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Shin SY, Petersen AK, Wahl S, Zhai G, Römisch-Margl W, Small KS, Döring A, Kato BS, Peters A, Grundberg E, Prehn C, Wang-Sattler R, Wichmann HE, de Angelis MH, Illig T, Adamski J, Deloukas P, Spector TD, Suhre K, Gieger C, Soranzo N. Interrogating causal pathways linking genetic variants, small molecule metabolites, and circulating lipids. Genome Med 2014; 6:25. [PMID: 24678845 PMCID: PMC4062056 DOI: 10.1186/gm542] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/14/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Emerging technologies based on mass spectrometry or nuclear magnetic resonance enable the monitoring of hundreds of small metabolites from tissues or body fluids. Profiling of metabolites can help elucidate causal pathways linking established genetic variants to known disease risk factors such as blood lipid traits. METHODS We applied statistical methodology to dissect causal relationships between single nucleotide polymorphisms, metabolite concentrations, and serum lipid traits, focusing on 95 genetic loci reproducibly associated with the four main serum lipids (total-, low-density lipoprotein-, and high-density lipoprotein- cholesterol and triglycerides). The dataset used included 2,973 individuals from two independent population-based cohorts with data for 151 small molecule metabolites and four main serum lipids. Three statistical approaches, namely conditional analysis, Mendelian randomization, and structural equation modeling, were compared to investigate causal relationship at sets of a single nucleotide polymorphism, a metabolite, and a lipid trait associated with one another. RESULTS A subset of three lipid-associated loci (FADS1, GCKR, and LPA) have a statistically significant association with at least one main lipid and one metabolite concentration in our data, defining a total of 38 cross-associated sets of a single nucleotide polymorphism, a metabolite and a lipid trait. Structural equation modeling provided sufficient discrimination to indicate that the association of a single nucleotide polymorphism with a lipid trait was mediated through a metabolite at 15 of the 38 sets, and involving variants at the FADS1 and GCKR loci. CONCLUSIONS These data provide a framework for evaluating the causal role of components of the metabolome (or other intermediate factors) in mediating the association between established genetic variants and diseases or traits.
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Affiliation(s)
- So-Youn Shin
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK ; MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
| | - Ann-Kristin Petersen
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg D-85764, Germany
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg D-85764, Germany ; Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg D-85764, Germany ; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Guangju Zhai
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK ; Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, Newfoundland, Canada
| | - Werner Römisch-Margl
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg D-85764, Germany
| | - Kerrin S Small
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Angela Döring
- Institute of Epidemiology I, Helmholtz Zentrum München, Neuherberg D-85764, Germany ; Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg D-85764, Germany
| | - Bernet S Kato
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK ; Respiratory Epidemiology, Occupational Medicine and Public Health, Imperial College London, London SW3 6LR, UK
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg D-85764, Germany
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montreal H3A 1A5, Canada ; Genome Quebec Innovation Centre, McGill University, Montreal H3A 1A5, Canada
| | - Cornelia Prehn
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, Neuherberg D-85764, Germany
| | - Rui Wang-Sattler
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg D-85764, Germany
| | - H-Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum München, Neuherberg D-85764, Germany ; Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, München D-81377, Germany ; Klinikum Grosshadern, München D-81377, Germany
| | - Martin Hrabé de Angelis
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, Neuherberg D-85764, Germany ; Institute of Experimental Genetics, Life and Food Science Center Weihenstephan, Technische Universität München, Freising D-85354, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Jerzy Adamski
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, Neuherberg D-85764, Germany ; Institute of Experimental Genetics, Life and Food Science Center Weihenstephan, Technische Universität München, Freising D-85354, Germany
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK ; Willian Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK ; Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg D-85764, Germany ; Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City - Qatar Foundation, Doha, Qatar
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg D-85764, Germany
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1HH, UK ; Department of Hematology, Long Road, Cambridge CB2 0PT, UK
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Keildson S, Fadista J, Ladenvall C, Hedman ÅK, Elgzyri T, Small KS, Grundberg E, Nica AC, Glass D, Richards JB, Barrett A, Nisbet J, Zheng HF, Rönn T, Ström K, Eriksson KF, Prokopenko I, Spector TD, Dermitzakis ET, Deloukas P, McCarthy MI, Rung J, Groop L, Franks PW, Lindgren CM, Hansson O. Expression of phosphofructokinase in skeletal muscle is influenced by genetic variation and associated with insulin sensitivity. Diabetes 2014; 63:1154-65. [PMID: 24306210 PMCID: PMC3931395 DOI: 10.2337/db13-1301] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Using an integrative approach in which genetic variation, gene expression, and clinical phenotypes are assessed in relevant tissues may help functionally characterize the contribution of genetics to disease susceptibility. We sought to identify genetic variation influencing skeletal muscle gene expression (expression quantitative trait loci [eQTLs]) as well as expression associated with measures of insulin sensitivity. We investigated associations of 3,799,401 genetic variants in expression of >7,000 genes from three cohorts (n = 104). We identified 287 genes with cis-acting eQTLs (false discovery rate [FDR] <5%; P < 1.96 × 10(-5)) and 49 expression-insulin sensitivity phenotype associations (i.e., fasting insulin, homeostasis model assessment-insulin resistance, and BMI) (FDR <5%; P = 1.34 × 10(-4)). One of these associations, fasting insulin/phosphofructokinase (PFKM), overlaps with an eQTL. Furthermore, the expression of PFKM, a rate-limiting enzyme in glycolysis, was nominally associated with glucose uptake in skeletal muscle (P = 0.026; n = 42) and overexpressed (Bonferroni-corrected P = 0.03) in skeletal muscle of patients with T2D (n = 102) compared with normoglycemic controls (n = 87). The PFKM eQTL (rs4547172; P = 7.69 × 10(-6)) was nominally associated with glucose uptake, glucose oxidation rate, intramuscular triglyceride content, and metabolic flexibility (P = 0.016-0.048; n = 178). We explored eQTL results using published data from genome-wide association studies (DIAGRAM and MAGIC), and a proxy for the PFKM eQTL (rs11168327; r(2) = 0.75) was nominally associated with T2D (DIAGRAM P = 2.7 × 10(-3)). Taken together, our analysis highlights PFKM as a potential regulator of skeletal muscle insulin sensitivity.
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Affiliation(s)
- Sarah Keildson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Joao Fadista
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Åsa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | - Targ Elgzyri
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, U.K
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
| | - Elin Grundberg
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, U.K
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
| | - Alexandra C. Nica
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Daniel Glass
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, U.K
| | - J. Brent Richards
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, U.K
- Department of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Churchill Hospital, Oxford, U.K
| | - James Nisbet
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
| | - Hou-Feng Zheng
- Department of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Tina Rönn
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Kristoffer Ström
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
- Swedish Winter Sports Research Centre, Department of Health Sciences, Mid Sweden University, Östersund, Sweden
| | - Karl-Fredrik Eriksson
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | | | | | | | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, U.K
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, U.K
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Churchill Hospital, Oxford, U.K
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - Johan Rung
- European Molecular Biology Laboratory–European Bioinformatics Institute, Cambridge, U.K
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Paul W. Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Ola Hansson
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Skåne University Hospital Malmö, Lund University, Malmö, Sweden
- Corresponding author: Ola Hansson,
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Mahajan A, Go MJ, Zhang W, Below JE, Gaulton KJ, Ferreira T, Horikoshi M, Johnson AD, Ng MCY, Prokopenko I, Saleheen D, Wang X, Zeggini E, Abecasis GR, Adair LS, Almgren P, Atalay M, Aung T, Baldassarre D, Balkau B, Bao Y, Barnett AH, Barroso I, Basit A, Been LF, Beilby J, Bell GI, Benediktsson R, Bergman RN, Boehm BO, Boerwinkle E, Bonnycastle LL, Burtt N, Cai Q, Campbell H, Carey J, Cauchi S, Caulfield M, Chan JCN, Chang LC, Chang TJ, Chang YC, Charpentier G, Chen CH, Chen H, Chen YT, Chia KS, Chidambaram M, Chines PS, Cho NH, Cho YM, Chuang LM, Collins FS, Cornelis MC, Couper DJ, Crenshaw AT, van Dam RM, Danesh J, Das D, de Faire U, Dedoussis G, Deloukas P, Dimas AS, Dina C, Doney AS, Donnelly PJ, Dorkhan M, van Duijn C, Dupuis J, Edkins S, Elliott P, Emilsson V, Erbel R, Eriksson JG, Escobedo J, Esko T, Eury E, Florez JC, Fontanillas P, Forouhi NG, Forsen T, Fox C, Fraser RM, Frayling TM, Froguel P, Frossard P, Gao Y, Gertow K, Gieger C, Gigante B, Grallert H, Grant GB, Grrop LC, Groves CJ, Grundberg E, Guiducci C, Hamsten A, Han BG, Hara K, Hassanali N, Hattersley AT, Hayward C, Hedman AK, Herder C, Hofman A, Holmen OL, Hovingh K, Hreidarsson AB, Hu C, Hu FB, Hui J, Humphries SE, Hunt SE, Hunter DJ, Hveem K, Hydrie ZI, Ikegami H, Illig T, Ingelsson E, Islam M, Isomaa B, Jackson AU, Jafar T, James A, Jia W, Jöckel KH, Jonsson A, Jowett JBM, Kadowaki T, Kang HM, Kanoni S, Kao WHL, Kathiresan S, Kato N, Katulanda P, Keinanen-Kiukaanniemi KM, Kelly AM, Khan H, Khaw KT, Khor CC, Kim HL, Kim S, Kim YJ, Kinnunen L, Klopp N, Kong A, Korpi-Hyövälti E, Kowlessur S, Kraft P, Kravic J, Kristensen MM, Krithika S, Kumar A, Kumate J, Kuusisto J, Kwak SH, Laakso M, Lagou V, Lakka TA, Langenberg C, Langford C, Lawrence R, Leander K, Lee JM, Lee NR, Li M, Li X, Li Y, Liang J, Liju S, Lim WY, Lind L, Lindgren CM, Lindholm E, Liu CT, Liu JJ, Lobbens S, Long J, Loos RJF, Lu W, Luan J, Lyssenko V, Ma RCW, Maeda S, Mägi R, Männisto S, Matthews DR, Meigs JB, Melander O, Metspalu A, Meyer J, Mirza G, Mihailov E, Moebus S, Mohan V, Mohlke KL, Morris AD, Mühleisen TW, Müller-Nurasyid M, Musk B, Nakamura J, Nakashima E, Navarro P, Ng PK, Nica AC, Nilsson PM, Njølstad I, Nöthen MM, Ohnaka K, Ong TH, Owen KR, Palmer CNA, Pankow JS, Park KS, Parkin M, Pechlivanis S, Pedersen NL, Peltonen L, Perry JRB, Peters A, Pinidiyapathirage JM, Platou CG, Potter S, Price JF, Qi L, Radha V, Rallidis L, Rasheed A, Rathman W, Rauramaa R, Raychaudhuri S, Rayner NW, Rees SD, Rehnberg E, Ripatti S, Robertson N, Roden M, Rossin EJ, Rudan I, Rybin D, Saaristo TE, Salomaa V, Saltevo J, Samuel M, Sanghera DK, Saramies J, Scott J, Scott LJ, Scott RA, Segrè AV, Sehmi J, Sennblad B, Shah N, Shah S, Shera AS, Shu XO, Shuldiner AR, Sigurđsson G, Sijbrands E, Silveira A, Sim X, Sivapalaratnam S, Small KS, So WY, Stančáková A, Stefansson K, Steinbach G, Steinthorsdottir V, Stirrups K, Strawbridge RJ, Stringham HM, Sun Q, Suo C, Syvänen AC, Takayanagi R, Takeuchi F, Tay WT, Teslovich TM, Thorand B, Thorleifsson G, Thorsteinsdottir U, Tikkanen E, Trakalo J, Tremoli E, Trip MD, Tsai FJ, Tuomi T, Tuomilehto J, Uitterlinden AG, Valladares-Salgado A, Vedantam S, Veglia F, Voight BF, Wang C, Wareham NJ, Wennauer R, Wickremasinghe AR, Wilsgaard T, Wilson JF, Wiltshire S, Winckler W, Wong TY, Wood AR, Wu JY, Wu Y, Yamamoto K, Yamauchi T, Yang M, Yengo L, Yokota M, Young R, Zabaneh D, Zhang F, Zhang R, Zheng W, Zimmet PZ, Altshuler D, Bowden DW, Cho YS, Cox NJ, Cruz M, Hanis CL, Kooner J, Lee JY, Seielstad M, Teo YY, Boehnke M, Parra EJ, Chambers JC, Tai ES, McCarthy MI, Morris AP. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nat Genet 2014; 46:234-44. [PMID: 24509480 PMCID: PMC3969612 DOI: 10.1038/ng.2897] [Citation(s) in RCA: 777] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/17/2014] [Indexed: 11/18/2022]
Abstract
To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS) including 26,488 cases and 83,964 controls of European, East Asian, South Asian, and Mexican and Mexican American ancestry. We observed significant excess in directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven novel T2D susceptibility loci. Furthermore, we observed considerable improvements in fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterisation of complex trait loci, and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry.
