1
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Shah SA, Deng L, Thorsen J, Pedersen AG, Dion MB, Castro-Mejía JL, Silins R, Romme FO, Sausset R, Jessen LE, Ndela EO, Hjelmsø M, Rasmussen MA, Redgwell TA, Leal Rodríguez C, Vestergaard G, Zhang Y, Chawes B, Bønnelykke K, Sørensen SJ, Bisgaard H, Enault F, Stokholm J, Moineau S, Petit MA, Nielsen DS. Expanding known viral diversity in the healthy infant gut. Nat Microbiol 2023; 8:986-998. [PMID: 37037943 PMCID: PMC10159846 DOI: 10.1038/s41564-023-01345-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/17/2023] [Indexed: 04/12/2023]
Abstract
The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother-child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.
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Affiliation(s)
- Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark.
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders G Pedersen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Moïra B Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
| | | | - Ronalds Silins
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Fie O Romme
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Romain Sausset
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Leon E Jessen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Eric Olo Ndela
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mathis Hjelmsø
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Morten A Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Tamsin A Redgwell
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Cristina Leal Rodríguez
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Gisle Vestergaard
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Yichang Zhang
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Francois Enault
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Quebec, Canada
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark.
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2
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Chronister WD, Crinklaw A, Mahajan S, Vita R, Koşaloğlu-Yalçın Z, Yan Z, Greenbaum JA, Jessen LE, Nielsen M, Christley S, Cowell LG, Sette A, Peters B. TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors. Front Immunol 2021; 12:640725. [PMID: 33777034 PMCID: PMC7991084 DOI: 10.3389/fimmu.2021.640725] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
The adaptive immune system in vertebrates has evolved to recognize non-self antigens, such as proteins expressed by infectious agents and mutated cancer cells. T cells play an important role in antigen recognition by expressing a diverse repertoire of antigen-specific receptors, which bind epitopes to mount targeted immune responses. Recent advances in high-throughput sequencing have enabled the routine generation of T-cell receptor (TCR) repertoire data. Identifying the specific epitopes targeted by different TCRs in these data would be valuable. To accomplish that, we took advantage of the ever-increasing number of TCRs with known epitope specificity curated in the Immune Epitope Database (IEDB) since 2004. We compared seven metrics of sequence similarity to determine their power to predict if two TCRs have the same epitope specificity. We found that a comprehensive k-mer matching approach produced the best results, which we have implemented into TCRMatch, an openly accessible tool (http://tools.iedb.org/tcrmatch/) that takes TCR β-chain CDR3 sequences as an input, identifies TCRs with a match in the IEDB, and reports the specificity of each match. We anticipate that this tool will provide new insights into T cell responses captured in receptor repertoire and single cell sequencing experiments and will facilitate the development of new strategies for monitoring and treatment of infectious, allergic, and autoimmune diseases, as well as cancer.
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Affiliation(s)
| | - Austin Crinklaw
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Swapnil Mahajan
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Randi Vita
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | | | - Zhen Yan
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Jason A Greenbaum
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Leon E Jessen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Morten Nielsen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Argentina
| | - Scott Christley
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, United States
| | - Lindsay G Cowell
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, United States
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
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3
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Bønnelykke K, Coleman AT, Evans MD, Thorsen J, Waage J, Vissing NH, Carlsson CJ, Stokholm J, Chawes BL, Jessen LE, Fischer TK, Bochkov YA, Ober C, Lemanske RF, Jackson DJ, Gern JE, Bisgaard H. Cadherin-related Family Member 3 Genetics and Rhinovirus C Respiratory Illnesses. Am J Respir Crit Care Med 2019; 197:589-594. [PMID: 29121479 DOI: 10.1164/rccm.201705-1021oc] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Experimental evidence suggests that CDHR3 (cadherin-related family member 3) is a receptor for rhinovirus (RV)-C, and a missense variant in this gene (rs6967330) is associated with childhood asthma with severe exacerbations. OBJECTIVES To determine whether rs6967330 influences RV-C infections and illnesses in early childhood. METHODS We studied associations between rs6967330 and respiratory infections and illnesses in the COPSAC2010 (Copenhagen Prospective Studies on Asthma in Childhood 2010) and COAST (Childhood Origins of Asthma Birth Cohort Study) birth cohorts, where respiratory infections were monitored prospectively for the first 3 years of life. Nasal samples were collected during acute infections in both cohorts and during asymptomatic periods in COAST and analyzed for RV-A, RV-B, and RV-C, and other common respiratory viruses. MEASUREMENTS AND MAIN RESULTS The CDHR3 asthma risk allele (rs6967330-A) was associated with increased risk of respiratory tract illnesses (incidence risk ratio [IRR] = 1.14 [95% confidence interval, 1.05-1.23]; P = 0.003). In particular, this variant was associated with risk of respiratory episodes with detection of RV-C in COPSAC2010 (IRR = 1.89 [1.14-3.05]; P = 0.01) and in COAST (IRR = 1.37 [1.02-1.82]; P = 0.03) children, and in a combined meta-analysis (IRR = 1.51 [1.13-2.02]; P = 0.006). In contrast, the variant was not associated with illnesses related to other viruses (IRR = 1.07 [0.92-1.25]; P = 0.37). Consistent with these observations, the CDHR3 variant was associated with increased detection of RV-C, but not of other viruses during scheduled visits at specific ages. CONCLUSIONS The CDHR3 asthma risk allele is associated specifically with RV-C illnesses in two birth cohorts. This clinical evidence supports earlier molecular evidence indicating that CDHR3 functions as an RV-C receptor, and raises the possibility of preventing RV-C infections by targeting CDHR3.
