (sorting nexin 29), eicosenoic (intergenic) and capric (component of oligomeric Golgi complex 3) acids; and six additional loci at genomewide significance (<5×10-8). CONCLUSIONS AA is the primary FA in breast milk influenced by genetic variation at the FADS1/2/3 locus, extending the potential phenotypes under genetic selection to include breast milk composition, thereby possibly affecting infant growth or cognition. Breast milk FA composition is influenced by maternal genetics in addition to diet and body composition.
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Affiliation(s)
- Josyf C Mychaleckyj
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Uma Nayak
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - E Ross Colgate
- Department of Medicine, Vaccine Testing Center, University of Vermont, College of Medicine, Burlington, Vermont, USA
| | - Dadong Zhang
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | | | - Shahnawaz Ahmed
- Center for Nutrition and Food Security, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - Masud Alam
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Beth D Kirkpatrick
- Department of Medicine, Vaccine Testing Center, University of Vermont, College of Medicine, Burlington, Vermont, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Abu Syed Golam Faruque
- Center for Nutrition and Food Security, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - William A Petri
- Division of Infectious Diseases and International Health, Department of Medicine, Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
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48
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Armstrong C, Richardson DS, Hipperson H, Horsburgh GJ, Küpper C, Percival‐Alwyn L, Clark M, Burke T, Spurgin LG. Genomic associations with bill length and disease reveal drift and selection across island bird populations. Evol Lett 2018; 2:22-36. [PMID: 30283662 PMCID: PMC6121843 DOI: 10.1002/evl3.38] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/15/2022] Open
Abstract
Island species provide excellent models for investigating how selection and drift operate in wild populations, and for determining how these processes act to influence local adaptation and speciation. Here, we examine the role of selection and drift in shaping genomic and phenotypic variation across recently separated populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three archipelagos in the Atlantic. We first characterized genetic diversity and population structuring that supported previous inferences of a history of recent colonizations and bottlenecks. We then tested for regions of the genome associated with the ecologically important traits of bill length and malaria infection, both of which vary substantially across populations in this species. We identified a SNP associated with variation in bill length among individuals, islands, and archipelagos; patterns of variation at this SNP suggest that both phenotypic and genotypic variation in bill length is largely shaped by founder effects. Malaria was associated with SNPs near/within genes involved in the immune response, but this relationship was not consistent among archipelagos, supporting the view that disease resistance is complex and rapidly evolving. Although we found little evidence for divergent selection at candidate loci for bill length and malaria resistance, genome scan analyses pointed to several genes related to immunity and metabolism as having important roles in divergence and adaptation. Our findings highlight the utility and challenges involved with combining association mapping and population genetic analysis in nonequilibrium populations, to disentangle the effects of drift and selection on shaping genotypes and phenotypes.
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Affiliation(s)
- Claire Armstrong
- School of Biological Sciences, University of East AngliaNorwich Research ParkNorwich NR4 7TJUnited Kingdom
| | - David S. Richardson
- School of Biological Sciences, University of East AngliaNorwich Research ParkNorwich NR4 7TJUnited Kingdom
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffield S10 2TNUnited Kingdom
| | - Gavin J. Horsburgh
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffield S10 2TNUnited Kingdom
| | - Clemens Küpper
- Max Planck Institute for Ornithology82319 SeewiesenGermany
| | | | - Matt Clark
- Earlham InstituteNorwich Research ParkNorwich NR4 7UZUnited Kingdom
| | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffield S10 2TNUnited Kingdom
| | - Lewis G. Spurgin
- School of Biological Sciences, University of East AngliaNorwich Research ParkNorwich NR4 7TJUnited Kingdom
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49
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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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50
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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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