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Grundberg E, Meduri E, Sandling JK, Hedman ÅK, Keildson S, Buil A, Busche S, Yuan W, Nisbet J, Sekowska M, Wilk A, Barrett A, Small KS, Ge B, Caron M, Shin SY, Lathrop M, Dermitzakis ET, McCarthy MI, Spector TD, Bell JT, Deloukas P, Ahmadi KR, Ainali C, Barrett A, Bataille V, Bell JT, Buil A, Deloukas P, Dermitzakis ET, Dimas AS, Durbin R, Glass D, Grundberg E, Hassanali N, Hedman ÅK, Ingle C, Knowles D, Krestyaninova M, Lindgren CM, Lowe CE, McCarthy MI, Meduri E, di Meglio P, Min JL, Montgomery SB, Nestle FO, Nica AC, Nisbet J, O’Rahilly S, Parts L, Potter S, Sandling J, Sekowska M, Shin SY, Small KS, Soranzo N, Spector TD, Surdulescu G, Travers ME, Tsaprouni L, Tsoka S, Wilk A, Yang TP, Zondervan KT. Global Analysis of DNA Methylation Variation in Adipose Tissue from Twins Reveals Links to Disease-Associated Variants in Distal Regulatory Elements. Am J Hum Genet 2013. [DOI: 10.1016/j.ajhg.2013.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Grundberg E, Meduri E, Sandling J, Hedman Å, Keildson S, Buil A, Busche S, Yuan W, Nisbet J, Sekowska M, Wilk A, Barrett A, Small K, Ge B, Caron M, Shin SY, Lathrop M, Dermitzakis ET, McCarthy MI, Spector TD, Bell JT, Deloukas P. Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet 2013; 93:876-90. [PMID: 24183450 PMCID: PMC3824131 DOI: 10.1016/j.ajhg.2013.10.004] [Citation(s) in RCA: 288] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/13/2013] [Accepted: 10/04/2013] [Indexed: 12/28/2022] Open
Abstract
Epigenetic modifications such as DNA methylation play a key role in gene regulation and disease susceptibility. However, little is known about the genome-wide frequency, localization, and function of methylation variation and how it is regulated by genetic and environmental factors. We utilized the Multiple Tissue Human Expression Resource (MuTHER) and generated Illumina 450K adipose methylome data from 648 twins. We found that individual CpGs had low variance and that variability was suppressed in promoters. We noted that DNA methylation variation was highly heritable (h(2)median = 0.34) and that shared environmental effects correlated with metabolic phenotype-associated CpGs. Analysis of methylation quantitative-trait loci (metQTL) revealed that 28% of CpGs were associated with nearby SNPs, and when overlapping them with adipose expression quantitative-trait loci (eQTL) from the same individuals, we found that 6% of the loci played a role in regulating both gene expression and DNA methylation. These associations were bidirectional, but there were pronounced negative associations for promoter CpGs. Integration of metQTL with adipose reference epigenomes and disease associations revealed significant enrichment of metQTL overlapping metabolic-trait or disease loci in enhancers (the strongest effects were for high-density lipoprotein cholesterol and body mass index [BMI]). We followed up with the BMI SNP rs713586, a cg01884057 metQTL that overlaps an enhancer upstream of ADCY3, and used bisulphite sequencing to refine this region. Our results showed widespread population invariability yet sequence dependence on adipose DNA methylation but that incorporating maps of regulatory elements aid in linking CpG variation to gene regulation and disease risk in a tissue-dependent manner.
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Affiliation(s)
- Elin Grundberg
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Eshwar Meduri
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Johanna K. Sandling
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Molecular Medicine, Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, 751 23 Uppsala, Sweden
| | - Åsa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
| | - Sarah Keildson
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
| | - Alfonso Buil
- Department of Genetic Medicine and Development and Institute for Genetics and Genomics in Geneva, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Stephan Busche
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Wei Yuan
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - James Nisbet
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | | | - Alicja Wilk
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, OX37LJ Oxford, UK
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Bing Ge
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | - Mark Lathrop
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development and Institute for Genetics and Genomics in Geneva, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, OX37LJ Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, OX3 7LE Oxford, UK
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
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Glass D, Viñuela A, Davies MN, Ramasamy A, Parts L, Knowles D, Brown AA, Hedman ÅK, Small KS, Buil A, Grundberg E, Nica AC, Di Meglio P, Nestle FO, Ryten M, Durbin R, McCarthy MI, Deloukas P, Dermitzakis ET, Weale ME, Bataille V, Spector TD. Gene expression changes with age in skin, adipose tissue, blood and brain. Genome Biol 2013; 14:R75. [PMID: 23889843 PMCID: PMC4054017 DOI: 10.1186/gb-2013-14-7-r75] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 05/13/2013] [Accepted: 07/26/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Previous studies have demonstrated that gene expression levels change with age. These changes are hypothesized to influence the aging rate of an individual. We analyzed gene expression changes with age in abdominal skin, subcutaneous adipose tissue and lymphoblastoid cell lines in 856 female twins in the age range of 39-85 years. Additionally, we investigated genotypic variants involved in genotype-by-age interactions to understand how the genomic regulation of gene expression alters with age. RESULTS Using a linear mixed model, differential expression with age was identified in 1,672 genes in skin and 188 genes in adipose tissue. Only two genes expressed in lymphoblastoid cell lines showed significant changes with age. Genes significantly regulated by age were compared with expression profiles in 10 brain regions from 100 postmortem brains aged 16 to 83 years. We identified only one age-related gene common to the three tissues. There were 12 genes that showed differential expression with age in both skin and brain tissue and three common to adipose and brain tissues. CONCLUSIONS Skin showed the most age-related gene expression changes of all the tissues investigated, with many of the genes being previously implicated in fatty acid metabolism, mitochondrial activity, cancer and splicing. A significant proportion of age-related changes in gene expression appear to be tissue-specific with only a few genes sharing an age effect in expression across tissues. More research is needed to improve our understanding of the genetic influences on aging and the relationship with age-related diseases.
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Affiliation(s)
- Daniel Glass
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
- North West London Hospitals NHS Trust, Northwick Park Hospital, Watford Road, Harrow HA1 3UJ, UK
| | - Ana Viñuela
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
| | - Matthew N Davies
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
| | - Adaikalavan Ramasamy
- Department of Medical ƒ Molecular Genetics, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | | | - David Knowles
- Stanford University, 450 Serra MallStanford, CA 94305, USA
| | | | - Åsa K Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
- Wellcome Trust Sanger Institute, HinxtonCB10 1SA,UK
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet (CMU office 9088), Geneva 1211, Switzerland
| | - Elin Grundberg
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
- Wellcome Trust Sanger Institute, HinxtonCB10 1SA,UK
| | - Alexandra C Nica
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet (CMU office 9088), Geneva 1211, Switzerland
| | - Paola Di Meglio
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Frank O Nestle
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Mina Ryten
- Department of Medical ƒ Molecular Genetics, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - the UK Brain Expression consortium
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
| | | | | | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology ƒ Metabolism, University of Oxford, Churchill Hospital, Oxford, Headington OX3 7LJ,UK
| | | | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet (CMU office 9088), Geneva 1211, Switzerland
| | - Michael E Weale
- Department of Medical ƒ Molecular Genetics, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Veronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Westminster Bridge Road, London SE1 7EH, UK
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Drong AW, Nicholson G, Hedman ÅK, Meduri E, Grundberg E, Small KS, Shin SY, Bell JT, Karpe F, Soranzo N, Spector TD, McCarthy MI, Deloukas P, Rantalainen M, Lindgren CM. The presence of methylation quantitative trait loci indicates a direct genetic influence on the level of DNA methylation in adipose tissue. PLoS One 2013; 8:e55923. [PMID: 23431366 PMCID: PMC3576415 DOI: 10.1371/journal.pone.0055923] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/03/2013] [Indexed: 11/19/2022] Open
Abstract
Genetic variants that associate with DNA methylation at CpG sites (methylation quantitative trait loci, meQTLs) offer a potential biological mechanism of action for disease associated SNPs. We investigated whether meQTLs exist in abdominal subcutaneous adipose tissue (SAT) and if CpG methylation associates with metabolic syndrome (MetSyn) phenotypes. We profiled 27,718 genomic regions in abdominal SAT samples of 38 unrelated individuals using differential methylation hybridization (DMH) together with genotypes at 5,227,243 SNPs and expression of 17,209 mRNA transcripts. Validation and replication of significant meQTLs was pursued in an independent cohort of 181 female twins. We find that, at 5% false discovery rate, methylation levels of 149 DMH regions associate with at least one SNP in a ±500 kilobase cis-region in our primary study. We sought to validate 19 of these in the replication study and find that five of these significantly associate with the corresponding meQTL SNPs from the primary study. We find that none of the 149 meQTL top SNPs is a significant expression quantitative trait locus in our expression data, but we observed association between expression levels of two mRNA transcripts and cis-methylation status. Our results indicate that DNA CpG methylation in abdominal SAT is partly under genetic control. This study provides a starting point for future investigations of DNA methylation in adipose tissue.
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Affiliation(s)
- Alexander W. Drong
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - George Nicholson
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Åsa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Eshwar Meduri
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Elin Grundberg
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Twin Research, King's College London, London, United Kingdom
| | - Kerrin S. Small
- Department of Twin Research, King's College London, London, United Kingdom
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Jordana T. Bell
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Twin Research, King's College London, London, United Kingdom
| | - Fredrik Karpe
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Tim D. Spector
- Department of Twin Research, King's College London, London, United Kingdom
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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58
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Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR, Ingelsson E, Saleheen D, Erdmann J, Goldstein BA, Stirrups K, König IR, Cazier JB, Johansson A, Hall AS, Lee JY, Willer CJ, Chambers JC, Esko T, Folkersen L, Goel A, Grundberg E, Havulinna AS, Ho WK, Hopewell JC, Eriksson N, Kleber ME, Kristiansson K, Lundmark P, Lyytikäinen LP, Rafelt S, Shungin D, Strawbridge RJ, Thorleifsson G, Tikkanen E, Van Zuydam N, Voight BF, Waite LL, Zhang W, Ziegler A, Absher D, Altshuler D, Balmforth AJ, Barroso I, Braund PS, Burgdorf C, Claudi-Boehm S, Cox D, Dimitriou M, Do R, Doney ASF, El Mokhtari N, Eriksson P, Fischer K, Fontanillas P, Franco-Cereceda A, Gigante B, Groop L, Gustafsson S, Hager J, Hallmans G, Han BG, Hunt SE, Kang HM, Illig T, Kessler T, Knowles JW, Kolovou G, Kuusisto J, Langenberg C, Langford C, Leander K, Lokki ML, Lundmark A, McCarthy MI, Meisinger C, Melander O, Mihailov E, Maouche S, Morris AD, Müller-Nurasyid M, Nikus K, Peden JF, Rayner NW, Rasheed A, Rosinger S, Rubin D, Rumpf MP, Schäfer A, Sivananthan M, Song C, Stewart AFR, Tan ST, Thorgeirsson G, van der Schoot CE, Wagner PJ, Wells GA, Wild PS, Yang TP, Amouyel P, Arveiler D, Basart H, Boehnke M, Boerwinkle E, Brambilla P, Cambien F, Cupples AL, de Faire U, Dehghan A, Diemert P, Epstein SE, Evans A, Ferrario MM, Ferrières J, Gauguier D, Go AS, Goodall AH, Gudnason V, Hazen SL, Holm H, Iribarren C, Jang Y, Kähönen M, Kee F, Kim HS, Klopp N, Koenig W, Kratzer W, Kuulasmaa K, Laakso M, Laaksonen R, Lee JY, Lind L, Ouwehand WH, Parish S, Park JE, Pedersen NL, Peters A, Quertermous T, Rader DJ, Salomaa V, Schadt E, Shah SH, Sinisalo J, Stark K, Stefansson K, Trégouët DA, Virtamo J, Wallentin L, Wareham N, Zimmermann ME, Nieminen MS, Hengstenberg C, Sandhu MS, Pastinen T, Syvänen AC, Hovingh GK, Dedoussis G, Franks PW, Lehtimäki T, Metspalu A, Zalloua PA, Siegbahn A, Schreiber S, Ripatti S, Blankenberg SS, Perola M, Clarke R, Boehm BO, O'Donnell C, Reilly MP, März W, Collins R, Kathiresan S, Hamsten A, Kooner JS, Thorsteinsdottir U, Danesh J, Palmer CNA, Roberts R, Watkins H, Schunkert H, Samani NJ. Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet 2012. [PMID: 23202125 DOI: 10.1038/ng.2480] [Citation(s) in RCA: 1227] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coronary artery disease (CAD) is the commonest cause of death. Here, we report an association analysis in 63,746 CAD cases and 130,681 controls identifying 15 loci reaching genome-wide significance, taking the number of susceptibility loci for CAD to 46, and a further 104 independent variants (r(2) < 0.2) strongly associated with CAD at a 5% false discovery rate (FDR). Together, these variants explain approximately 10.6% of CAD heritability. Of the 46 genome-wide significant lead SNPs, 12 show a significant association with a lipid trait, and 5 show a significant association with blood pressure, but none is significantly associated with diabetes. Network analysis with 233 candidate genes (loci at 10% FDR) generated 5 interaction networks comprising 85% of these putative genes involved in CAD. The four most significant pathways mapping to these networks are linked to lipid metabolism and inflammation, underscoring the causal role of these activities in the genetic etiology of CAD. Our study provides insights into the genetic basis of CAD and identifies key biological pathways.
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59
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Clark C, Palta P, Joyce CJ, Scott C, Grundberg E, Deloukas P, Palotie A, Coffey AJ. A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profiling. PLoS One 2012; 7:e50233. [PMID: 23209683 PMCID: PMC3510246 DOI: 10.1371/journal.pone.0050233] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 10/17/2012] [Indexed: 02/04/2023] Open
Abstract
DNA methylation is one of the most studied epigenetic marks in the human genome, with the result that the desire to map the human methylome has driven the development of several methods to map DNA methylation on a genomic scale. Our study presents the first comparison of two of these techniques - the targeted approach of the Infinium HumanMethylation450 BeadChip® with the immunoprecipitation and sequencing-based method, MeDIP-seq. Both methods were initially validated with respect to bisulfite sequencing as the gold standard and then assessed in terms of coverage, resolution and accuracy. The regions of the methylome that can be assayed by both methods and those that can only be assayed by one method were determined and the discovery of differentially methylated regions (DMRs) by both techniques was examined. Our results show that the Infinium HumanMethylation450 BeadChip® and MeDIP-seq show a good positive correlation (Spearman correlation of 0.68) on a genome-wide scale and can both be used successfully to determine differentially methylated loci in RefSeq genes, CpG islands, shores and shelves. MeDIP-seq however, allows a wider interrogation of methylated regions of the human genome, including thousands of non-RefSeq genes and repetitive elements, all of which may be of importance in disease. In our study MeDIP-seq allowed the detection of 15,709 differentially methylated regions, nearly twice as many as the array-based method (8070), which may result in a more comprehensive study of the methylome.