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Affiliation(s)
- Klaus Bønnelykke
- 1 Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael D Evans
- 3 Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin
| | - Jonathan Thorsen
- 1 Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Johannes Waage
- 1 Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Nadja H Vissing
- 1 Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Christian J Carlsson
- 1 Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- 1 Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Bo L Chawes
- 1 Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Leon E Jessen
- 1 Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Thea K Fischer
- 4 World Health Organization National Reference Laboratories for Polio, Influenza, Measles and Rubella, Statens Serum Institut, Copenhagen, Denmark.,5 Department of Infectious Diseases and Center for Global Health, University of Southern Denmark, Odense, Denmark; and
| | | | - Carole Ober
- 6 Department of Human Genetics, University of Chicago, Chicago, Illinois
| | | | | | | | - Hans Bisgaard
- 1 Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
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4
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Bentzen AK, Such L, Jensen KK, Marquard AM, Jessen LE, Miller NJ, Church CD, Lyngaa R, Koelle DM, Becker JC, Linnemann C, Schumacher TNM, Marcatili P, Nghiem P, Nielsen M, Hadrup SR. T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide-MHC complexes. Nat Biotechnol 2018; 36:nbt.4303. [PMID: 30451992 PMCID: PMC9452375 DOI: 10.1038/nbt.4303] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/24/2018] [Indexed: 02/08/2023]
Abstract
The promiscuous nature of T-cell receptors (TCRs) allows T cells to recognize a large variety of pathogens, but makes it challenging to understand and control T-cell recognition. Existing technologies provide limited information about the key requirements for T-cell recognition and the ability of TCRs to cross-recognize structurally related elements. Here we present a 'one-pot' strategy for determining the interactions that govern TCR recognition of peptide-major histocompatibility complex (pMHC). We measured the relative affinities of TCRs to libraries of barcoded peptide-MHC variants and applied this knowledge to understand the recognition motif, here termed the TCR fingerprint. The TCR fingerprints of 16 different TCRs were identified and used to predict and validate cross-recognized peptides from the human proteome. The identified fingerprints differed among TCRs recognizing the same epitope, demonstrating the value of this strategy for understanding T-cell interactions and assessing potential cross-recognition before selection of TCRs for clinical development.
