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Anwar MY, Graff M, Highland HM, Smit R, Wang Z, Buchanan VL, Young KL, Kenny EE, Fernandez-Rhodes L, Liu S, Assimes T, Garcia DO, Daeeun K, Gignoux CR, Justice AE, Haiman CA, Buyske S, Peters U, Loos RJF, Kooperberg C, North KE. Assessing efficiency of fine-mapping obesity-associated variants through leveraging ancestry architecture and functional annotation using PAGE and UKBB cohorts. Hum Genet 2023; 142:1477-1489. [PMID: 37658231 DOI: 10.1007/s00439-023-02593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/10/2023] [Indexed: 09/03/2023]
Abstract
Inadequate representation of non-European ancestry populations in genome-wide association studies (GWAS) has limited opportunities to isolate functional variants. Fine-mapping in multi-ancestry populations should improve the efficiency of prioritizing variants for functional interrogation. To evaluate this hypothesis, we leveraged ancestry architecture to perform comparative GWAS and fine-mapping of obesity-related phenotypes in European ancestry populations from the UK Biobank (UKBB) and multi-ancestry samples from the Population Architecture for Genetic Epidemiology (PAGE) consortium with comparable sample sizes. In the investigated regions with genome-wide significant associations for obesity-related traits, fine-mapping in our ancestrally diverse sample led to 95% and 99% credible sets (CS) with fewer variants than in the European ancestry sample. Lead fine-mapped variants in PAGE regions had higher average coding scores, and higher average posterior probabilities for causality compared to UKBB. Importantly, 99% CS in PAGE loci contained strong expression quantitative trait loci (eQTLs) in adipose tissues or harbored more variants in tighter linkage disequilibrium (LD) with eQTLs. Leveraging ancestrally diverse populations with heterogeneous ancestry architectures, coupled with functional annotation, increased fine-mapping efficiency and performance, and reduced the set of candidate variants for consideration for future functional studies. Significant overlap in genetic causal variants across populations suggests generalizability of genetic mechanisms underpinning obesity-related traits across populations.
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Affiliation(s)
- Mohammad Yaser Anwar
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Roelof Smit
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Victoria L Buchanan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kristin L Young
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Eimear E Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lindsay Fernandez-Rhodes
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA, 16802, USA
| | - Simin Liu
- Department of Epidemiology and Center for Global Cardiometabolic Health, School of Public Health, Brown University, Providence, RI, 02903, USA
| | - Themistocles Assimes
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - David O Garcia
- Department of Health Promotion Sciences, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, 85724, USA
| | - Kim Daeeun
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Anne E Justice
- Department of Population Health Sciences, Geisinger Health, Danville, PA, 17822, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Steve Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Valvi D, Christiani DC, Coull B, Højlund K, Nielsen F, Audouze K, Su L, Weihe P, Grandjean P. Gene-environment interactions in the associations of PFAS exposure with insulin sensitivity and beta-cell function in a Faroese cohort followed from birth to adulthood. ENVIRONMENTAL RESEARCH 2023; 226:115600. [PMID: 36868448 PMCID: PMC10101920 DOI: 10.1016/j.envres.2023.115600] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Exposure to perfluoroalkyl substances (PFAS) has been associated with changes in insulin sensitivity and pancreatic beta-cell function in humans. Genetic predisposition to diabetes may modify these associations; however, this hypothesis has not been yet studied. OBJECTIVES To evaluate genetic heterogeneity as a modifier in the PFAS association with insulin sensitivity and pancreatic beta-cell function, using a targeted gene-environment (GxE) approach. METHODS We studied 85 single-nucleotide polymorphisms (SNPs) associated with type 2 diabetes, in 665 Faroese adults born in 1986-1987. Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) were measured in cord whole blood at birth and in participants' serum from age 28 years. We calculated the Matsuda-insulin sensitivity index (ISI) and the insulinogenic index (IGI) based on a 2 h-oral glucose tolerance test performed at age 28. Effect modification was evaluated in linear regression models adjusted for cross-product terms (PFAS*SNP) and important covariates. RESULTS Prenatal and adult PFOS exposures were significantly associated with decreased insulin sensitivity and increased beta-cell function. PFOA associations were in the same direction but attenuated compared to PFOS. A total of 58 SNPs were associated with at least one PFAS exposure variable and/or Matsuda-ISI or IGI in the Faroese population and were subsequently tested as modifiers in the PFAS-clinical outcome associations. Eighteen SNPs showed interaction p-values (PGxE) < 0.05 in at least one PFAS-clinical outcome association, five of which passed False Discovery Rate (FDR) correction (PGxE-FDR<0.20). SNPs for which we found stronger evidence for GxE interactions included ABCA1 rs3890182, FTO rs9939609, FTO rs3751812, PPARG rs170036314 and SLC12A3 rs2289116 and were more clearly shown to modify the PFAS associations with insulin sensitivity, rather than with beta-cell function. DISCUSSION Findings from this study suggest that PFAS-associated changes in insulin sensitivity could vary between individuals as a result of genetic predisposition and warrant replication in independent larger populations.