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Affiliation(s)
- Christine Clark
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Priit Palta
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Christopher J. Joyce
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Carol Scott
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Elin Grundberg
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Panos Deloukas
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Aarno Palotie
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Medical Genetics, University of Helsinki and University Central Hospital, Helsinki, Finland
| | - Alison J. Coffey
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- * E-mail:
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60
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Liu CT, Estrada K, Yerges-Armstrong LM, Amin N, Evangelou E, Li G, Minster RL, Carless MA, Kammerer CM, Oei L, Zhou Y, Alonso N, Dailiana Z, Eriksson J, García-Giralt N, Giroux S, Husted LB, Khusainova RI, Koromila T, Kung AW, Lewis JR, Masi L, Mencej-Bedrac S, Nogues X, Patel MS, Prezelj J, Richards JB, Sham PC, Spector T, Vandenput L, Xiao SM, Zheng HF, Zhu K, Balcells S, Brandi ML, Frost M, Goltzman D, González-Macías J, Karlsson M, Khusnutdinova EK, Kollia P, Langdahl BL, Ljunggren Ö, Lorentzon M, Marc J, Mellström D, Ohlsson C, Olmos JM, Ralston SH, Riancho JA, Rousseau F, Urreizti R, Van Hul W, Zarrabeitia MT, Castano-Betancourt M, Demissie S, Grundberg E, Herrera L, Kwan T, Medina-Gómez C, Pastinen T, Sigurdsson G, Thorleifsson G, vanMeurs JB, Blangero J, Hofman A, Liu Y, Mitchell BD, O’Connell JR, Oostra BA, Rotter JI, Stefansson K, Streeten EA, Styrkarsdottir U, Thorsteinsdottir U, Tylavsky FA, Uitterlinden A, Cauley JA, Harris TB, Ioannidis JP, Psaty BM, Robbins JA, Zillikens MC, vanDuijn CM, Prince RL, Karasik D, Rivadeneira F, Kiel DP, Cupples LA, Hsu YH. Assessment of gene-by-sex interaction effect on bone mineral density. J Bone Miner Res 2012; 27:2051-64. [PMID: 22692763 PMCID: PMC3447125 DOI: 10.1002/jbmr.1679] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Sexual dimorphism in various bone phenotypes, including bone mineral density (BMD), is widely observed; however, the extent to which genes explain these sex differences is unclear. To identify variants with different effects by sex, we examined gene-by-sex autosomal interactions genome-wide, and performed expression quantitative trait loci (eQTL) analysis and bioinformatics network analysis. We conducted an autosomal genome-wide meta-analysis of gene-by-sex interaction on lumbar spine (LS) and femoral neck (FN) BMD in 25,353 individuals from 8 cohorts. In a second stage, we followed up the 12 top single-nucleotide polymorphisms (SNPs; p < 1 × 10(-5) ) in an additional set of 24,763 individuals. Gene-by-sex interaction and sex-specific effects were examined in these 12 SNPs. We detected one novel genome-wide significant interaction associated with LS-BMD at the Chr3p26.1-p25.1 locus, near the GRM7 gene (male effect = 0.02 and p = 3.0 × 10(-5) ; female effect = -0.007 and p = 3.3 × 10(-2) ), and 11 suggestive loci associated with either FN- or LS-BMD in discovery cohorts. However, there was no evidence for genome-wide significant (p < 5 × 10(-8) ) gene-by-sex interaction in the joint analysis of discovery and replication cohorts. Despite the large collaborative effort, no genome-wide significant evidence for gene-by-sex interaction was found to influence BMD variation in this screen of autosomal markers. If they exist, gene-by-sex interactions for BMD probably have weak effects, accounting for less than 0.08% of the variation in these traits per implicated SNP. © 2012 American Society for Bone and Mineral Research.
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Affiliation(s)
- Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Karol Estrada
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Laura M. Yerges-Armstrong
- Department of Medicine; Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Guo Li
- Cardiovascular Health Research Unit, Dept. Med, University of Washington, Seattle, WA, USA
| | - Ryan L. Minster
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Melanie A. Carless
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Candace M. Kammerer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ling Oei
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Yanhua Zhou
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Nerea Alonso
- Rheumatic Diseases Unit, Centre for Molecular Medicine, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Zoe Dailiana
- Department of Orthopaedic Surgery, Medical School University of Thessalia, Larissa, Greece
| | - Joel Eriksson
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Sylvie Giroux
- URGHM, Centre de recherche du CHUQ/HSFA, Québec City, Canada
| | - Lise Bjerre Husted
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus C, Denmark
| | - Rita I. Khusainova
- Ufa Scientific Centre of RAS, Institute of Biochemistry and Genetics, Russia, Ufa
- Biological, Bashkir State University, Russia, Ufa
| | - Theodora Koromila
- Department of Human Genetics, School of Biology, University of Athens, Athens, Greece
| | - Annie WaiChee Kung
- Department of Medicine, The University of Hong Kong, Hong Kong, China
- Research Centre of Heart, Brain, Hormone & Healthy Aging, The University of Hong Kong, Hong Kong, China
| | - Joshua R. Lewis
- School of Medicine and Pharmacology, University of Western Australia, Perth, Australia
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Perth, Australia
| | - Laura Masi
- Department of Internal Medicine, University of Florence, Florence, Italy
| | - Simona Mencej-Bedrac
- Department of Clinical Biochemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Xavier Nogues
- Department of Internal Medicine, Hospital del Mar-IMIM, UAB, Barcelone, Spain
| | - Millan S. Patel
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Janez Prezelj
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Medical Center, Ljubljana, Slovenia
| | - J Brent Richards
- Department of Medicine, Human genetics and epidemiology & biostatistics, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Canada
- Department of Twin Research and Genetic Epidemiology, King’s College, London, UK
| | - Pak Chung Sham
- Department of Psychiatry, The University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development and Growth, The University of Hong Kong, Hong Kong, China
| | - Timothy Spector
- Department of Twin Research and Genetic Epidemiology, King’s College, London, UK
| | - Liesbeth Vandenput
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Su-Mei Xiao
- Department of Medicine, The University of Hong Kong, Hong Kong, China
- Research Centre of Heart, Brain, Hormone & Healthy Aging, The University of Hong Kong, Hong Kong, China
| | - Hou-Feng Zheng
- Department of Medicine, Human genetics and epidemiology & biostatistics, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Canada
| | - Kun Zhu
- School of Medicine and Pharmacology, University of Western Australia, Perth, Australia
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Perth, Australia
| | - Susana Balcells
- Department of Genetics, University of Barcelona, CIBERER, IBUB, Barcelone, Spain
| | - Maria Luisa Brandi
- Department of Internal Medicine, University of Florence, Florence, Italy
| | - Morten Frost
- Department of Endocrinology, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - David Goltzman
- Department of Medicine, McGill University, Montreal, Canada
| | - Jesús González-Macías
- Department of Medicine, University of Cantabria, Santander, Spain
- Department of Internal Medicine, Hospital U.M. Valdecilla-IFIMAV, RETICEF, Santander, Spain
| | - Magnus Karlsson
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences and Department of Orthopaedics, Lund university, Malmö, Sweden
| | - Elza K. Khusnutdinova
- Ufa Scientific Centre of RAS, Institute of Biochemistry and Genetics, Russia, Ufa
- Biological, Bashkir State University, Russia, Ufa
| | - Panagoula Kollia
- Department of Human Genetics, School of Biology, University of Athens, Athens, Greece
| | - Bente Lomholt Langdahl
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus C, Denmark
| | - Östen Ljunggren
- Department of Medical Sciences, University of Uppsala, Uppsala, Sweden
| | - Mattias Lorentzon
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Janja Marc
- Department of Clinical Biochemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Dan Mellström
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - José M. Olmos
- Department of Medicine, University of Cantabria, Santander, Spain
- Department of Internal Medicine, Hospital U.M. Valdecilla-IFIMAV, RETICEF, Santander, Spain
| | - Stuart H. Ralston
- Rheumatic Diseases Unit, Centre for Molecular Medicine, MRC IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - José A. Riancho
- Department of Medicine, University of Cantabria, Santander, Spain
- Department of Internal Medicine, Hospital U.M. Valdecilla-IFIMAV, RETICEF, Santander, Spain
| | - François Rousseau
- URGHM, Centre de recherche du CHUQ/HSFA, Québec City, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, Canada
- The APOGEE-Net/CanGèneTest Network on Genetic Health Services and Policy, Université Laval, Québec City, Canada
| | - Roser Urreizti
- Department of Genetics, University of Barcelona, CIBERER, IBUB, Barcelone, Spain
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | | - Martha Castano-Betancourt
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Serkalem Demissie
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Elin Grundberg
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Lizbeth Herrera
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Tony Kwan
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre
| | - Carolina Medina-Gómez
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre
| | - Gunnar Sigurdsson
- Department of Endocrinology and Metabolism, University Hospital, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Joyce B.J. vanMeurs
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Yongmei Liu
- Center for Human Genomics, School of Medicine, Wake Forest University, Winston-Salem, NC, USA
| | - Braxton D. Mitchell
- Department of Medicine; Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jeffrey R. O’Connell
- Department of Medicine; Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Centre for Medical Systems Biology & Netherlands Consortium on Healthy Aging, Leiden, The Netherlands
- Netherlands Genomic Initiative, the Hague, The Netherlands
| | - Jerome I Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kari Stefansson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- deCODE Genetics, Reykjavik, Iceland
| | - Elizabeth A. Streeten
- Department of Medicine; Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatric Research and Education Clinical Center (GRECC), Veterans Administration Medical Center, Baltimore, MD, USA
| | | | - Unnur Thorsteinsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- deCODE Genetics, Reykjavik, Iceland
| | - Frances A. Tylavsky
- Department of Preventive Medicine, College of Medicine, University of Tennessee, Memphis, TN, USA
| | - Andre Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Jane A. Cauley
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, Intramural Research Program, National Institute on Aging, Bethesda, MD,USA
| | - John P.A. Ioannidis
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
- Stanford Prevention Research Center, Department of Medicine and Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, USA
- Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
| | | | - M. Carola Zillikens
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cornelia M. vanDuijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Centre for Medical Systems Biology & Netherlands Consortium on Healthy Aging, Leiden, The Netherlands
- Netherlands Genomic Initiative, the Hague, The Netherlands
| | - Richard L. Prince
- School of Medicine and Pharmacology, University of Western Australia, Perth, Australia
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Perth, Australia
| | - David Karasik
- Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Douglas P. Kiel
- Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Yi-Hsiang Hsu
- Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, MA, USA
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61
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Grundberg E, Small KS, Hedman ÅK, Nica AC, Buil A, Keildson S, Bell JT, Yang TP, Meduri E, Barrett A, Nisbett J, Sekowska M, Wilk A, Shin SY, Glass D, Travers M, Min JL, Ring S, Ho K, Thorleifsson G, Kong A, Thorsteindottir U, Ainali C, Dimas AS, Hassanali N, Ingle C, Knowles D, Krestyaninova M, Lowe CE, Di Meglio P, Montgomery SB, Parts L, Potter S, Surdulescu G, Tsaprouni L, Tsoka S, Bataille V, Durbin R, Nestle FO, O'Rahilly S, Soranzo N, Lindgren CM, Zondervan KT, Ahmadi KR, Schadt EE, Stefansson K, Smith GD, McCarthy MI, Deloukas P, Dermitzakis ET, Spector TD. Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet 2012; 44:1084-9. [PMID: 22941192 PMCID: PMC3784328 DOI: 10.1038/ng.2394] [Citation(s) in RCA: 575] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 08/08/2012] [Indexed: 12/16/2022]
Abstract
Sequence-based variation in gene expression is a key driver of disease risk. Common variants regulating expression in cis have been mapped in many expression quantitative trait locus (eQTL) studies, typically in single tissues from unrelated individuals. Here, we present a comprehensive analysis of gene expression across multiple tissues conducted in a large set of mono- and dizygotic twins that allows systematic dissection of genetic (cis and trans) and non-genetic effects on gene expression. Using identity-by-descent estimates, we show that at least 40% of the total heritable cis effect on expression cannot be accounted for by common cis variants, a finding that reveals the contribution of low-frequency and rare regulatory variants with respect to both transcriptional regulation and complex trait susceptibility. We show that a substantial proportion of gene expression heritability is trans to the structural gene, and we identify several replicating trans variants that act predominantly in a tissue-restricted manner and may regulate the transcription of many genes.
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62
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Billings LK, Hsu YH, Ackerman RJ, Dupuis J, Voight BF, Rasmussen-Torvik LJ, Hercberg S, Lathrop M, Barnes D, Langenberg C, Hui J, Fu M, Bouatia-Naji N, Lecoeur C, An P, Magnusson PK, Surakka I, Ripatti S, Christiansen L, Dalgård C, Folkersen L, Grundberg E, Eriksson P, Kaprio J, Ohm Kyvik K, Pedersen NL, Borecki IB, Province MA, Balkau B, Froguel P, Shuldiner AR, Palmer LJ, Wareham N, Meneton P, Johnson T, Pankow JS, Karasik D, Meigs JB, Kiel DP, Florez JC. Impact of common variation in bone-related genes on type 2 diabetes and related traits. Diabetes 2012; 61:2176-86. [PMID: 22698912 PMCID: PMC3402303 DOI: 10.2337/db11-1515] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Exploring genetic pleiotropy can provide clues to a mechanism underlying the observed epidemiological association between type 2 diabetes and heightened fracture risk. We examined genetic variants associated with bone mineral density (BMD) for association with type 2 diabetes and glycemic traits in large well-phenotyped and -genotyped consortia. We undertook follow-up analysis in ∼19,000 individuals and assessed gene expression. We queried single nucleotide polymorphisms (SNPs) associated with BMD at levels of genome-wide significance, variants in linkage disequilibrium (r(2) > 0.5), and BMD candidate genes. SNP rs6867040, at the ITGA1 locus, was associated with a 0.0166 mmol/L (0.004) increase in fasting glucose per C allele in the combined analysis. Genetic variants in the ITGA1 locus were associated with its expression in the liver but not in adipose tissue. ITGA1 variants appeared among the top loci associated with type 2 diabetes, fasting insulin, β-cell function by homeostasis model assessment, and 2-h post-oral glucose tolerance test glucose and insulin levels. ITGA1 has demonstrated genetic pleiotropy in prior studies, and its suggested role in liver fibrosis, insulin secretion, and bone healing lends credence to its contribution to both osteoporosis and type 2 diabetes. These findings further underscore the link between skeletal and glucose metabolism and highlight a locus to direct future investigations.