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Affiliation(s)
- Amalie K Bentzen
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| | - Lina Such
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| | - Kamilla K Jensen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Andrea M Marquard
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| | - Leon E Jessen
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Natalie J Miller
- Department of Medicine, Divisions of Dermatology, University of Washington, Seattle, Washington, USA
| | - Candice D Church
- Department of Medicine, Divisions of Dermatology, University of Washington, Seattle, Washington, USA
| | - Rikke Lyngaa
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Division of Vaccine and Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jürgen C Becker
- Translational Skin Cancer Research, University Hospital Essen and University of Duisburg-Essen, Essen, Germany
| | - Carsten Linnemann
- Department of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ton N M Schumacher
- Department of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paolo Marcatili
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Paul Nghiem
- Department of Medicine, Divisions of Dermatology, University of Washington, Seattle, Washington, USA
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Sine R Hadrup
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
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5
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Waage J, Standl M, Curtin JA, Jessen LE, Thorsen J, Tian C, Schoettler N, Flores C, Abdellaoui A, Ahluwalia TS, Alves AC, Amaral AFS, Antó JM, Arnold A, Barreto-Luis A, Baurecht H, van Beijsterveldt CEM, Bleecker ER, Bonàs-Guarch S, Boomsma DI, Brix S, Bunyavanich S, Burchard EG, Chen Z, Curjuric I, Custovic A, den Dekker HT, Dharmage SC, Dmitrieva J, Duijts L, Ege MJ, Gauderman WJ, Georges M, Gieger C, Gilliland F, Granell R, Gui H, Hansen T, Heinrich J, Henderson J, Hernandez-Pacheco N, Holt P, Imboden M, Jaddoe VWV, Jarvelin MR, Jarvis DL, Jensen KK, Jónsdóttir I, Kabesch M, Kaprio J, Kumar A, Lee YA, Levin AM, Li X, Lorenzo-Diaz F, Melén E, Mercader JM, Meyers DA, Myers R, Nicolae DL, Nohr EA, Palviainen T, Paternoster L, Pennell CE, Pershagen G, Pino-Yanes M, Probst-Hensch NM, Rüschendorf F, Simpson A, Stefansson K, Sunyer J, Sveinbjornsson G, Thiering E, Thompson PJ, Torrent M, Torrents D, Tung JY, Wang CA, Weidinger S, Weiss S, Willemsen G, Williams LK, Ober C, Hinds DA, Ferreira MA, Bisgaard H, Strachan DP, Bønnelykke K. Author Correction: Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis. Nat Genet 2018; 50:1343. [PMID: 30116036 DOI: 10.1038/s41588-018-0197-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In the version of this article initially published, in Fig. 3, the y-axis numbering did not match the log scale indicated in the axis label. The error has been corrected in the HTML and PDF version of the article.
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Affiliation(s)
- Johannes Waage
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - John A Curtin
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Leon E Jessen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Chao Tian
- 23andMe, Inc., Mountain View, CA, USA
| | - Nathan Schoettler
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Tenerife, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Abdel Abdellaoui
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands
- Department of Psychiatry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Alexessander C Alves
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Andre F S Amaral
- Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College London, London, UK
| | - Josep M Antó
- ISGlobal, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Andreas Arnold
- Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | - Amalia Barreto-Luis
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Tenerife, Spain
| | - Hansjörg Baurecht
- Department of Dermatology, Venereology and Allergology, University-Hospital Schleswig-Hostein, Campus Kiel, Kiel, Germany
| | | | - Eugene R Bleecker
- Divisions of Pharmacogenomics and Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Sílvia Bonàs-Guarch
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona, Spain
| | - Dorret I Boomsma
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands
- APH Amsterdam Public Health, Amsterdam, The Netherlands
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Zhanghua Chen
- Department of Preventive Medicine, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - Ivan Curjuric
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Adnan Custovic
- Department of Paediatrics, Imperial College London, London, UK
| | - Herman T den Dekker
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Pediatrics, Division of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Shyamali C Dharmage
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Julia Dmitrieva
- Laboratory of Animal Genomics, Unit of Medical Genomics, GIGA Institute, University of Liège, Liège, Belgium
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Pediatrics, Division of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Pediatrics, Division of Neonatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Markus J Ege
- LMU Munich, Dr von Hauner Children's Hospital, Munich, and German Center for Lung Research (DZL), Munich, Germany
| | - W James Gauderman
- Department of Preventive Medicine, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - Michel Georges
- Laboratory of Animal Genomics, Unit of Medical Genomics, GIGA Institute, University of Liège, Liège, Belgium