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Affiliation(s)
- Damaskini Valvi
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Brent Coull
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kurt Højlund
- Steno Diabetes Center Odense, Odense University Hospital, Odense, Denmark
| | - Flemming Nielsen
- Department of Public Health, Clinical Pharmacology, Pharmacy and Environmental Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Li Su
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Pal Weihe
- Department of Occupational Medicine and Public Health, The Faroese Hospital System, Tórshavn, Faroe Islands; Centre of Health Science, Faculty of Health Sciences, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Philippe Grandjean
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States; Department of Public Health, Clinical Pharmacology, Pharmacy and Environmental Medicine, University of Southern Denmark, Odense, Denmark
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3
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Pahl MC, Grant SFA, Leibel RL, Stratigopoulos G. Technologies, strategies, and cautions when deconvoluting genome-wide association signals: FTO in focus. Obes Rev 2023; 24:e13558. [PMID: 36882962 DOI: 10.1111/obr.13558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 10/08/2022] [Accepted: 01/31/2023] [Indexed: 03/09/2023]
Abstract
Genome-wide association studies have revealed a plethora of genetic variants that correlate with polygenic conditions. However, causal molecular mechanisms have proven challenging to fully define. Without such information, the associations are not physiologically useful or clinically actionable. By reviewing studies of the FTO locus in the genetic etiology of obesity, we wish to highlight advances in the field fueled by the evolution of technical and analytic strategies in assessing the molecular bases for genetic associations. Particular attention is drawn to extrapolating experimental findings from animal models and cell types to humans, as well as technical aspects used to identify long-range DNA interactions and their biological relevance with regard to the associated trait. A unifying model is proposed by which independent obesogenic pathways regulated by multiple FTO variants and genes are integrated at the primary cilium, a cellular antenna where signaling molecules that control energy balance convene.
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Affiliation(s)
- Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Diabetes and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.,Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rudolph L Leibel
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, USA.,Naomi Berrie Diabetes Center, Columbia University Medical Center, New York, New York, USA
| | - George Stratigopoulos
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, USA.,Naomi Berrie Diabetes Center, Columbia University Medical Center, New York, New York, USA
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4
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Park S, Lee S, Kim Y, Lee Y, Kang MW, Kim K, Kim YC, Han SS, Lee H, Lee JP, Joo KW, Lim CS, Kim YS, Kim DK. Relation of Poor Handgrip Strength or Slow Walking Pace to Risk of Myocardial Infarction and Fatality. Am J Cardiol 2022; 162:58-65. [PMID: 34903347 DOI: 10.1016/j.amjcard.2021.08.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 12/22/2022]
Abstract
We aimed to investigate a causal effect of functional sarcopenia status, including poor handgrip strength and slow walking pace, on cardiovascular diseases. This study was an observational cohort study including observational analysis and Mendelian randomization. We studied the UK Biobank prospective cohort (n = 324,486) for observational analysis with poor handgrip strength or self-reported slow walking pace as the exposures, investigating risk of myocardial infarction or mortality. Genetic instruments for the exposures were developed in 337,138 individuals of white British ancestries, and coronary artery disease outcome (60,801 cases/123,504 controls) from the independent CARDIoGRAMplustC4D cohort was studied by two-sample Mendelian randomization. The findings were replicated by one-sample analysis by polygenic risk score analysis within the UK Biobank. Both slow walking pace and poor handgrip strength were significantly associated with higher risks of incident myocardial infarction and mortality, particularly from cardiovascular deaths, in the observational investigation. Genetically predicted poor handgrip strength (odds ratio: 1.128 [1.041 to 1.222]) and slow walking pace (odds ratio: 1.171 [1.022 to 1.342]) showed causal effects on the coronary artery disease risks in the independent cohort. The results were again identified by the one-sample Mendelian randomization, as the higher polygenic risk score for poor handgrip strength and slow walking pace was associated with a higher risk of mortality. In conclusion, this study supports the causal effects of slow walking pace and poor handgrip strength on the risks of cardiovascular disease and mortality. The functional sarcopenia status are targetable causative factors for interventions aiming to reduce risks of cardiovascular disease or mortality.