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Affiliation(s)
- Liana K. Billings
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts
| | - Yi-Hsiang Hsu
- Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, Massachusetts
- Molecular and Integrative Physiological Sciences Program, Harvard School of Public Health, Boston, Massachusetts
- Framingham Heart Study, Framingham, Massachusetts
| | - Rachel J. Ackerman
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Josée Dupuis
- Framingham Heart Study, Framingham, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Benjamin F. Voight
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Laura J. Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Serge Hercberg
- INSERM, National Institute of Agronomic Research, University of Paris, Bobigny, France
| | - Mark Lathrop
- National Genotyping Center, Atomic Energy Commission, Institute of Genomics, Evry, France
| | - Daniel Barnes
- Medical Research Council Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, U.K
| | - Claudia Langenberg
- Medical Research Council Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, U.K
| | - Jennie Hui
- Molecular Genetics, PathWest Laboratory Medicine of Western Australia, Nedlands, Western Australia, Australia
- School of Population Health and School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Western Australia, Australia
- Busselton Population Medical Research Foundation, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Mao Fu
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - Nabila Bouatia-Naji
- National Center for Scientific Research, UMR 8199, Genomics and Metabolic Diseases, Lille Pasteur Institute, Lille Nord de France University, Lille, France
| | - Cecile Lecoeur
- National Center for Scientific Research, UMR 8199, Genomics and Metabolic Diseases, Lille Pasteur Institute, Lille Nord de France University, Lille, France
| | - Ping An
- Division of Statistical Genomics and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Patrik K. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Ida Surakka
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Lene Christiansen
- Danish Twin Registry, Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Christine Dalgård
- Department of Environmental Medicine, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Lasse Folkersen
- Atherosclerosis Research Unit, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Elin Grundberg
- Wellcome Trust Sanger Institute, Hinxton, U.K
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, U.K
| | | | | | | | | | | | - Per Eriksson
- Atherosclerosis Research Unit, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Unit for Child and Adolescent Mental Health, National Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Kirsten Ohm Kyvik
- Institute of Regional Health Services Research, University of Southern Denmark, Odense, Denmark
- Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Ingrid B. Borecki
- Division of Statistical Genomics and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Michael A. Province
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Beverley Balkau
- INSERM, CESP Center for Research in Epidemiology and Health of Populations, U1018, Epidemiology of Diabetes, Obesity and Chronic Kidney Disease Over the Life Course, INSERM, Villejuif, France and Université Paris-Sud 11, UMRS 1018, Villejuif, France
| | - Philippe Froguel
- National Center for Scientific Research, UMR 8199, Genomics and Metabolic Diseases, Lille Pasteur Institute, Lille Nord de France University, Lille, France
- Genomic Medicine, Hammersmith Hospital, Imperial College London, London, U.K
| | - Alan R. Shuldiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
- Geriatrics Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, Maryland
| | - Lyle J. Palmer
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Nick Wareham
- Medical Research Council Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, U.K
| | | | - Toby Johnson
- Clinical Pharmacology and the Genome Centre, William Harvey Research Institute, Barts and London School of Medicine and Dentistry, Queen Mary University of London, London, U.K
| | - James S. Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota
| | - David Karasik
- Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, Massachusetts
- Framingham Heart Study, Framingham, Massachusetts
| | - James B. Meigs
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Framingham Heart Study, Framingham, Massachusetts
| | - Douglas P. Kiel
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, Massachusetts
- Framingham Heart Study, Framingham, Massachusetts
| | - Jose C. Florez
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
- Corresponding author: Jose C. Florez,
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63
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Bell JT, Tsai PC, Yang TP, Pidsley R, Nisbet J, Glass D, Mangino M, Zhai G, Zhang F, Valdes A, Shin SY, Dempster EL, Murray RM, Grundberg E, Hedman AK, Nica A, Small KS, Dermitzakis ET, McCarthy MI, Mill J, Spector TD, Deloukas P. Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet 2012; 8:e1002629. [PMID: 22532803 PMCID: PMC3330116 DOI: 10.1371/journal.pgen.1002629] [Citation(s) in RCA: 491] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 02/22/2012] [Indexed: 12/18/2022] Open
Abstract
Age-related changes in DNA methylation have been implicated in cellular senescence and longevity, yet the causes and functional consequences of these variants remain unclear. To elucidate the role of age-related epigenetic changes in healthy ageing and potential longevity, we tested for association between whole-blood DNA methylation patterns in 172 female twins aged 32 to 80 with age and age-related phenotypes. Twin-based DNA methylation levels at 26,690 CpG-sites showed evidence for mean genome-wide heritability of 18%, which was supported by the identification of 1,537 CpG-sites with methylation QTLs in cis at FDR 5%. We performed genome-wide analyses to discover differentially methylated regions (DMRs) for sixteen age-related phenotypes (ap-DMRs) and chronological age (a-DMRs). Epigenome-wide association scans (EWAS) identified age-related phenotype DMRs (ap-DMRs) associated with LDL (STAT5A), lung function (WT1), and maternal longevity (ARL4A, TBX20). In contrast, EWAS for chronological age identified hundreds of predominantly hyper-methylated age DMRs (490 a-DMRs at FDR 5%), of which only one (TBX20) was also associated with an age-related phenotype. Therefore, the majority of age-related changes in DNA methylation are not associated with phenotypic measures of healthy ageing in later life. We replicated a large proportion of a-DMRs in a sample of 44 younger adult MZ twins aged 20 to 61, suggesting that a-DMRs may initiate at an earlier age. We next explored potential genetic and environmental mechanisms underlying a-DMRs and ap-DMRs. Genome-wide overlap across cis-meQTLs, genotype-phenotype associations, and EWAS ap-DMRs identified CpG-sites that had cis-meQTLs with evidence for genotype–phenotype association, where the CpG-site was also an ap-DMR for the same phenotype. Monozygotic twin methylation difference analyses identified one potential environmentally-mediated ap-DMR associated with total cholesterol and LDL (CSMD1). Our results suggest that in a small set of genes DNA methylation may be a candidate mechanism of mediating not only environmental, but also genetic effects on age-related phenotypes. Epigenetic patterns vary during healthy ageing and development. Age-related DNA methylation changes have been implicated in cellular senescence and longevity, yet the causes and functional consequences of these variants remain unclear. To understand the biological mechanisms involved in potential longevity and rate of healthy ageing, we performed genome-wide association of epigenetic and genetic variation with both chronological age and age-related phenotypes. We identified hundreds of DNA methylation variants significantly associated with age and replicated these in an independent sample of young adult twins. Only a small proportion of these variants were also associated with age-related phenotypes. Therefore, the majority of age-related epigenetic changes do not contribute to rate of healthy ageing at later stages in life. Our results suggest that age-related changes in methylation occur throughout an individual's lifespan and that a proportion of these may be initiated from an early age. Intriguingly, a fraction of the age differentially methylated regions also associated with genetic variants in our sample, suggesting that DNA methylation may be a candidate mechanism of mediating not only environmental but also genetic effects on age-related phenotypes.
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Affiliation(s)
- Jordana T. Bell
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
- * E-mail: (JTB); (TDS); (PD)
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Tsun-Po Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Ruth Pidsley
- MRC Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
| | - James Nisbet
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Daniel Glass
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Guangju Zhai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Feng Zhang
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Ana Valdes
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Emma L. Dempster
- MRC Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Robin M. Murray
- Department of Psychosis Studies, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Elin Grundberg
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Asa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Alexandra Nica
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | | | | | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Churchill Hospital, Oxford, United Kingdom
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford, United Kingdom
| | - Jonathan Mill
- MRC Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
- * E-mail: (JTB); (TDS); (PD)
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- * E-mail: (JTB); (TDS); (PD)
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64
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Suhre K, Shin SY, Petersen AK, Mohney RP, Meredith D, Wägele B, Altmaier E, Deloukas P, Erdmann J, Grundberg E, Hammond CJ, de Angelis MH, Kastenmüller G, Köttgen A, Kronenberg F, Mangino M, Meisinger C, Meitinger T, Mewes HW, Milburn MV, Prehn C, Raffler J, Ried JS, Römisch-Margl W, Samani NJ, Small KS, Wichmann HE, Zhai G, Illig T, Spector TD, Adamski J, Soranzo N, Gieger C. Human metabolic individuality in biomedical and pharmaceutical research. Nature 2011; 477:54-60. [PMID: 21886157 DOI: 10.1038/nature10354] [Citation(s) in RCA: 792] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 06/30/2011] [Indexed: 01/08/2023]
Abstract
Genome-wide association studies (GWAS) have identified many risk loci for complex diseases, but effect sizes are typically small and information on the underlying biological processes is often lacking. Associations with metabolic traits as functional intermediates can overcome these problems and potentially inform individualized therapy. Here we report a comprehensive analysis of genotype-dependent metabolic phenotypes using a GWAS with non-targeted metabolomics. We identified 37 genetic loci associated with blood metabolite concentrations, of which 25 show effect sizes that are unusually high for GWAS and account for 10-60% differences in metabolite levels per allele copy. Our associations provide new functional insights for many disease-related associations that have been reported in previous studies, including those for cardiovascular and kidney disorders, type 2 diabetes, cancer, gout, venous thromboembolism and Crohn's disease. The study advances our knowledge of the genetic basis of metabolic individuality in humans and generates many new hypotheses for biomedical and pharmaceutical research.
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Affiliation(s)
- Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Faculty of Biology, Ludwig-Maximilians-Universität, Planegg-Martinsried, Germany.,Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City - Qatar Foundation, Doha, Qatar
| | - So-Youn Shin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton UK
| | - Ann-Kristin Petersen
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - David Meredith
- School of Life Sciences, Oxford Brookes University, Headington, Oxford, UK
| | - Brigitte Wägele
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Department of Genome-oriented Bioinformatics, Life and Food Science Center Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Elisabeth Altmaier
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Panos Deloukas
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton UK
| | | | - Elin Grundberg
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton UK.,Department of Twin Research & Genetic Epidemiology, King's College London, UK
| | | | - Martin Hrabé de Angelis
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Experimental Genetics, Life and Food Science Center Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Anna Köttgen
- Renal Division, University Hospital Freiburg, Germany
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, UK
| | - Christa Meisinger
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Hans-Werner Mewes
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Department of Genome-oriented Bioinformatics, Life and Food Science Center Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | | | - Cornelia Prehn
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Raffler
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Faculty of Biology, Ludwig-Maximilians-Universität, Planegg-Martinsried, Germany
| | - Janina S Ried
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton UK
| | - Werner Römisch-Margl
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, and Leicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, UK
| | - Kerrin S Small
- Department of Twin Research & Genetic Epidemiology, King's College London, UK
| | - H-Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany.,Klinikum Grosshadern, Munich, Germany
| | - Guangju Zhai
- Department of Twin Research & Genetic Epidemiology, King's College London, UK
| | - Thomas Illig
- Unit for Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, UK
| | - Jerzy Adamski
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nicole Soranzo
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton UK
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
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65
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Nica AC, Parts L, Glass D, Nisbet J, Barrett A, Sekowska M, Travers M, Potter S, Grundberg E, Small K, Hedman ÅK, Bataille V, Tzenova Bell J, Surdulescu G, Dimas AS, Ingle C, Nestle FO, di Meglio P, Min JL, Wilk A, Hammond CJ, Hassanali N, Yang TP, Montgomery SB, O'Rahilly S, Lindgren CM, Zondervan KT, Soranzo N, Barroso I, Durbin R, Ahmadi K, Deloukas P, McCarthy MI, Dermitzakis ET, Spector TD. The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet 2011; 7:e1002003. [PMID: 21304890 PMCID: PMC3033383 DOI: 10.1371/journal.pgen.1002003] [Citation(s) in RCA: 355] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 12/15/2010] [Indexed: 12/16/2022] Open
Abstract
While there have been studies exploring regulatory variation in one or more tissues, the complexity of tissue-specificity in multiple primary tissues is not yet well understood. We explore in depth the role of cis-regulatory variation in three human tissues: lymphoblastoid cell lines (LCL), skin, and fat. The samples (156 LCL, 160 skin, 166 fat) were derived simultaneously from a subset of well-phenotyped healthy female twins of the MuTHER resource. We discover an abundance of cis-eQTLs in each tissue similar to previous estimates (858 or 4.7% of genes). In addition, we apply factor analysis (FA) to remove effects of latent variables, thus more than doubling the number of our discoveries (1,822 eQTL genes). The unique study design (Matched Co-Twin Analysis—MCTA) permits immediate replication of eQTLs using co-twins (93%–98%) and validation of the considerable gain in eQTL discovery after FA correction. We highlight the challenges of comparing eQTLs between tissues. After verifying previous significance threshold-based estimates of tissue-specificity, we show their limitations given their dependency on statistical power. We propose that continuous estimates of the proportion of tissue-shared signals and direct comparison of the magnitude of effect on the fold change in expression are essential properties that jointly provide a biologically realistic view of tissue-specificity. Under this framework we demonstrate that 30% of eQTLs are shared among the three tissues studied, while another 29% appear exclusively tissue-specific. However, even among the shared eQTLs, a substantial proportion (10%–20%) have significant differences in the magnitude of fold change between genotypic classes across tissues. Our results underline the need to account for the complexity of eQTL tissue-specificity in an effort to assess consequences of such variants for complex traits. Regulation of gene expression is a fundamental cellular process determining a large proportion of the phenotypic variance. Previous studies have identified genetic loci influencing gene expression levels (eQTLs), but the complexity of their tissue-specific properties has not yet been well-characterized. In this study, we perform cis-eQTL analysis in a unique matched co-twin design for three human tissues derived simultaneously from the same set of individuals. The study design allows validation of the substantial discoveries we make in each tissue. We explore in depth the tissue-dependent features of regulatory variants and estimate the proportions of shared and specific effects. We use continuous measures of eQTL sharing to circumvent the statistical power limitations of comparing direct overlap of eQTLs in multiple tissues. In this framework, we demonstrate that 30% of eQTLs are shared among tissues, while 29% are exclusively tissue-specific. Furthermore, we show that the fold change in expression between eQTL genotypic classes differs between tissues. Even among shared eQTLs, we report a substantial proportion (10%–20%) of significant tissue differences in magnitude of these effects. The complexities we highlight here are essential for understanding the impact of regulatory variants on complex traits.