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Frank Gilliland
- Department of Preventive Medicine, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - Raquel Granell
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hongsheng Gui
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, USA
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joachim Heinrich
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University of Munich Medical Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - John Henderson
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Tenerife, Spain
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Patrick Holt
- Telethon Kids Institute (TKI), Perth, Western Australia, Australia
| | - Medea Imboden
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Deborah L Jarvis
- Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College London, London, UK
| | - Kamilla K Jensen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ingileif Jónsdóttir
- deCODE genetics/Amgen Inc, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Ashish Kumar
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Young-Ae Lee
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany
- Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Xingnan Li
- Divisions of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Fabian Lorenzo-Diaz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children's Hospital, Stockholm, Sweden
| | - Josep M Mercader
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona, Spain
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Deborah A Meyers
- Divisions of Pharmacogenomics and Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Rachel Myers
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Ellen A Nohr
- Institute of Clinical Research, University of Southern Denmark, Department of Obstetrics & Gynecology, Odense University Hospital, Odense, Denmark
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Craig E Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Tenerife, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Nicole M Probst-Hensch
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Kari Stefansson
- deCODE genetics/Amgen Inc, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | | | - Elisabeth Thiering
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Ludwig-Maximilians-University of Munich, Dr. von Hauner Children's Hospital, Division of Metabolic Diseases and Nutritional Medicine, Munich, Germany
| | - Philip J Thompson
- Institute for Respiratory Health, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, Western Australia, Australia
| | - Maties Torrent
- Ib-Salut, Area de Salut de Menorca, Institut d'Investigacio Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergology, University-Hospital Schleswig-Hostein, Campus Kiel, Kiel, Germany
| | - Scott Weiss
- Channing Division of Network Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gonneke Willemsen
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands
| | - L Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, USA
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | | | - Manuel A Ferreira
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
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6
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Waage J, Standl M, Curtin JA, Jessen LE, Thorsen J, Tian C, Schoettler N, Flores C, Abdellaoui A, Ahluwalia TS, Alves AC, Amaral AFS, Antó JM, Arnold A, Barreto-Luis A, Baurecht H, van Beijsterveldt CEM, Bleecker ER, Bonàs-Guarch S, Boomsma DI, Brix S, Bunyavanich S, Burchard EG, Chen Z, Curjuric I, Custovic A, den Dekker HT, Dharmage SC, Dmitrieva J, Duijts L, Ege MJ, Gauderman WJ, Georges M, Gieger C, Gilliland F, Granell R, Gui H, Hansen T, Heinrich J, Henderson J, Hernandez-Pacheco N, Holt P, Imboden M, Jaddoe VWV, Jarvelin MR, Jarvis DL, Jensen KK, Jónsdóttir I, Kabesch M, Kaprio J, Kumar A, Lee YA, Levin AM, Li X, Lorenzo-Diaz F, Melén E, Mercader JM, Meyers DA, Myers R, Nicolae DL, Nohr EA, Palviainen T, Paternoster L, Pennell CE, Pershagen G, Pino-Yanes M, Probst-Hensch NM, Rüschendorf F, Simpson A, Stefansson K, Sunyer J, Sveinbjornsson G, Thiering E, Thompson PJ, Torrent M, Torrents D, Tung JY, Wang CA, Weidinger S, Weiss S, Willemsen G, Williams LK, Ober C, Hinds DA, Ferreira MA, Bisgaard H, Strachan DP, Bønnelykke K. Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis. Nat Genet 2018; 50:1072-1080. [PMID: 30013184 DOI: 10.1038/s41588-018-0157-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 05/10/2018] [Indexed: 11/09/2022]
Abstract
Allergic rhinitis is the most common clinical presentation of allergy, affecting 400 million people worldwide, with increasing incidence in westernized countries1,2. To elucidate the genetic architecture and understand the underlying disease mechanisms, we carried out a meta-analysis of allergic rhinitis in 59,762 cases and 152,358 controls of European ancestry and identified a total of 41 risk loci for allergic rhinitis, including 20 loci not previously associated with allergic rhinitis, which were confirmed in a replication phase of 60,720 cases and 618,527 controls. Functional annotation implicated genes involved in various immune pathways, and fine mapping of the HLA region suggested amino acid variants important for antigen binding. We further performed genome-wide association study (GWAS) analyses of allergic sensitization against inhalant allergens and nonallergic rhinitis, which suggested shared genetic mechanisms across rhinitis-related traits. Future studies of the identified loci and genes might identify novel targets for treatment and prevention of allergic rhinitis.