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Affiliation(s)
- Sehoon Park
- Department of Biomedical Sciences; Department of Internal Medicine, Armed Forces Capital Hospital, Gyeonggi-do, Korea
| | - Soojin Lee
- Division of Nephrology, Department of Internal Medicine, Uijeongbu Eulji University Medical Center
| | - Yaerim Kim
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Yeonhee Lee
- Division of Nephrology, Department of Internal Medicine, Uijeongbu Eulji University Medical Center
| | | | - Kwangsoo Kim
- Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Korea
| | | | - Seung Seok Han
- Department of Internal Medicine; Kidney Research Institute, Seoul National University, Seoul, Korea
| | - Hajeong Lee
- Department of Internal Medicine; Kidney Research Institute, Seoul National University, Seoul, Korea
| | - Jung Pyo Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea; Kidney Research Institute, Seoul National University, Seoul, Korea; Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Kwon Wook Joo
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea; Department of Internal Medicine; Kidney Research Institute, Seoul National University, Seoul, Korea
| | - Chun Soo Lim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea; Kidney Research Institute, Seoul National University, Seoul, Korea; Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Yon Su Kim
- Department of Biomedical Sciences; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea; Department of Internal Medicine; Kidney Research Institute, Seoul National University, Seoul, Korea
| | - Dong Ki Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea; Department of Internal Medicine; Kidney Research Institute, Seoul National University, Seoul, Korea.
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5
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Fernández-Rhodes L, Gong J, Haessler J, Franceschini N, Graff M, Nishimura KK, Wang Y, Highland HM, Yoneyama S, Bush WS, Goodloe R, Ritchie MD, Crawford D, Gross M, Fornage M, Buzkova P, Tao R, Isasi C, Avilés-Santa L, Daviglus M, Mackey RH, Houston D, Gu CC, Ehret G, Nguyen KDH, Lewis CE, Leppert M, Irvin MR, Lim U, Haiman CA, Le Marchand L, Schumacher F, Wilkens L, Lu Y, Bottinger EP, Loos RJL, Sheu WHH, Guo X, Lee WJ, Hai Y, Hung YJ, Absher D, Wu IC, Taylor KD, Lee IT, Liu Y, Wang TD, Quertermous T, Juang JMJ, Rotter JI, Assimes T, Hsiung CA, Chen YDI, Prentice R, Kuller LH, Manson JE, Kooperberg C, Smokowski P, Robinson WR, Gordon-Larsen P, Li R, Hindorff L, Buyske S, Matise TC, Peters U, North KE. Trans-ethnic fine-mapping of genetic loci for body mass index in the diverse ancestral populations of the Population Architecture using Genomics and Epidemiology (PAGE) Study reveals evidence for multiple signals at established loci. Hum Genet 2017; 136:771-800. [PMID: 28391526 PMCID: PMC5485655 DOI: 10.1007/s00439-017-1787-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/23/2017] [Indexed: 11/26/2022]
Abstract
Most body mass index (BMI) genetic loci have been identified in studies of primarily European ancestries. The effect of these loci in other racial/ethnic groups is less clear. Thus, we aimed to characterize the generalizability of 170 established BMI variants, or their proxies, to diverse US populations and trans-ethnically fine-map 36 BMI loci using a sample of >102,000 adults of African, Hispanic/Latino, Asian, European and American Indian/Alaskan Native descent from the Population Architecture using Genomics and Epidemiology Study. We performed linear regression of the natural log of BMI (18.5-70 kg/m2) on the additive single nucleotide polymorphisms (SNPs) at BMI loci on the MetaboChip (Illumina, Inc.), adjusting for age, sex, population stratification, study site, or relatedness. We then performed fixed-effect meta-analyses and a Bayesian trans-ethnic meta-analysis to empirically cluster by allele frequency differences. Finally, we approximated conditional and joint associations to test for the presence of secondary signals. We noted directional consistency with the previously reported risk alleles beyond what would have been expected by chance (binomial p < 0.05). Nearly, a quarter of the previously described BMI index SNPs and 29 of 36 densely-genotyped BMI loci on the MetaboChip replicated/generalized in trans-ethnic analyses. We observed multiple signals at nine loci, including the description of seven loci with novel multiple signals. This study supports the generalization of most common genetic loci to diverse ancestral populations and emphasizes the importance of dense multiethnic genomic data in refining the functional variation at genetic loci of interest and describing several loci with multiple underlying genetic variants.