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Affiliation(s)
- Alexandra C. Nica
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Leopold Parts
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Daniel Glass
- Department of Twin Research, King's College London, London, United Kingdom
| | - James Nisbet
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Amy Barrett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Magdalena Sekowska
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Mary Travers
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Simon Potter
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Elin Grundberg
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Twin Research, King's College London, London, United Kingdom
| | - Kerrin Small
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Twin Research, King's College London, London, United Kingdom
| | - Åsa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Veronique Bataille
- Department of Twin Research, King's College London, London, United Kingdom
| | - Jordana Tzenova Bell
- Department of Twin Research, King's College London, London, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Antigone S. Dimas
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Catherine Ingle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Frank O. Nestle
- St. John's Institute of Dermatology, King's College London, London, United Kingdom
| | - Paola di Meglio
- St. John's Institute of Dermatology, King's College London, London, United Kingdom
| | - Josine L. Min
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Alicja Wilk
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | | | - Neelam Hassanali
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tsun-Po Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Stephen B. Montgomery
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Steve O'Rahilly
- University of Cambridge Metabolic Research Labs, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Krina T. Zondervan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- Department of Twin Research, King's College London, London, United Kingdom
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- University of Cambridge Metabolic Research Labs, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Kourosh Ahmadi
- Department of Twin Research, King's College London, London, United Kingdom
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
- * E-mail: (ETD); (TDS); (MIM); (PD)
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Churchill Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, United Kingdom
- * E-mail: (ETD); (TDS); (MIM); (PD)
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- * E-mail: (ETD); (TDS); (MIM); (PD)
| | - Timothy D. Spector
- Department of Twin Research, King's College London, London, United Kingdom
- * E-mail: (ETD); (TDS); (MIM); (PD)
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Grundberg E, Adoue V, Kwan T, Ge B, Duan QL, Lam KCL, Koka V, Kindmark A, Weiss ST, Tantisira K, Mallmin H, Raby BA, Nilsson O, Pastinen T. Global analysis of the impact of environmental perturbation on cis-regulation of gene expression. PLoS Genet 2011; 7:e1001279. [PMID: 21283786 PMCID: PMC3024267 DOI: 10.1371/journal.pgen.1001279] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 12/17/2010] [Indexed: 12/30/2022] Open
Abstract
Genetic variants altering cis-regulation of normal gene expression (cis-eQTLs) have been extensively mapped in human cells and tissues, but the extent by which controlled, environmental perturbation influences cis-eQTLs is unclear. We carried out large-scale induction experiments using primary human bone cells derived from unrelated donors of Swedish origin treated with 18 different stimuli (7 treatments and 2 controls, each assessed at 2 time points). The treatments with the largest impact on the transcriptome, verified on two independent expression arrays, included BMP-2 (t = 2h), dexamethasone (DEX) (t = 24h), and PGE2 (t = 24h). Using these treatments and control, we performed expression profiling for 18,144 RefSeq transcripts on biological replicates of the complete study cohort of 113 individuals (ntotal = 782) and combined it with genome-wide SNP-genotyping data in order to map treatment-specific cis-eQTLs (defined as SNPs located within the gene ±250 kb). We found that 93% of cis-eQTLs at 1% FDR were observed in at least one additional treatment, and in fact, on average, only 1.4% of the cis-eQTLs were considered as treatment-specific at high confidence. The relative invariability of cis-regulation following perturbation was reiterated independently by genome-wide allelic expression tests where only a small proportion of variance could be attributed to treatment. Treatment-specific cis-regulatory effects were, however, 2- to 6-fold more abundant among differently expressed genes upon treatment. We further followed-up and validated the DEX–specific cis-regulation of the MYO6 and TNC loci and found top cis-regulatory variants located 180 kb and 250 kb upstream of the transcription start sites, respectively. Our results suggest that, as opposed to tissue-specificity of cis-eQTLs, the interactions between cellular environment and cis-variants are relatively rare (∼1.5%), but that detection of such specific interactions can be achieved by a combination of functional genomic approaches as described here. Population variation in normal gene expression has been convincingly shown to be under strong genetic control where the main genetic variants are located within close proximity to the gene itself (so called cis-acting). However, the extent to which controlled, environmental stimuli influences cis-regulation of gene expression is unclear. Here, we combine different functional genomic approaches and examine the role of common genetic variants on induced gene expression in a population panel of primary human cells derived from ∼100 unrelated donors treated under multiple conditions. Using these approaches, we find that the interaction between cellular environment and cis-variants are relatively rare, with only a small proportion of the identified genetic variants being specific to treatment. However, although treatment-specific genetic regulation of gene expression seems to be infrequent, we prove its existence by thorough validation of treatment-specific effects of the glucocorticoid-specific regulation of TNC expression. Taken together, these findings indicate that the regulatory landscape within a cell is very stable but, by combining functional genomic tools gene-environmental interactions of clinical importance, can be detected and possibly used as biomarkers in future pharmacogenomic studies.
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Affiliation(s)
- Elin Grundberg
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.
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67
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Abstract
Interindividual variation in gene expression has been convincingly shown to be controlled, in part, by genetic differences. Determining the architecture of genetic variation, the underlying gene expression may allow deeper insight into complex phenotypes, such as differences in disease susceptibility. Mapping genetic variants accounting for expression phenotypes in human cell and tissue panels has rapidly progressed from proof-of-principle experiments to general tools in biomedical discovery. We discuss the general approach and critical considerations for carrying out expression quantitative trait mapping in human tissues.
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Affiliation(s)
- Elin Grundberg
- Department of Human Genetics, McGill University and Génome Québec Innovation Centre, McGill University, Montréal, QC, Canada
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Richards JB, Waterworth D, O'Rahilly S, Hivert MF, Loos RJF, Perry JRB, Tanaka T, Timpson NJ, Semple RK, Soranzo N, Song K, Rocha N, Grundberg E, Dupuis J, Florez JC, Langenberg C, Prokopenko I, Saxena R, Sladek R, Aulchenko Y, Evans D, Waeber G, Erdmann J, Burnett MS, Sattar N, Devaney J, Willenborg C, Hingorani A, Witteman JCM, Vollenweider P, Glaser B, Hengstenberg C, Ferrucci L, Melzer D, Stark K, Deanfield J, Winogradow J, Grassl M, Hall AS, Egan JM, Thompson JR, Ricketts SL, König IR, Reinhard W, Grundy S, Wichmann HE, Barter P, Mahley R, Kesaniemi YA, Rader DJ, Reilly MP, Epstein SE, Stewart AFR, Van Duijn CM, Schunkert H, Burling K, Deloukas P, Pastinen T, Samani NJ, McPherson R, Davey Smith G, Frayling TM, Wareham NJ, Meigs JB, Mooser V, Spector TD. A genome-wide association study reveals variants in ARL15 that influence adiponectin levels. PLoS Genet 2009; 5:e1000768. [PMID: 20011104 PMCID: PMC2781107 DOI: 10.1371/journal.pgen.1000768] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 11/12/2009] [Indexed: 12/22/2022] Open
Abstract
The adipocyte-derived protein adiponectin is highly heritable and inversely associated with risk of type 2 diabetes mellitus (T2D) and coronary heart disease (CHD). We meta-analyzed 3 genome-wide association studies for circulating adiponectin levels (n = 8,531) and sought validation of the lead single nucleotide polymorphisms (SNPs) in 5 additional cohorts (n = 6,202). Five SNPs were genome-wide significant in their relationship with adiponectin (P< or =5x10(-8)). We then tested whether these 5 SNPs were associated with risk of T2D and CHD using a Bonferroni-corrected threshold of P< or =0.011 to declare statistical significance for these disease associations. SNPs at the adiponectin-encoding ADIPOQ locus demonstrated the strongest associations with adiponectin levels (P-combined = 9.2x10(-19) for lead SNP, rs266717, n = 14,733). A novel variant in the ARL15 (ADP-ribosylation factor-like 15) gene was associated with lower circulating levels of adiponectin (rs4311394-G, P-combined = 2.9x10(-8), n = 14,733). This same risk allele at ARL15 was also associated with a higher risk of CHD (odds ratio [OR] = 1.12, P = 8.5x10(-6), n = 22,421) more nominally, an increased risk of T2D (OR = 1.11, P = 3.2x10(-3), n = 10,128), and several metabolic traits. Expression studies in humans indicated that ARL15 is well-expressed in skeletal muscle. These findings identify a novel protein, ARL15, which influences circulating adiponectin levels and may impact upon CHD risk.
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Affiliation(s)
- J Brent Richards
- Departments of Medicine, Human Genetics, and Epidemiology and Biostatistics, Jewish General Hospital, McGill University, Montréal, Québec, Canada.
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69
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Ge B, Pokholok DK, Kwan T, Grundberg E, Morcos L, Verlaan DJ, Le J, Koka V, Lam KCL, Gagné V, Dias J, Hoberman R, Montpetit A, Joly MM, Harvey EJ, Sinnett D, Beaulieu P, Hamon R, Graziani A, Dewar K, Harmsen E, Majewski J, Göring HHH, Naumova AK, Blanchette M, Gunderson KL, Pastinen T. Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet 2009; 41:1216-22. [PMID: 19838192 DOI: 10.1038/ng.473] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 08/24/2009] [Indexed: 12/15/2022]
Abstract
Cis-acting variants altering gene expression are a source of phenotypic differences. The cis-acting components of expression variation can be identified through the mapping of differences in allelic expression (AE), which is the measure of relative expression between two allelic transcripts. We generated a map of AE associated SNPs using quantitative measurements of AE on Illumina Human1M BeadChips. In 53 lymphoblastoid cell lines derived from donors of European descent, we identified common cis variants affecting 30% (2935/9751) of the measured RefSeq transcripts at 0.001 permutation significance. The pervasive influence of cis-regulatory variants, which explain 50% of population variation in AE, extend to full-length transcripts and their isoforms as well as to unannotated transcripts. These strong effects facilitate fine mapping of cis-regulatory SNPs, as demonstrated by dissection of heritable control of transcripts in the systemic lupus erythematosus-associated C8orf13-BLK region in chromosome 8. The dense collection of associations will facilitate large-scale isolation of cis-regulatory SNPs.
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Affiliation(s)
- Bing Ge
- McGill University and Genome Québec Innovation Centre, Montréal, Québec, Canada
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70
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Rivadeneira F, Styrkársdottir U, Estrada K, Halldórsson BV, Hsu YH, Richards JB, Zillikens MC, Kavvoura FK, Amin N, Aulchenko YS, Cupples LA, Deloukas P, Demissie S, Grundberg E, Hofman A, Kong A, Karasik D, van Meurs JB, Oostra B, Pastinen T, Pols HAP, Sigurdsson G, Soranzo N, Thorleifsson G, Thorsteinsdottir U, Williams FMK, Wilson SG, Zhou Y, Ralston SH, van Duijn CM, Spector T, Kiel DP, Stefansson K, Ioannidis JPA, Uitterlinden AG. Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. Nat Genet 2009; 41:1199-206. [PMID: 19801982 PMCID: PMC2783489 DOI: 10.1038/ng.446] [Citation(s) in RCA: 585] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 07/21/2009] [Indexed: 12/15/2022]
Abstract
Bone mineral density (BMD) is a heritable complex trait used in the clinical diagnosis of osteoporosis and the assessment of fracture risk. We performed meta-analysis of five genome-wide association studies of femoral neck and lumbar spine BMD in 19,195 subjects of Northern European descent. We identified 20 BMD loci that reached genome-wide significance (GWS; P < 5 x 10(-8)), of which 13 map to regions not previously associated with this trait: 1p31.3 (GPR177), 2p21 (SPTBN1), 3p22 (CTNNB1), 4q21.1 (MEPE), 5q14 (MEF2C), 7p14 (STARD3NL), 7q21.3 (FLJ42280), 11p11.2 (LRP4, ARHGAP1, F2), 11p14.1 (DCDC5), 11p15 (SOX6), 16q24 (FOXL1), 17q21 (HDAC5) and 17q12 (CRHR1). The meta-analysis also confirmed at GWS level seven known BMD loci on 1p36 (ZBTB40), 6q25 (ESR1), 8q24 (TNFRSF11B), 11q13.4 (LRP5), 12q13 (SP7), 13q14 (TNFSF11) and 18q21 (TNFRSF11A). The many SNPs associated with BMD map to genes in signaling pathways with relevance to bone metabolism and highlight the complex genetic architecture that underlies osteoporosis and variation in BMD.
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71
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Lerner-Ellis JP, Anastasio N, Liu J, Coelho D, Suormala T, Stucki M, Loewy AD, Gurd S, Grundberg E, Morel CF, Watkins D, Baumgartner MR, Pastinen T, Rosenblatt DS, Fowler B. Spectrum of mutations in MMACHC, allelic expression, and evidence for genotype-phenotype correlations. Hum Mutat 2009; 30:1072-81. [PMID: 19370762 DOI: 10.1002/humu.21001] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Methylmalonic aciduria and homocystinuria, cblC type, is a rare disorder of intracellular vitamin B(12) (cobalamin [Cbl]) metabolism caused by mutations in the MMACHC gene. MMACHC was sequenced from the gDNA of 118 cblC individuals. Eleven novel mutations were identified, as well as 23 mutations that were observed previously. Six sequence variants capture haplotype diversity in individuals across the MMACHC interval. Genotype-phenotype correlations of common mutations were apparent; individuals with c.394C>T tend to present with late-onset disease whereas patients with c.331C>T and c.271dupA tend to present in infancy. Other missense variants were also associated with late- or early-onset disease. Allelic expression analysis was carried out on human cblC fibroblasts compound heterozygous for different combinations of mutations including c.271dupA, c.331C>T, c.394C>T, and c.482G>A. The early-onset c.271dupA mutation was consistently underexpressed when compared to control alleles and the late-onset c.394C>T and c.482G>A mutations. The early-onset c.331C>T mutation was also underexpressed when compared to control alleles and the c.394C>T mutation. Levels of MMACHC mRNA transcript in cell lines homozygous for c.271dupA, c.331C>T, and c.394C>T were assessed using quantitative real-time RT-PCR. Cell lines homozygous for the late onset c.394C>T mutation had significantly higher levels of transcript when compared to cell lines homozygous for the early-onset mutations. Differential or preferential MMACHC transcript levels may provide a clue as to why individuals carrying c.394C>T generally present later in life.