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Affiliation(s)
- Johannes Waage
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - John A Curtin
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Leon E Jessen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Chao Tian
- 23andMe, Inc., Mountain View, CA, USA
| | - Nathan Schoettler
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | | | | | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Tenerife, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Abdel Abdellaoui
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands.,Department of Psychiatry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Alexessander C Alves
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Andre F S Amaral
- Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College London, London, UK
| | - Josep M Antó
- ISGlobal, Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Andreas Arnold
- Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | - Amalia Barreto-Luis
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Tenerife, Spain
| | - Hansjörg Baurecht
- Department of Dermatology, Venereology and Allergology, University-Hospital Schleswig-Hostein, Campus Kiel, Kiel, Germany
| | | | - Eugene R Bleecker
- Divisions of Pharmacogenomics and Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Sílvia Bonàs-Guarch
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona, Spain
| | - Dorret I Boomsma
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands.,APH Amsterdam Public Health, Amsterdam, The Netherlands
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Zhanghua Chen
- Department of Preventive Medicine, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - Ivan Curjuric
- University of Basel, Basel, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Adnan Custovic
- Department of Paediatrics, Imperial College London, London, UK
| | - Herman T den Dekker
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Pediatrics, Division of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Shyamali C Dharmage
- Allergy and Lung Health Unit, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Julia Dmitrieva
- Laboratory of Animal Genomics, Unit of Medical Genomics, GIGA Institute, University of Liège, Liège, Belgium
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Pediatrics, Division of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Pediatrics, Division of Neonatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Markus J Ege
- LMU Munich, Dr von Hauner Children's Hospital, Munich, and German Center for Lung Research (DZL), Munich, Germany
| | - W James Gauderman
- Department of Preventive Medicine, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - Michel Georges
- Laboratory of Animal Genomics, Unit of Medical Genomics, GIGA Institute, University of Liège, Liège, Belgium
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Frank Gilliland
- Department of Preventive Medicine, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - Raquel Granell
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hongsheng Gui
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, USA
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joachim Heinrich
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University of Munich Medical Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - John Henderson
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Patrick Holt
- Telethon Kids Institute (TKI), Perth, Western Australia, Australia
| | - Medea Imboden
- University of Basel, Basel, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Deborah L Jarvis
- Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College London, London, UK
| | - Kamilla K Jensen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ingileif Jónsdóttir
- deCODE genetics/Amgen Inc, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland.,National Institute for Health and Welfare, Helsinki, Finland
| | - Ashish Kumar
- University of Basel, Basel, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland.,Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Young-Ae Lee
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Xingnan Li
- Divisions of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Fabian Lorenzo-Diaz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Sachs' Children's Hospital, Stockholm, Sweden
| | - Josep M Mercader
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona, Spain.,Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Deborah A Meyers
- Divisions of Pharmacogenomics and Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Rachel Myers
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Ellen A Nohr
- Institute of Clinical Research, University of Southern Denmark, Department of Obstetrics & Gynecology, Odense University Hospital, Odense, Denmark
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Craig E Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Tenerife, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Nicole M Probst-Hensch
- University of Basel, Basel, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Kari Stefansson
- deCODE genetics/Amgen Inc, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | | | - Elisabeth Thiering
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Ludwig-Maximilians-University of Munich, Dr. von Hauner Children's Hospital, Division of Metabolic Diseases and Nutritional Medicine, Munich, Germany
| | - Philip J Thompson
- Institute for Respiratory Health, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, Western Australia, Australia
| | - Maties Torrent
- Ib-Salut, Area de Salut de Menorca, Institut d'Investigacio Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergology, University-Hospital Schleswig-Hostein, Campus Kiel, Kiel, Germany