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Affiliation(s)
- Lindsay Fernández-Rhodes
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jian Gong
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mariaelisa Graff
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katherine K Nishimura
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yujie Wang
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heather M Highland
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sachiko Yoneyama
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William S Bush
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Robert Goodloe
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
| | - Marylyn D Ritchie
- Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Dana Crawford
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Myron Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Myriam Fornage
- Center for Human Genetics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Petra Buzkova
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Ran Tao
- Department of Biostatistics, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Carmen Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Martha Daviglus
- Insitute of Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Rachel H Mackey
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Denise Houston
- Geriatrics and Gerontology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - C Charles Gu
- Division of Biostatistics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Georg Ehret
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Division of Cardiology, Geneva University Hospital, Geneva, OH, Switzerland
| | - Khanh-Dung H Nguyen
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Cora E Lewis
- Department of Medicine, University of Alabama, Birmingham, AL, USA
| | - Mark Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Unhee Lim
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lynne Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Yingchang Lu
- Charles R. Bronfman Instituted for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erwin P Bottinger
- Charles R. Bronfman Instituted for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J L Loos
- Charles R. Bronfman Instituted for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wayne H-H Sheu
- Division of Endocrine and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Defense Medical Center, National Yang-Ming University, Taipei, Taiwan
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yang Hai
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yi-Jen Hung
- Division of Endocrinology and Metabolism, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - I-Chien Wu
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | - Kent D Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - I-Te Lee
- Division of Endocrine and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Defense Medical Center, National Yang-Ming University, Taipei, Taiwan
| | - Yeheng Liu
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Tzung-Dau Wang
- Division of Cardiology, Department of Internal Medicine, Cardiovascular Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Thomas Quertermous
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jyh-Ming J Juang
- Division of Cardiology, Department of Internal Medicine, Cardiovascular Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Jerome I Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Themistocles Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Chao A Hsiung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | - Yii-Der Ida Chen
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ross Prentice
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lewis H Kuller
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - JoAnn E Manson
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul Smokowski
- School of Social Welfare, The University of Kansas, Lawrence, KS, USA
| | - Whitney R Robinson
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Penny Gordon-Larsen
- Department of Nutrition, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rongling Li
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucia Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Steven Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, NJ, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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6
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Recent progress in genetics, epigenetics and metagenomics unveils the pathophysiology of human obesity. Clin Sci (Lond) 2017; 130:943-86. [PMID: 27154742 DOI: 10.1042/cs20160136] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/24/2016] [Indexed: 12/19/2022]
Abstract
In high-, middle- and low-income countries, the rising prevalence of obesity is the underlying cause of numerous health complications and increased mortality. Being a complex and heritable disorder, obesity results from the interplay between genetic susceptibility, epigenetics, metagenomics and the environment. Attempts at understanding the genetic basis of obesity have identified numerous genes associated with syndromic monogenic, non-syndromic monogenic, oligogenic and polygenic obesity. The genetics of leanness are also considered relevant as it mirrors some of obesity's aetiologies. In this report, we summarize ten genetically elucidated obesity syndromes, some of which are involved in ciliary functioning. We comprehensively review 11 monogenic obesity genes identified to date and their role in energy maintenance as part of the leptin-melanocortin pathway. With the emergence of genome-wide association studies over the last decade, 227 genetic variants involved in different biological pathways (central nervous system, food sensing and digestion, adipocyte differentiation, insulin signalling, lipid metabolism, muscle and liver biology, gut microbiota) have been associated with polygenic obesity. Advances in obligatory and facilitated epigenetic variation, and gene-environment interaction studies have partly accounted for the missing heritability of obesity and provided additional insight into its aetiology. The role of gut microbiota in obesity pathophysiology, as well as the 12 genes associated with lipodystrophies is discussed. Furthermore, in an attempt to improve future studies and merge the gap between research and clinical practice, we provide suggestions on how high-throughput '-omic' data can be integrated in order to get closer to the new age of personalized medicine.