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Affiliation(s)
- Jordan P Lerner-Ellis
- Department of Medical Genetics, McGill University Health Centre, Montreal, Quebec, Canada.
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72
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Verlaan DJ, Berlivet S, Hunninghake GM, Madore AM, Larivière M, Moussette S, Grundberg E, Kwan T, Ouimet M, Ge B, Hoberman R, Swiatek M, Dias J, Lam KC, Koka V, Harmsen E, Soto-Quiros M, Avila L, Celedón JC, Weiss ST, Dewar K, Sinnett D, Laprise C, Raby BA, Pastinen T, Naumova AK. Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease. Am J Hum Genet 2009; 85:377-93. [PMID: 19732864 DOI: 10.1016/j.ajhg.2009.08.007] [Citation(s) in RCA: 226] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 07/31/2009] [Accepted: 08/12/2009] [Indexed: 02/05/2023] Open
Abstract
Common SNPs in the chromosome 17q12-q21 region alter the risk for asthma, type 1 diabetes, primary biliary cirrhosis, and Crohn disease. Previous reports by us and others have linked the disease-associated genetic variants with changes in expression of GSDMB and ORMDL3 transcripts in human lymphoblastoid cell lines (LCLs). The variants also alter regulation of other transcripts, and this domain-wide cis-regulatory effect suggests a mechanism involving long-range chromatin interactions. Here, we further dissect the disease-linked haplotype and identify putative causal DNA variants via a combination of genetic and functional analyses. First, high-throughput resequencing of the region and genotyping of potential candidate variants were performed. Next, additional mapping of allelic expression differences in Yoruba HapMap LCLs allowed us to fine-map the basis of the cis-regulatory differences to a handful of candidate functional variants. Functional assays identified allele-specific differences in nucleosome distribution, an allele-specific association with the insulator protein CTCF, as well as a weak promoter activity for rs12936231. Overall, this study shows a common disease allele linked to changes in CTCF binding and nucleosome occupancy leading to altered domain-wide cis-regulation. Finally, a strong association between asthma and cis-regulatory haplotypes was observed in three independent family-based cohorts (p = 1.78 x 10(-8)). This study demonstrates the requirement of multiple parallel allele-specific tools for the investigation of noncoding disease variants and functional fine-mapping of human disease-associated haplotypes.
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73
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Kwan T, Grundberg E, Koka V, Ge B, Lam KCL, Dias C, Kindmark A, Mallmin H, Ljunggren O, Rivadeneira F, Estrada K, van Meurs JB, Uitterlinden A, Karlsson M, Ohlsson C, Mellström D, Nilsson O, Pastinen T, Majewski J. Tissue effect on genetic control of transcript isoform variation. PLoS Genet 2009; 5:e1000608. [PMID: 19680542 PMCID: PMC2719916 DOI: 10.1371/journal.pgen.1000608] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 07/20/2009] [Indexed: 11/26/2022] Open
Abstract
Current genome-wide association studies (GWAS) are moving towards the use of large cohorts of primary cell lines to study a disease of interest and to assign biological relevance to the genetic signals identified. Here, we use a panel of human osteoblasts (HObs) to carry out a transcriptomic survey, similar to recent studies in lymphoblastoid cell lines (LCLs). The distinct nature of HObs and LCLs is reflected by the preferential grouping of cell type–specific genes within biologically and functionally relevant pathways unique to each tissue type. We performed cis-association analysis with SNP genotypes to identify genetic variations of transcript isoforms, and our analysis indicates that differential expression of transcript isoforms in HObs is also partly controlled by cis-regulatory genetic variants. These isoforms are regulated by genetic variants in both a tissue-specific and tissue-independent fashion, and these associations have been confirmed by RT–PCR validation. Our study suggests that multiple transcript isoforms are often present in both tissues and that genetic control may affect the relative expression of one isoform to another, rather than having an all-or-none effect. Examination of the top SNPs from a GWAS of bone mineral density show overlap with probeset associations observed in this study. The top hit corresponding to the FAM118A gene was tested for association studies in two additional clinical studies, revealing a novel transcript isoform variant. Our approach to examining transcriptome variation in multiple tissue types is useful for detecting the proportion of genetic variation common to different cell types and for the identification of cell-specific isoform variants that may be functionally relevant, an important follow-up step for GWAS. The transcriptome of any given cell type is a complex program of controlled gene expression underlying its biological function. An additional layer of molecular complexity involving individual genetic variation can modulate the transcriptome within the same tissue type, conferring potential phenotypic differences between individuals at the cellular level. This study highlights common and unique aspects of the transcriptome between the well-characterized lymphoblastoid cell lines from the International HapMap Project and those of a cultured primary cell type, human osteoblasts. We observe that inter-individual genetic variation can regulate transcript isoform expression in tissue-specific and tissue-independent manners, indicating that genetic differences among individuals can alter the transcriptome in one or more tissues, ultimately leading to altered biological functions within the lymphoblasts and/or osteoblasts. Pursuant to this, genome wide association studies on bone mineral density (BMD) have identified a number of significant loci and polymorphisms highly linked to the BMD quantitative phenotype. A small proportion of these polymorphisms overlap with our highly significant SNPs regulating the osteoblast transcriptome, revealing a potential molecular basis for this phenotype at the transcriptional level. This study highlights the importance of examining the differing transcriptomes and cis-regulatory mechanisms governing the biological and functional roles of varied tissue types.
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Affiliation(s)
- Tony Kwan
- Department of Human Genetics, McGill University, Montréal, Canada.
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Grundberg E, Kwan T, Ge B, Lam KCL, Koka V, Kindmark A, Mallmin H, Dias J, Verlaan DJ, Ouimet M, Sinnett D, Rivadeneira F, Estrada K, Hofman A, van Meurs JM, Uitterlinden A, Beaulieu P, Graziani A, Harmsen E, Ljunggren O, Ohlsson C, Mellström D, Karlsson MK, Nilsson O, Pastinen T. Population genomics in a disease targeted primary cell model. Genome Res 2009; 19:1942-52. [PMID: 19654370 DOI: 10.1101/gr.095224.109] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The common genetic variants associated with complex traits typically lie in noncoding DNA and may alter gene regulation in a cell type-specific manner. Consequently, the choice of tissue or cell model in the dissection of disease associations is important. We carried out an expression quantitative trait loci (eQTL) study of primary human osteoblasts (HOb) derived from 95 unrelated donors of Swedish origin, each represented by two independently derived primary lines to provide biological replication. We combined our data with publicly available information from a genome-wide association study (GWAS) of bone mineral density (BMD). The top 2000 BMD-associated SNPs (P < approximately 10(-3)) were tested for cis-association of gene expression in HObs and in lymphoblastoid cell lines (LCLs) using publicly available data and showed that HObs have a significantly greater enrichment (threefold) of converging cis-eQTLs as compared to LCLs. The top 10 BMD loci with SNPs showing strong cis-effects on gene expression in HObs (P = 6 x 10(-10) - 7 x 10(-16)) were selected for further validation using a staged design in two cohorts of Caucasian male subjects. All 10 variants were tested in the Swedish MrOS Cohort (n = 3014), providing evidence for two novel BMD loci (SRR and MSH3). These variants were then tested in the Rotterdam Study (n = 2090), yielding converging evidence for BMD association at the 17p13.3 SRR locus (P(combined) = 5.6 x 10(-5)). The cis-regulatory effect was further fine-mapped to the proximal promoter of the SRR gene (rs3744270, r(2) = 0.5, P = 2.6 x 10(-15)). Our results suggest that primary cells relevant to disease phenotypes complement traditional approaches for prioritization and validation of GWAS hits for follow-up studies.
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Affiliation(s)
- Elin Grundberg
- Department of Human Genetics, McGill University, Montréal H3A 1B1, Canada
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75
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Khoschnau S, Melhus H, Jacobson A, Rahme H, Bengtsson H, Ribom E, Grundberg E, Mallmin H, Michaëlsson K. Type I collagen alpha1 Sp1 polymorphism and the risk of cruciate ligament ruptures or shoulder dislocations. Am J Sports Med 2008; 36:2432-6. [PMID: 18669982 DOI: 10.1177/0363546508320805] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Cruciate ligament ruptures and shoulder dislocations are often caused by trauma, but predisposing intrinsic factors might also influence the risk. These injuries are more common in those with a previously injured sibling, an observation that might indicate a genetic predisposition. It is well known that polymorphisms in the collagen I gene are associated not only with osteoporosis and osteoporotic fracture risk, but also with osteoarthritis. HYPOTHESIS Because collagen I is abundant in ligaments and tendons, the authors hypothesized that collagen I alpha1 Sp1 polymorphism also was related to the occurrence of cruciate ligament ruptures and shoulder dislocations. STUDY DESIGN Case-control study; Level of evidence, 3. METHODS A total of 358 patients and 325 randomly selected population-based female controls were included in the study. Of the cases, 233 had a cruciate ligament rupture and 126 had had a shoulder dislocation. Age-adjusted odds ratios (ORs) with 95% confidence intervals (CIs) estimated by unconditional logistic regression were used as measures of association. RESULTS Compared with the homozygous SS category, the heterozygous participants displayed a similar risk (OR, 1.06; 95% CI, 0.76-1.49), whereas the ss genotype was underrepresented in the injured population compared with the controls (OR, 0.15; 95% CI, 0.03-0.68). This latter estimate was similar for both cruciate ligament ruptures and shoulder dislocations, and was furthermore not modified by general joint laxity. CONCLUSION The authors found a substantially decreased risk of these injuries associated with collagen type I alpha1 Sp1 polymorphism. The study might encourage other investigators to consider further research in the area of genes and soft tissue injuries.
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Affiliation(s)
- Shwan Khoschnau
- Department of Surgical Sciences, Section of Orthopedics, University Hospital, Uppsala, Sweden.
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76
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Grundberg E, Lau EM, Lorentzon M, Karlsson M, Holmberg A, Groop L, Mellström D, Orwoll E, Mallmin H, Ohlsson C, Ljunggren Ö, Åkesson K. Erratum to: Large-scale association study between two coding LRP5 gene polymorphisms and bone phenotypes and fractures in men. Osteoporos Int 2008; 19:1647. [PMID: 27730267 DOI: 10.1007/s00198-008-0705-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- E Grundberg
- Department of Medical Sciences, Uppsala University Hospital, 75185, Uppsala, Sweden.
| | - E M Lau
- Hong Kong Orthopedic and Osteoporosis, Center for Treatment and research, Hong Kong, China
| | - M Lorentzon
- Center for Bone Research at the Sahlgrenska Academy, Department of Internal Medicine, Göteborg University, Gothenburg, Sweden
| | - M Karlsson
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Science, Lund University, Malmö, Sweden
- Department of Orthopaedics, Malmö University Hospital, Malmö, Sweden
| | - A Holmberg
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Science, Lund University, Malmö, Sweden
- Department of Orthopaedics, Malmö University Hospital, Malmö, Sweden
| | - L Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Clinical Research Center, Malmö University Hospital, Lund University, Malmö, Sweden
| | - D Mellström
- Center for Bone Research at the Sahlgrenska Academy, Department of Internal Medicine, Göteborg University, Gothenburg, Sweden
| | - E Orwoll
- Bone and Mineral Research Unit, Oregon Health and Science University, Portland, OR, USA
| | - H Mallmin
- Department of Surgical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | - C Ohlsson
- Center for Bone Research at the Sahlgrenska Academy, Department of Internal Medicine, Göteborg University, Gothenburg, Sweden
| | - Ö Ljunggren
- Department of Medical Sciences, Uppsala University Hospital, 75185, Uppsala, Sweden
| | - K Åkesson
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Science, Lund University, Malmö, Sweden
- Department of Orthopaedics, Malmö University Hospital, Malmö, Sweden
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77
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Verlaan DJ, Ge B, Grundberg E, Hoberman R, Lam KCL, Koka V, Dias J, Gurd S, Martin NW, Mallmin H, Nilsson O, Harmsen E, Dewar K, Kwan T, Pastinen T. Targeted screening of cis-regulatory variation in human haplotypes. Genome Res 2008; 19:118-27. [PMID: 18971308 DOI: 10.1101/gr.084798.108] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Regulatory cis-acting variants account for a large proportion of gene expression variability in populations. Cis-acting differences can be specifically measured by comparing relative levels of allelic transcripts within a sample. Allelic expression (AE) mapping for cis-regulatory variant discovery has been hindered by the requirements of having informative or heterozygous single nucleotide polymorphisms (SNPs) within genes in order to assign the allelic origin of each transcript. In this study we have developed an approach to systematically screen for heritable cis-variants in common human haplotypes across >1,000 genes. In order to achieve the highest level of information per haplotype studied, we carried out allelic expression measurements by using both intronic and exonic SNPs in primary transcripts. We used a novel RNA pooling strategy in immortalized lymphoblastoid cell lines (LCLs) and primary human osteoblast cell lines (HObs) to allow for high-throughput AE. Screening hits from RNA pools were further validated by performing allelic expression mapping in individual samples. Our results indicate that >10% of expressed genes in human LCLs show genotype-linked AE. In addition, we have validated cis-acting variants in over 20 genes linked with common disease susceptibility in recent genome-wide studies. More generally, our results indicate that RNA pooling coupled with AE read-out by second generation sequencing or by other methods provides a high-throughput tool for cataloging the impact of common noncoding variants in the human genome.