| | - Scott Weiss
- Channing Division of Network Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gonneke Willemsen
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands
| | - L Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, USA.,Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | | | - Manuel A Ferreira
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
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7
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Medina-Gomez C, Kemp JP, Trajanoska K, Luan J, Chesi A, Ahluwalia TS, Mook-Kanamori DO, Ham A, Hartwig FP, Evans DS, Joro R, Nedeljkovic I, Zheng HF, Zhu K, Atalay M, Liu CT, Nethander M, Broer L, Porleifsson G, Mullin BH, Handelman SK, Nalls MA, Jessen LE, Heppe DH, Richards JB, Wang C, Chawes B, Schraut KE, Amin N, Wareham N, Karasik D, Van der Velde N, Ikram MA, Zemel BS, Zhou Y, Carlsson CJ, Liu Y, McGuigan FE, Boer CG, Bønnelykke K, Ralston SH, Robbins JA, Walsh JP, Zillikens MC, Langenberg C, Li-Gao R, Williams FM, Harris TB, Akesson K, Jackson RD, Sigurdsson G, den Heijer M, van der Eerden BC, van de Peppel J, Spector TD, Pennell C, Horta BL, Felix JF, Zhao JH, Wilson SG, de Mutsert R, Bisgaard H, Styrkársdóttir U, Jaddoe VW, Orwoll E, Lakka TA, Scott R, Grant SF, Lorentzon M, van Duijn CM, Wilson JF, Stefansson K, Psaty BM, Kiel DP, Ohlsson C, Ntzani E, van Wijnen AJ, Forgetta V, Ghanbari M, Logan JG, Williams GR, Bassett JD, Croucher PI, Evangelou E, Uitterlinden AG, Ackert-Bicknell CL, Tobias JH, Evans DM, Rivadeneira F. Life-Course Genome-wide Association Study Meta-analysis of Total Body BMD and Assessment of Age-Specific Effects. Am J Hum Genet 2018; 102:88-102. [PMID: 29304378 DOI: 10.1016/j.ajhg.2017.12.005] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/30/2017] [Indexed: 12/22/2022] Open
Abstract
Bone mineral density (BMD) assessed by DXA is used to evaluate bone health. In children, total body (TB) measurements are commonly used; in older individuals, BMD at the lumbar spine (LS) and femoral neck (FN) is used to diagnose osteoporosis. To date, genetic variants in more than 60 loci have been identified as associated with BMD. To investigate the genetic determinants of TB-BMD variation along the life course and test for age-specific effects, we performed a meta-analysis of 30 genome-wide association studies (GWASs) of TB-BMD including 66,628 individuals overall and divided across five age strata, each spanning 15 years. We identified variants associated with TB-BMD at 80 loci, of which 36 have not been previously identified; overall, they explain approximately 10% of the TB-BMD variance when combining all age groups and influence the risk of fracture. Pathway and enrichment analysis of the association signals showed clustering within gene sets implicated in the regulation of cell growth and SMAD proteins, overexpressed in the musculoskeletal system, and enriched in enhancer and promoter regions. These findings reveal TB-BMD as a relevant trait for genetic studies of osteoporosis, enabling the identification of variants and pathways influencing different bone compartments. Only variants in ESR1 and close proximity to RANKL showed a clear effect dependency on age. This most likely indicates that the majority of genetic variants identified influence BMD early in life and that their effect can be captured throughout the life course.
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8
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Skaaby T, Taylor AE, Jacobsen RK, Paternoster L, Thuesen BH, Ahluwalia TS, Larsen SC, Zhou A, Wong A, Gabrielsen ME, Bjørngaard JH, Flexeder C, Männistö S, Hardy R, Kuh D, Barry SJ, Tang Møllehave L, Cerqueira C, Friedrich N, Bonten TN, Noordam R, Mook-Kanamori DO, Taube C, Jessen LE, McConnachie A, Sattar N, Upton MN, McSharry C, Bønnelykke K, Bisgaard H, Schulz H, Strauch K, Meitinger T, Peters A, Grallert H, Nohr EA, Kivimaki M, Kumari M, Völker U, Nauck M, Völzke H, Power C, Hyppönen E, Hansen T, Jørgensen T, Pedersen O, Salomaa V, Grarup N, Langhammer A, Romundstad PR, Skorpen F, Kaprio J, R Munafò M, Linneberg A. Investigating the causal effect of smoking on hay fever and asthma: a Mendelian randomization meta-analysis in the CARTA consortium. Sci Rep 2017; 7:2224. [PMID: 28533558 PMCID: PMC5440386 DOI: 10.1038/s41598-017-01977-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 10/04/2016] [Accepted: 04/05/2017] [Indexed: 01/08/2023] Open
Abstract
Observational studies on smoking and risk of hay fever and asthma have shown inconsistent results. However, observational studies may be biased by confounding and reverse causation. Mendelian randomization uses genetic variants as markers of exposures to examine causal effects. We examined the causal effect of smoking on hay fever and asthma by using the smoking-associated single nucleotide polymorphism (SNP) rs16969968/rs1051730. We included 231,020 participants from 22 population-based studies. Observational analyses showed that current vs never smokers had lower risk of hay fever (odds ratio (OR) = 0·68, 95% confidence interval (CI): 0·61, 0·76; P < 0·001) and allergic sensitization (OR = 0·74, 95% CI: 0·64, 0·86; P < 0·001), but similar asthma risk (OR = 1·00, 95% CI: 0·91, 1·09; P = 0·967). Mendelian randomization analyses in current smokers showed a slightly lower risk of hay fever (OR = 0·958, 95% CI: 0·920, 0·998; P = 0·041), a lower risk of allergic sensitization (OR = 0·92, 95% CI: 0·84, 1·02; P = 0·117), but higher risk of asthma (OR = 1·06, 95% CI: 1·01, 1·11; P = 0·020) per smoking-increasing allele. Our results suggest that smoking may be causally related to a higher risk of asthma and a slightly lower risk of hay fever. However, the adverse events associated with smoking limit its clinical significance.