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7
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Association of FTO and near MC4R variants with obesity measures in urban and rural dwelling Sri Lankans. Obes Res Clin Pract 2016; 10 Suppl 1:S117-S124. [PMID: 26948330 DOI: 10.1016/j.orcp.2016.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/25/2016] [Accepted: 02/04/2016] [Indexed: 12/26/2022]
Abstract
OBJECTIVES To investigate the association between the fat mass and obesity related (FTO) gene rs9939609 and near melanocortin-4-receptor (MC4R) gene rs17782313 polymorphisms with obesity measures and metabolic parameters in urban and rural dwelling Sri Lankans. METHODS 535 subjects (60.9% female) from the general adult population (ages 18-70 years) representative of both urban (28.4%) and rural areas of residence were recruited by multi-stage random sampling. Body mass index (BMI), waist circumference (WC) and waist-to-hip ratio (WHR) was obtained by standard methods. DNA extracted from whole blood was genotyped using real-time PCR. RESULTS The FTO risk genotypes (AA+AT) were associated with higher BMI (p=0.03) and WC (p=0.05) measures as well as categorical obesity (BMI ≥27.5kgm-2 definition) (OR 1.69 95% CI 1.11-2.56, p=0.01). The near MC4R risk genotypes (CC+CT) were associated with greater BMI (p=0.03) as well as categorical obesity (BMI ≥25kgm-2 definition) (OR 1.57 95% CI 1.11-2.22, p=0.01). In addition the MC4R risk genotype carriers (CC+CT) had significantly higher fasting blood sugar (FBS) levels compared to the 'TT' genotype carriers independent of BMI (p=0.05). Urban living was associated with significantly greater BMI values for FTO risk genotypes compared to rural living (p=0.02). CONCLUSIONS FTO and near MC4R variants are associated with obesity measures in Sri Lankan populations whilst urban living accentuates the obesogenic effect of the FTO polymorphism.
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Hunt LE, Noyvert B, Bhaw-Rosun L, Sesay AK, Paternoster L, Nohr EA, Davey Smith G, Tommerup N, Sørensen TIA, Elgar G. Complete re-sequencing of a 2Mb topological domain encompassing the FTO/IRXB genes identifies a novel obesity-associated region upstream of IRX5. Genome Med 2015; 7:126. [PMID: 26642925 PMCID: PMC4671217 DOI: 10.1186/s13073-015-0250-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/17/2015] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Association studies have identified a number of loci that contribute to an increased body mass index (BMI), the strongest of which is in the first intron of the FTO gene on human chromosome 16q12.2. However, this region is both non-coding and under strong linkage disequilibrium, making it recalcitrant to functional interpretation. Furthermore, the FTO gene is located within a complex cis-regulatory landscape defined by a topologically associated domain that includes the IRXB gene cluster, a trio of developmental regulators. Consequently, at least three genes in this interval have been implicated in the aetiology of obesity. METHODS Here, we sequence a 2 Mb region encompassing the FTO, RPGRIP1L and IRXB cluster genes in 284 individuals from a well-characterised study group of Danish men containing extremely overweight young adults and controls. We further replicate our findings both in an expanded male cohort and an independent female study group. Finally, we compare our variant data with a previous study describing IRX3 and FTO interactions in this region. RESULTS We obtain deep coverage across the entire region, allowing accurate and unequivocal determination of almost every single nucleotide polymorphism and short insertion/deletion. As well as confirming previous findings across the interval, we identify a further novel age-dependent association upstream of IRX5 that imposes a similar burden on BMI to the FTO locus. CONCLUSIONS Our findings are consistent with the hypothesis that chromatin architectures play a role in regulating gene expression levels across topological domains while our targeted sequence approach represents a widely applicable methodology for high-resolution analysis of regional variation across candidate genomic loci.