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78
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Sigurdsson S, Nordmark G, Garnier S, Grundberg E, Kwan T, Nilsson O, Eloranta ML, Gunnarsson I, Svenungsson E, Sturfelt G, Bengtsson AA, Jönsen A, Truedsson L, Rantapää-Dahlqvist S, Eriksson C, Alm G, Göring HHH, Pastinen T, Syvänen AC, Rönnblom L. A risk haplotype of STAT4 for systemic lupus erythematosus is over-expressed, correlates with anti-dsDNA and shows additive effects with two risk alleles of IRF5. Hum Mol Genet 2008; 17:2868-76. [PMID: 18579578 PMCID: PMC2525501 DOI: 10.1093/hmg/ddn184] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is the prototype autoimmune disease where genes regulated by type I interferon (IFN) are over-expressed and contribute to the disease pathogenesis. Because signal transducer and activator of transcription 4 (STAT4) plays a key role in the type I IFN receptor signaling, we performed a candidate gene study of a comprehensive set of single nucleotide polymorphism (SNPs) in STAT4 in Swedish patients with SLE. We found that 10 out of 53 analyzed SNPs in STAT4 were associated with SLE, with the strongest signal of association (P = 7.1 x 10(-8)) for two perfectly linked SNPs rs10181656 and rs7582694. The risk alleles of these 10 SNPs form a common risk haplotype for SLE (P = 1.7 x 10(-5)). According to conditional logistic regression analysis the SNP rs10181656 or rs7582694 accounts for all of the observed association signal. By quantitative analysis of the allelic expression of STAT4 we found that the risk allele of STAT4 was over-expressed in primary human cells of mesenchymal origin, but not in B-cells, and that the risk allele of STAT4 was over-expressed (P = 8.4 x 10(-5)) in cells carrying the risk haplotype for SLE compared with cells with a non-risk haplotype. The risk allele of the SNP rs7582694 in STAT4 correlated to production of anti-dsDNA (double-stranded DNA) antibodies and displayed a multiplicatively increased, 1.82-fold risk of SLE with two independent risk alleles of the IRF5 (interferon regulatory factor 5) gene.
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Affiliation(s)
- Snaevar Sigurdsson
- Molecular Medicine, Department of Medical Sciences, Uppsala University, SE-75185 Uppsala, Sweden
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79
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Grundberg E, Lau EM, Lorentzon M, Karlsson M, Holmberg A, Groop L, Mellström D, Orwoll E, Mallmin H, Ohlsson C, Ljunggren O, Akesson K. Large-scale association study between two coding LRP5 gene polymorphisms and bone phenotypes and fractures in men. Osteoporos Int 2008; 19:829-37. [PMID: 18026682 DOI: 10.1007/s00198-007-0512-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 10/24/2007] [Indexed: 11/25/2022]
Abstract
UNLABELLED Herein we investigated the association between polymorphisms in the LRP5 gene and bone phenotypes and fractures in three large male cohorts based on the rationale that mutations in LRP5 cause severe bone phenotypes. Results showed an association of the Val667Met SNP with spine BMD in 3,800 young and elderly men. INTRODUCTION The low-density lipoprotein receptor-related protein 5 (LRP5)-Wnt signalling system is of importance for regulating osteoblastic activity, which became clear after findings that inactivating mutations in LRP5 cause osteoporosis. The overall aim of this study was to investigate the association between polymorphisms in the LRP5 gene and bone mineral density (BMD) in three large cohorts of young and elderly men. METHODS The cohorts used were MrOS Sweden (n = 3014, aged 69-81 years) and MrOs Hong Kong (n = 2000, aged > 65 years) and the Swedish GOOD study (n = 1068, aged 18-20 years). The polymorphisms Val667Met and Ala1330Val were genotyped using a TaqMan assay. RESULTS When combining the data from the Swedish cohorts in a meta-analysis (n = 3,800), men carrying the 667Met-allele had 3% lower BMD at lumbar spine compared with non-carriers (p < 0.05). The Val667Met SNP was not polymorphic in the Hong Kong population and thus were not included. There were no associations between the Ala1330Val SNP and bone phenotypes in the study populations. No associations between the LRP5 polymorphisms and self-reported fractures were seen in MrOs Sweden. CONCLUSIONS Results from these three large cohorts indicate that the Val667Met polymorphism but not the Ala1330Val contributes to the observed variability in BMD in the Swedish populations.
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Affiliation(s)
- E Grundberg
- Department of Medical Sciences, Uppsala University Hospital, 75185 Uppsala, Sweden.
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80
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Grundberg E, Brändström H, Lam KCL, Gurd S, Ge B, Harmsen E, Kindmark A, Ljunggren O, Mallmin H, Nilsson O, Pastinen T. Systematic assessment of the human osteoblast transcriptome in resting and induced primary cells. Physiol Genomics 2008; 33:301-11. [PMID: 18334548 DOI: 10.1152/physiolgenomics.00028.2008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Osteoblasts are key players in bone remodeling. The accessibility of human primary osteoblast-like cells (HObs) from bone explants makes them a lucrative model for studying molecular physiology of bone turnover, for discovering novel anabolic therapeutics, and for mesenchymal cell biology in general. Relatively little is known about resting and dynamic expression profiles of HObs, and to date no studies have been conducted to systematically assess the osteoblast transcriptome. The aim of this study was to characterize HObs and investigate signaling cascades and gene networks with genomewide expression profiling in resting and bone morphogenic protein (BMP)-2- and dexamethasone-induced cells. In addition, we compared HOb gene expression with publicly available samples from the Gene Expression Omnibus. Our data show a vast number of genes and networks expressed predominantly in HObs compared with closely related cells such as fibroblasts or chondrocytes. For instance, genes in the insulin-like growth factor (IGF) signaling pathway were enriched in HObs (P = 0.003) and included the binding proteins (IGFBP-1, -2, -5) and IGF-II and its receptor. Another HOb-specific expression pattern included leptin and its receptor (P < 10(-8)). Furthermore, after stimulation of HObs with BMP-2 or dexamethasone, the expression of several interesting genes and pathways was observed. For instance, our data support the role of peripheral leptin signaling in bone cell function. In conclusion, we provide the landscape of tissue-specific and dynamic gene expression in HObs. This resource will allow utilization of osteoblasts as a model to study specific gene networks and gene families related to human bone physiology and diseases.
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Affiliation(s)
- Elin Grundberg
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
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81
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Strandberg L, Mellström D, Ljunggren O, Grundberg E, Karlsson MK, Holmberg AH, Orwoll ES, Eriksson AL, Svedberg J, Bengtsson M, Ohlsson C, Jansson JO. IL6 and IL1B polymorphisms are associated with fat mass in older men: the MrOS Study Sweden. Obesity (Silver Spring) 2008; 16:710-3. [PMID: 18239554 DOI: 10.1038/oby.2007.95] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is growing evidence that immune functions are linked to the regulation of body fat. Our studies of knockout mice indicate that both endogenous interleukin (IL)-6 and IL-1 can suppress mature-onset obesity. We now investigated whether four common polymorphisms of the IL6 and IL1 systems are associated with the fat mass measured with dual-energy X-ray absorptiometry (DXA) in elderly men (n = 3,014). The study subjects were from the Swedish part of the MrOS multicenter population study and 69-81 years of age. The IL6 -174 G>C (Minor allele frequency (MAF) = 48%) gene promoter polymorphism was associated with the primary outcome total fat mass (P = 0.006) and regional fat masses, but not with lean body mass. The IL1B -31T>C (MAF = 34%) polymorphism was also associated with total fat (P = 0.007) and regional fat masses, but not lean body mass. The IL-1 receptor antagonist (IL-1ra) gene (IL1RN) +2018 T>C (MAF = 27%) polymorphism (in linkage disequilibrium (LD) with a well-studied variable number tandem repeat of 86 base pair (bp)) and IL1B +3953 C>T (MAF = 26%) polymorphism were not associated with total fat mass. In conclusion, the IL-1 and IL-6 systems, shown to suppress mature-onset obesity in experimental animals, contain gene polymorphisms that are associated with fat, but not lean, mass in elderly men.
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Affiliation(s)
- Louise Strandberg
- Institute of Neuroscience and Physiology/Endocrinology, Sahlgrenska Academy, Göteborg University, Göteborg, Sweden
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82
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Marsell R, Grundberg E, Krajisnik T, Mallmin H, Karlsson M, Mellström D, Orwoll E, Ohlsson C, Jonsson KB, Ljunggren O, Larsson TE. Fibroblast growth factor-23 is associated with parathyroid hormone and renal function in a population-based cohort of elderly men. Eur J Endocrinol 2008; 158:125-9. [PMID: 18166826 DOI: 10.1530/eje-07-0534] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Fibroblast growth factor-23 (FGF23) is a circulating factor involved in phosphate (Pi) and vitamin D metabolism. Serum FGF23 is increased at later stages of chronic kidney disease due to chronic hyperphosphatemia and decreased renal clearance. Recent studies also indicate that FGF23 may directly regulate the expression of parathyroid hormone (PTH) in vitro. Therefore, the objective of the current study was to determine the relationship between FGF23, PTH, and other biochemistries in vivo in subjects with no history of renal disease. DESIGN Serum biochemistries were measured in a subsample of the population-based Swedish part of the MrOS study. In total, 1000 Caucasian men aged 70-80 years were randomly selected from the population. METHODS Intact FGF23, Pi, calcium, albumin, estimated glomerular filtration rate (eGFR, calculated from cystatin C), PTH, and 25(OH)D3 were measured. Association studies were performed using linear univariate and multivariate regression analyses. RESULTS The median FGF23 level was 36.6 pg/ml, ranging from 0.63 to 957 pg/ml. There was a significant correlation between log FGF23 and eGFR (r=-0.21; P<0.00001) and log PTH (r=0.13; P<0.001). These variables remained as independent predictors of FGF23 in multivariate analysis. In addition, log PTH (beta=0.082; P<0.05) and eGFR (beta=-0.090; P<0.05) were associated with log FGF23 in subjects with eGFR>60 ml/min. Only eGFR (beta=-0.35; P<0.0001) remained as a predictor of log FGF23 in subjects with eGFR<60 ml/min. CONCLUSIONS Serum FGF23 and PTH are associated in vivo, supporting recent findings that FGF23 directly regulates PTH expression in vitro. Additionally, eGFR is associated with FGF23 in subjects with normal or mildly impaired renal function, indicating that GFR may modulate FGF23 levels independent of serum Pi.
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Affiliation(s)
- Richard Marsell
- Department of Surgical Sciences, Uppsala University Hospital, Uppsala, Sweden
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83
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Eriksson AL, Mellström D, Lorentzon M, Orwoll ES, Redlund-Johnell I, Grundberg E, Holmberg A, Ljunggren O, Karlsson MK, Ohlsson C. The COMT val158met polymorphism is associated with prevalent fractures in Swedish men. Bone 2008; 42:107-12. [PMID: 17962094 DOI: 10.1016/j.bone.2007.08.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 06/01/2007] [Accepted: 08/27/2007] [Indexed: 11/21/2022]
Abstract
INTRODUCTION Sex steroids are important for growth and maintenance of the skeleton. Catechol-O-methyltransferase (COMT) is an estrogen degrading enzyme. The COMT val158met polymorphism results in a 60-75% difference in enzyme activity between the val (high activity=H) and met (low activity=L) variants. We have previously reported that this polymorphism is associated with bone mineral density (BMD) in young men. The aim of this study was to investigate associations between COMT val158met, BMD and fractures in elderly men. METHODS Population-based study of Swedish men 75.4, SD 3.2, years of age. Fractures were reported using standardized questionnaires. Fracture and genotype data were available from 2,822 individuals. RESULTS Total number of individuals with self-reported fracture was 989 (35.0%). Prevalence of >or=1 fracture was 37.2% in COMT(LL), 35.7% in COMT(HL) and 30.4% in COMT(HH) (p<0.05). Early fractures (<or=50 years of age) were less common in COMT(HH) than in the combined COMT(LL+HL) genotype, OR 0.78 (95% CI 0.63-0.97). No associations were found for late fractures (>50 years of age). The OR for fracture of the non-weight bearing skeleton in COMT(HH) compared with COMT(LL+HL) was 0.74 (95% CI 0.59-0.92). No associations between COMT val158met and BMD were found in this cohort of elderly men. CONCLUSIONS The COMT val158met polymorphism is associated with life time fracture prevalence in elderly Swedish men. This association is mainly driven by early fractures (<or=50 years of age).
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Affiliation(s)
- Anna L Eriksson
- Center for Bone Research at the Sahlgrenska Academy, Departments of Internal Medicine and Geriatrics, The Sahlgrenska Academy at Göteborg University, Göteborg, Sweden.
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84
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Grundberg E, Lau EMC, Pastinen T, Kindmark A, Nilsson O, Ljunggren O, Mellström D, Orwoll E, Redlund-Johnell I, Holmberg A, Gurd S, Leung PC, Kwok T, Ohlsson C, Mallmin H, Brändström H. Vitamin D receptor 3' haplotypes are unequally expressed in primary human bone cells and associated with increased fracture risk: the MrOS Study in Sweden and Hong Kong. J Bone Miner Res 2007; 22:832-40. [PMID: 17371163 DOI: 10.1359/jbmr.070317] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
UNLABELLED The VDR is a prime candidate gene for osteoporosis. Here, we studied three common VDR haplotypes in relation to bone phenotypes in 5014 participants of the global MrOS Study. We also studied the relative expression of the haplotypes in human bone cells. One haplotype was associated with increased fracture risk and differently expressed in primary human bone cells. INTRODUCTION Vitamin D plays an essential role in skeletal metabolism by binding to its nuclear steroid receptor, the vitamin D receptor (VDR). The heritability of BMD is well established, and the VDR gene is considered a prime candidate suggested to partially account for genetically controlled BMD variance in the population. MATERIALS AND METHODS Here, we reconstructed common haplotypes in the VDR 3' untranslated region (UTR) and studied the association to BMD and risk of vertebral fractures in elderly men from Sweden (n = 3014) and Hong Kong (n = 2000), all participants of the global MrOS Study. To assess any functional implications of the VDR polymorphisms, we studied allele-specific expressions of the different VDR 3' UTR haplotypes in the normal chromosomal context of 70 unrelated human trabecular bone samples. This was performed by quantitative genotyping of coding polymorphisms in RNA samples and in corresponding DNA samples isolated from the bone samples. RESULTS Three major haplotypes were reconstructed and in agreement with the previously well-defined baT, BAt, and bAT haplotypes, herein denoted Hap1, Hap2, and Hap3. The Hap1 haplotype was independently associated with increased risk of vertebral fractures in Swedish men (OR, 1.655; 95% CI, 1.146-2.391; p < 0.01) and with lower lumbar spine BMD in elderly men from Sweden (p < 0.01) and Hong Kong (p < 0.05). The VDR gene was also shown to exhibit a 3' UTR haplotype dependent allelic imbalance, indicating that the VDR Hap1 allele was overexpressed in human trabecular bone samples. CONCLUSIONS The results indicate that the relatively overexpressed VDR Hap1 haplotype could be considered a risk allele for osteoporosis regardless of ethnicity.