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Affiliation(s)
- Tea Skaaby
- Research Centre for Prevention and Health, Centre for Health, Capital Region of Denmark, Copenhagen, Denmark.
| | - Amy E Taylor
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- UK Centre for Tobacco and Alcohol Studies, School of Experimental Psychology, University of Bristol, Bristol, UK
| | - Rikke K Jacobsen
- Research Centre for Prevention and Health, Centre for Health, Capital Region of Denmark, Copenhagen, Denmark
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Betina H Thuesen
- Research Centre for Prevention and Health, Centre for Health, Capital Region of Denmark, Copenhagen, Denmark
| | - Tarunveer S Ahluwalia
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - Sofus C Larsen
- Research unit for Dietary Studies, the Parker Institute, Frederiksberg and Bispebjerg Hospitals, The Capital Region, Frederiksberg, Denmark
| | - Ang Zhou
- Centre for Population Health Research, School of Health Sciences and Sansom Institute of Health Research, University of South Australia, Adelaide, Australia
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
- Department of laboratory medicine, children's and women's health, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Johan H Bjørngaard
- Forensic Department and Research Centre Bröset St. Olav's University Hospital Trondheim, Trondheim, Norway
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Claudia Flexeder
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Satu Männistö
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Rebecca Hardy
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
| | - Sarah J Barry
- Robertson Centre for Biostatistics, Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Line Tang Møllehave
- Research Centre for Prevention and Health, Centre for Health, Capital Region of Denmark, Copenhagen, Denmark
| | - Charlotte Cerqueira
- Research Centre for Prevention and Health, Centre for Health, Capital Region of Denmark, Copenhagen, Denmark
| | - Nele Friedrich
- Research Centre for Prevention and Health, Centre for Health, Capital Region of Denmark, Copenhagen, Denmark
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Tobias N Bonten
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Raymond Noordam
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Dennis O Mook-Kanamori
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of BESC, Epidemiology Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Christian Taube
- Department of Pulmonary Medicine, Ruhrlandklinik, West German Lung Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Leon E Jessen
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Alex McConnachie
- Robertson Centre for Biostatistics, Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences & Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | | | - Charles McSharry
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- German Center for Cardiovascular Research (DZHK e.V.), Partner Site Munich Heart Alliance, München, Germany
| | - Annette Peters
- German Center for Cardiovascular Research (DZHK e.V.), Partner Site Munich Heart Alliance, München, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Harald Grallert
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mika Kivimaki
- Department of Epidemiology & Public Health, University College London, London, UK
| | | | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Chris Power
- Population, Policy and Practice, University College London Institute of Child Health, London, UK
| | - Elina Hyppönen
- Centre for Population Health Research, School of Health Sciences and Sansom Institute of Health Research, University of South Australia, Adelaide, Australia
- Population, Policy and Practice, University College London Institute of Child Health, London, UK
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Jørgensen
- Research Centre for Prevention and Health, Centre for Health, Capital Region of Denmark, Copenhagen, Denmark
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Medicine, Aalborg University, Aalborg, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Veikko Salomaa
- National Institute for Health and Welfare, Dept. of Health, Helsinki, Finland
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Arnulf Langhammer
- HUNT Research Centre, Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Norwegian, Norway
| | - Pål R Romundstad
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Frank Skorpen
- Department of laboratory medicine, children's and women's health, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Jaakko Kaprio
- University of Helsinki, Dept. of Public Health, Helsinki, Finland
- National Institute for Health and Welfare, Dept. of Health, Helsinki, Finland
- University of Helsinki, Institute for Molecular Medicine, Helsinki, Finland
| | - Marcus R Munafò
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
- UK Centre for Tobacco and Alcohol Studies, School of Experimental Psychology, University of Bristol, Bristol, UK
| | - Allan Linneberg
- Research Centre for Prevention and Health, Centre for Health, Capital Region of Denmark, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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