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Affiliation(s)
- Lilian E Hunt
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Boris Noyvert
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Leena Bhaw-Rosun
- Genomics Facility, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Abdul K Sesay
- Genomics Facility, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol, UK
| | - Ellen A Nohr
- Research Unit for Gynecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol, UK
| | - Niels Tommerup
- Willhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, The Faculty of Health Sciences, The University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol, UK.,The Novo Nordisk Foundation Centre for Basic Metabolic Research, Section on Metabolic genetics, The Faculty of Health and Medical Sciences, University of Copenhagen, DK2100, Copenhagen Ø, Denmark.,Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospitals, The Capital Region, DK2000, Frederiksberg, Denmark
| | - Greg Elgar
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK.
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Livingstone KM, Celis-Morales C, Lara J, Ashor AW, Lovegrove JA, Martinez JA, Saris WH, Gibney M, Manios Y, Traczyk I, Drevon CA, Daniel H, Gibney ER, Brennan L, Bouwman J, Grimaldi KA, Mathers JC. Associations between FTO genotype and total energy and macronutrient intake in adults: a systematic review and meta-analysis. Obes Rev 2015; 16:666-78. [PMID: 26016642 DOI: 10.1111/obr.12290] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/09/2015] [Accepted: 04/09/2015] [Indexed: 12/30/2022]
Abstract
Risk variants of fat mass and obesity-associated (FTO) gene have been associated with increased obesity. However, the evidence for associations between FTO genotype and macronutrient intake has not been reviewed systematically. Our aim was to evaluate the potential associations between FTO genotype and intakes of total energy, fat, carbohydrate and protein. We undertook a systematic literature search in OVID MEDLINE, Scopus, EMBASE and Cochrane of associations between macronutrient intake and FTO genotype in adults. Beta coefficients and confidence intervals (CIs) were used for per allele comparisons. Random-effect models assessed the pooled effect sizes. We identified 56 eligible studies reporting on 213,173 adults. For each copy of the FTO risk allele, individuals reported 6.46 kcal day(-1) (95% CI: 10.76, 2.16) lower total energy intake (P = 0.003). Total fat (P = 0.028) and protein (P = 0.006), but not carbohydrate intakes, were higher in those carrying the FTO risk allele. After adjustment for body weight, total energy intakes remained significantly lower in individuals with the FTO risk genotype (P = 0.028). The FTO risk allele is associated with a lower reported total energy intake and with altered patterns of macronutrient intake. Although significant, these differences are small and further research is needed to determine whether the associations are independent of dietary misreporting.
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Affiliation(s)
- K M Livingstone
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | - C Celis-Morales
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | - J Lara
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | - A W Ashor
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | - J A Lovegrove
- Hugh Sinclair Unit of Human Nutrition and Institute for Cardiovascular and Metabolic Research, University of Reading, Reading, UK
| | - J A Martinez
- Department of Nutrition, Food Science and Physiology, University of Navarra, CIBER Fisiopatología Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Pamplona, Spain
| | - W H Saris
- Department of Human Biology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - M Gibney
- UCD Institute of Food and Health, University College Dublin, Dublin, Republic of Ireland
| | - Y Manios
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - I Traczyk
- ZIEL Research Center of Nutrition and Food Sciences, Technische Universität München, München, Germany
| | - C A Drevon
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - H Daniel
- National Food and Nutrition Institute (IZZ), Warsaw, Poland
| | - E R Gibney
- UCD Institute of Food and Health, University College Dublin, Dublin, Republic of Ireland
| | - L Brennan
- UCD Institute of Food and Health, University College Dublin, Dublin, Republic of Ireland
| | - J Bouwman
- Microbiology and Systems Biology Group, TNO, Zeist, The Netherlands
| | | | - J C Mathers
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
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