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Affiliation(s)
- Elin Grundberg
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
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Grundberg E, Akesson K, Kindmark A, Gerdhem P, Holmberg A, Mellström D, Ljunggren O, Orwoll E, Mallmin H, Ohlsson C, Brändström H. The impact of estradiol on bone mineral density is modulated by the specific estrogen receptor-alpha cofactor retinoblastoma-interacting zinc finger protein-1 insertion/deletion polymorphism. J Clin Endocrinol Metab 2007; 92:2300-6. [PMID: 17356055 DOI: 10.1210/jc.2006-1572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT Estrogens regulate bone mass by binding to the estrogen receptor (ER)-alpha as well as ER-beta. The specific ERalpha cofactor retinoblastoma-interacting zinc finger protein (RIZ)-1 enhances ERalpha function in the presence of estrogen. OBJECTIVE The objective of the study was to determine whether a RIZ P704 insertion (+)/deletion (-) (indel) polymorphism modulates the impact of estradiol on bone mineral density (BMD) and study the association between the polymorphism and BMD in elderly subjects. DESIGN This was a population-based, prospective, and cross-sectional study, the Swedish MrOS Study, and the Malmö OPRA Study, respectively. SETTING The study was conducted at three academic medical centers: Sahlgrenska Academy in Gothenburg, Malmö University Hospital, and Uppsala University Hospital. PARTICIPANTS In total, 4058 men and women, aged 69-81 yr, were randomly selected from population registries. MAIN OUTCOME MEASURES BMD (grams per square centimeter) was measured at femoral neck, trochanter, lumbar spine, and total body. RESULTS The RIZ P704(+/+) genotype was associated with low BMD in both women (femoral neck, P < 0.001; trochanter, P < 0.01; lumbar spine, P < 0.05; total body, P < 0.01) and men (lumbar spine, P < 0.05). However, the association between the polymorphism and BMD was dependent on estradiol status. The positive correlation between serum estradiol and BMD was significantly modulated by the genotype with a stronger correlation in the P704(+/+) group than the P704(-/-) group (r = 0.19 vs. r = 0.08, P < 0.05). CONCLUSIONS These large-scale studies of elderly men and women indicate that the ERalpha cofactor RIZ gene has a prominent effect on BMD, and the P704 genotype modulates the impact of estradiol on BMD. Further studies are required to determine whether this polymorphism modulates the estrogenic response to estradiol treatment.
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Affiliation(s)
- Elin Grundberg
- Department of Medical Sciences, Uppsala University Hospital, Ing 70, 3 tr, Uppsala, Sweden.
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Figtree GA, Kindmark A, Lind L, Grundberg E, Speller B, Robinson BG, Channon KM, Watkins H. Novel estrogen receptor alpha promoter polymorphism increases ventricular hypertrophic response to hypertension. J Steroid Biochem Mol Biol 2007; 103:110-8. [PMID: 17095210 DOI: 10.1016/j.jsbmb.2006.09.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Accepted: 09/05/2006] [Indexed: 11/16/2022]
Abstract
Given the strong genetic contribution to blood pressure and left ventricular hypertrophy (LVH), and the influence of estrogen on these parameters, we hypothesized that polymorphisms in the estrogen receptor alpha (ERalpha) promoter may influence LVH. Three novel polymorphisms were identified upstream of the ERalpha alternatively spliced exon 1E, within sequence which demonstrated significant promoter activity in vitro. Demonstration of ERalpha E isoform expression in human ventricle by RT-PCR supported a possible functional role for the 1E novel polymorphisms in estrogen signaling in the heart. Indeed, G>A (-721 E) was significantly associated with LVH after controlling for systolic blood pressure and sex in a healthy population (n=74), contributing to 23% of interventricular septum (IVS) width variance (p<0.001) and 9.4% of left ventricular mass index (LVMI) variance (p=0.035). In a separate hypertensive cohort, male carriers of the A allele (n=8) had a 17% increase in IVS (95% CI: 6-28%) and a 19% increase in LVMI (3-34%) compared to GG homozygotes (n=84). We conclude that a novel polymorphism in the promoter of a cardiac mRNA splice isoform of ERalpha is associated with LVH.
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Affiliation(s)
- G A Figtree
- Department of Cardiovascular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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87
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Michaëlsson K, Wolk A, Jacobsson A, Kindmark A, Grundberg E, Stiger F, Mallmin H, Ljunghall S, Melhus H. The positive effect of dietary vitamin D intake on bone mineral density in men is modulated by the polyadenosine repeat polymorphism of the vitamin D receptor. Bone 2006; 39:1343-51. [PMID: 16860619 DOI: 10.1016/j.bone.2006.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 04/10/2006] [Accepted: 06/08/2006] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Few studies have considered the dietary influence of vitamin D intake on bone mineral density (BMD). Numerous studies have examined the association between VDR polymorphism and BMD, but no previous study has examined the joint influence of dietary vitamin D intake and VDR polymorphism on BMD. METHODS We therefore conducted a study in 230 men aged 41-76 years of age. BMD was measured with DXA. A second bone scan was performed on average 2.7 years after the first investigation. Dietary habits were assessed by 14 dietary 24-h recall interviews. The polyadenosine (A) VDR genotypes were determined. RESULTS Dietary vitamin D intake was associated with BMD at all sites, also after multivariate adjustment. Those in the highest quintile of intake had 9% higher femoral neck BMD (p = 0.004), 6% higher BMD at the lumbar spine (p = 0.06) and 5% higher total body BMD (p = 0.003) compared to men in the lowest quintile of dietary vitamin D intake. However, the positive association between vitamin D intake and BMD was especially apparent among those with the L/L polyadenosine (A) VDR genotype explaining between 10 and 15% of the variability in BMD depending on site (p < 0.004). There was furthermore a trend, in the lumbar spine, of less reduction in BMD with increasing vitamin D intake (p = 0.07) but not at the other sites. Calcium intake conferred no association with BMD. CONCLUSIONS Our results indicate that the extent of positive association between dietary vitamin D intake and BMD in men is dependent on VDR polymorphism, a novel conceivable important gene-environmental interaction.
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Affiliation(s)
- Karl Michaëlsson
- Department of Surgical Sciences, Section of Orthopaedics, University Hospital, S-751 85 Uppsala, Sweden.
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88
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Grundberg E, Ribom EL, Brändström H, Ljunggren O, Mallmin H, Kindmark A. A TA-repeat polymorphism in the gene for the estrogen receptor alpha does not correlate with muscle strength or body composition in young adult Swedish women. Maturitas 2005; 50:153-60. [PMID: 15734595 DOI: 10.1016/j.maturitas.2004.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2003] [Revised: 02/02/2004] [Accepted: 05/01/2004] [Indexed: 12/01/2022]
Abstract
OBJECTIVES There are conflicting data in the literature whether estrogens affect muscle strength. Prospective studies with hormone replacement therapy have not been able to convincingly demonstrate a muscular effect and the putative role of estrogen in the development of lean body mass is not established. Both lean mass and fat mass are known to be under strong genetic control and therefore we have investigated the relation between a TA-repeat in the gene for the estrogen receptor alpha (ERalpha) and muscle strength and body composition. METHODS 175 healthy Swedish women, aged 20-39 were randomly selected from the population registry and included in the study. Body mass measurements (lean mass, fat mass, body weight and BMI) and muscle strength (quadriceps, hamstring and grip strength) were evaluated. The TA-repeat in the ERalpha gene was amplified by polymerase chain reaction. RESULTS Alleles with a TA-repeat length of 16 repeats or shorter were denoted short (e), and repeat length of 17 repeats or longer were denoted long (E). Women homozygous for the short and long genotype were denoted ee (31%) and EE (21%), respectively, while heterozygous individuals were denoted Ee (48%). The frequencies were in Hardy-Weinberg equilibrium. No associations were found between ERalpha genotypes and muscle strength or body composition. CONCLUSION The TA-repeat in the human ERalpha gene does not correlate with muscle strength or body mass measurements, indicating that body composition is not as sensitive to genetic variation in this receptor as other target organs for estrogen.
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Affiliation(s)
- Elin Grundberg
- Department of Medical Sciences, Uppsala University Hospital, Uppsala SE-751 85, Sweden.
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89
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Grundberg E, Carling T, Brändström H, Huang S, Ribom EL, Ljunggren O, Mallmin H, Kindmark A. A deletion polymorphism in the RIZ gene, a female sex steroid hormone receptor coactivator, exhibits decreased response to estrogen in vitro and associates with low bone mineral density in young Swedish women. J Clin Endocrinol Metab 2004; 89:6173-8. [PMID: 15579774 DOI: 10.1210/jc.2004-0403] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Low bone mineral density (BMD) is a major risk factor for osteoporotic fracture, and the trait is under genetic control by a large number of genes. It is recognized that estrogen plays an important role in the maintenance of bone mass by binding to estrogen receptor alpha (ERalpha). RIZ1 has previously been shown to be a specific ERalpha coactivator and strongly enhances its function both in vivo and in vitro. We performed in vitro studies comparing the abilities of RIZ1 P704 polymorphic variants (homozygous presence, P704+; absence, P704-; heterozygosity P704(+/-) of a proline at position 704) to coactivate the ERalpha and also examined the polymorphism associated to BMD of 343 Swedish women, aged 20-39 yr. The expression vector containing P704- RIZ1 showed an impaired response in coactivating ERalpha in a ligand- and dose-dependent manner compared with P704+ RIZ (P < 0.0001). The genotype frequencies were 19% (P704+), 32% (P704-), and 49% (P704(+/-)) and were in Hardy-Weinberg equilibrium. BMD at the heel was higher in the P704+ genotype group than in the P704(+/-) group (P = 0.02), which was evident also after corrections for fat and lean mass (P = 0.03). We conclude that RIZ1 may be a new candidate gene for involvement in the variation seen in BMD.
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Affiliation(s)
- E Grundberg
- Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden.
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90
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Grundberg E, Brändström H, Ribom EL, Ljunggren O, Mallmin H, Kindmark A. Genetic variation in the human vitamin D receptor is associated with muscle strength, fat mass and body weight in Swedish women. Eur J Endocrinol 2004; 150:323-8. [PMID: 15012617 DOI: 10.1530/eje.0.1500323] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Bone mineral density (BMD) is under strong genetic control and a number of candidate genes have been associated with BMD. Both muscle strength and body weight are considered to be important predictors of BMD but far less is known about the genes affecting muscle strength and fat mass. The purpose of this study was to investigate the poly adenosine (A) repeat and the BsmI SNP in the vitamin D receptor (VDR) in relation to muscle strength and body composition in healthy women. DESIGN A population-based study of 175 healthy women aged 20-39 years was used. METHODS The polymorphic regions in the VDR gene (the poly A repeat and the BsmI SNP) were amplified by PCR. Body mass measurements (fat mass, lean mass, body weight and body mass index) and muscle strength (quadriceps, hamstring and grip strength) were evaluated. RESULTS Individuals with shorter poly A repeat, ss and/or absence of the linked BsmI restriction site (BB) have higher hamstring strength (ss vs LL, P=0.02), body weight (ss vs LL, P=0.049) and fat mass (ss vs LL, P=0.04) compared with women with a longer poly A repeat (LL) and/or the presence of the linked BsmI restriction site (bb). CONCLUSIONS Genetic variation in the VDR is correlated with muscle strength, fat mass and body weight in premenopausal women. Further functional studies on the poly A microsatellite are needed to elucidate whether this is the functionally relevant locus or if the polymorphism is in linkage disequilibrium with a functional variant in a closely situated gene further downstream of the VDR 3'UTR.
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Affiliation(s)
- Elin Grundberg
- Department of Medical Sciences, Uppsala University Hospital, SE-75185 Uppsala, Sweden.
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91
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Grundberg E, Brändström H, Ribom EL, Ljunggren O, Kindmark A, Mallmin H. A poly adenosine repeat in the human vitamin D receptor gene is associated with bone mineral density in young Swedish women. Calcif Tissue Int 2003; 73:455-62. [PMID: 12958689 DOI: 10.1007/s00223-002-0032-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2002] [Accepted: 03/05/2003] [Indexed: 10/26/2022]
Abstract
Peak bone mass (PBM) and subsequent bone loss are important risk factors for development of osteoporosis later in life, and twin studies have reported strong genetic influence on PBM. The genetic factor influencing PBM is polygenetic, and many genes most likely exert relatively small effects on bone mass. The poly adenosine (A) microsatellite in the 3' untranslated region (UTR) of the VDR gene has been associated with both prostate and breast cancer risk but little is known about the effect of bone mineral density (BMD). In this report the poly A microsatellite and the linked BsmI SNP have been investigated in a population-based cohort of 343 Swedish women, aged 20-39. BMD was measured by dual x-ray absorptiometry at the spine, proximal femur, total body and heel and by quantitative ultrasound at the heel. Correlations were found between VDR genotypes and BMD at lumbar spine L2-L4, (ss versus LL, P = 0.03 and BB versus bb, P = 0.02, respectively), with a similar pattern concerning total hip (ss versus LL, P = 0.12 and BB versus bb, P = 0.16 respectively). After corrections for age, height, fat and lean mass, the VDR BsmI genotype was still associated to BMD at the lumbar spine (BB versus bb, P = 0.03). The polymorphisms were in linkage disequilibrium (Chi-square = 566, P < 0.0001). In conclusion, genetic variation in the VDR is associated with BMD in premenopausal women, and further studies are needed to evaluate a possible functional role of the VDR 3'UTR poly A repeat, a region that has shown to be of important for mRNA stability.
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Affiliation(s)
- E Grundberg
- Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden.
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