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A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1

Nature Genetics volume 42, pages 985–990 (2010)Cite this article

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Abstract

To identify new susceptibility loci for psoriasis, we undertook a genome-wide association study of 594,224 SNPs in 2,622 individuals with psoriasis and 5,667 controls. We identified associations at eight previously unreported genomic loci. Seven loci harbored genes with recognized immune functions (IL28RA, REL, IFIH1, ERAP1, TRAF3IP2, NFKBIA and TYK2). These associations were replicated in 9,079 European samples (six loci with a combined P < 5 × 10−8 and two loci with a combined P < 5 × 10−7). We also report compelling evidence for an interaction between the HLA-C and ERAP1 loci (combined P = 6.95 × 10−6). ERAP1 plays an important role in MHC class I peptide processing. ERAP1 variants only influenced psoriasis susceptibility in individuals carrying the HLA-C risk allele. Our findings implicate pathways that integrate epidermal barrier dysfunction with innate and adaptive immune dysregulation in psoriasis pathogenesis.

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Figure 1: Plot of genome-wide association results.
Figure 2: Regional association plots.
Figure 3: Statistical interaction between ERAP1 and HLA-C genotypes.

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Acknowledgements

The principal funding for this study was provided by the Wellcome Trust, as part of the Wellcome Trust Case Control Consortium 2 project (083948/Z/07/Z). We also thank S. Bertrand, J. Bryant, S.L. Clark, J.S. Conquer, T. Dibling, J.C. Eldred, S. Gamble, C. Hind, A. Wilk, C.R. Stribling and S. Taylor of the Wellcome Trust Sanger Institute's Sample and Genotyping Facilities for technical assistance. We thank D. Davison for making available his program 'Shellfish' for calculating principal components in large genetic datasets. Case collections were supported by the Netherlands Organization for Health Research and Development (P.L.J.M.Z.); the Swedish Medical Research Council, Karolinska Institutet, Karolinska University Hospital, Psoriasis Foundation, AFA Insurance and Welander Finsen Foundation (M.S.); the Association for the Defence of Psoriasis Patients (G.N.); Psoriasis Association and the Cecil King Memorial Foundation (M.J.C.); the Swedish Psoriasis Association (L.S.); the German Research Foundation (Tr 228/5-4 and Re 679/10-4) and The Interdisciplinary Centre for Clinical Research (IZKF B32/A8) of the University of Erlangen-Nuremberg (A. Reis); the Spanish Ministry of Science and Innovation (grant SAF 2008-00357) and the 'Generalitat de Catalunya' Departments of Health and Universities and Innovation (X.E.); the Genetic Repository in Ireland for Psoriasis and Psoriatic Arthritis (GRIPPsA), the Dublin Centre for Clinical Research (DCCR, funded by the Irish Health Research Board), The Wellcome Trust and Science Foundation Ireland (R. McManus); National Institute for Health Research, Manchester Biomedical Research Centre (J.W., C.E.M.G., R.B.W., H.S.Y.); and Arthritis Research UK (J.W., grant 17552). P. Donnelly was supported in part by a Wolfson-Royal Society Merit Award, and A.O. was supported by a PhD studentship from The Generation Trust. We also acknowledge support from the UK Medical Research Council (to R.C.T., F.O.N., A.H. and J.N.B., grant G0601387), the Wellcome Trust (F.O.N., grant 078173/Z/05/Z) and the Department of Health through the National Institute for Health Research (NIHR) comprehensive Biomedical Research Centre awards to Guy's and St. Thomas' National Health Service (NHS) Foundation Trust in partnership with King's College London (J. Knight., M.E.W., C.G.M., F.O.N., A. Hayday and J.N.B.) and the NIHR award to Moorfields Eye Hospital NHS Foundation Trust and University College London Institute of Ophthalmology for a Specialist Biomedical Research Centre for Ophthalmology (A.C.V.). We acknowledge use of the British 1958 Birth Cohort DNA collection, funded by the Medical Research Council grant G0000934 and the Wellcome Trust grant 068545/Z/02, and of the UK National Blood Service controls funded by the Wellcome Trust. We thank W. Bodmer and B. Winney for use of the People of the British Isles DNA collection, which was funded by the Wellcome Trust.

Author information

Author notes

  1. Amy Strange and Francesca Capon: These authors contributed equally to this work.

  2. Peter Donnelly and Richard C Trembath: These authors jointly supervised this work.

Authors and Affiliations

  1. Wellcome Trust Centre for Human Genetics, Oxford, UK

    Amy Strange, Chris C A Spencer, Gavin Band, Céline Bellenguez, Colin Freeman, Matti Pirinen, Anna Rautanen, Zhan Su & Peter Donnelly

  2. Division of Genetics and Molecular Medicine, King's College London, London, UK

    Francesca Capon, Jo Knight, Michael E Weale, Michael H Allen, Christopher G Mathew, Frank O Nestle, Alexandros Onoufriadis, Catherine H Smith, Jonathan N Barker & Richard C Trembath

  3. National Institute for Health Research (NIHR), Biomedical Research Centre, Guy's and St. Thomas' National Health Service (NHS) Foundation Trust and King's College London, London, UK

    Jo Knight, Frank O Nestle & Richard C Trembath

  4. Arthritis Research, UK Epidemiology Unit, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK

    Anne Barton & Jane Worthington

  5. Department of Dermatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands

    Judith G M Bergboer, Joost Schalkwijk & Patrick L J M Zeeuwen

  6. Genetics and Infection Laboratory, Cambridge Institute of Medical Research, Addenbrooke's Hospital, Cambridge, UK

    Jenefer M Blackwell

  7. Division of Psychological Medicine and Psychiatry, Biomedical Research Centre for Mental Health at the Institute of Psychiatry, King's College London and The South London and Maudsley NHS Foundation Trust, Denmark Hill, London, UK

    Elvira Bramon

  8. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,

    Suzannah J Bumpstead, Panos Deloukas, Sarah Edkins, Emma Gray, Sarah E Hunt, Cordelia Langford, Simon C Potter & Leena Peltonen

  9. Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK

    Juan P Casas

  10. Department of Infection and Immunity, Academic Unit of Dermatology Research, The University of Sheffield, Sheffield, UK

    Michael J Cork & Rachid Tazi-Ahnini

  11. Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland

    Aiden Corvin

  12. Department of Statistics, University of Oxford, Oxford, UK

    Alexander Dilthey, Stephen Leslie, Loukas Moutsianas, Gilean McVean & Peter Donnelly

  13. Molecular and Physiological Sciences, The Wellcome Trust, London, UK

    Audrey Duncanson

  14. Genes and Disease Programme, Centre for Genomic Regulation (CRG) and Public Health and Epidemiology Network Biomedical Research Center (CIBERESP), Barcelona, Spain

    Xavier Estivill & Eva Riveira-Munoz

  15. St. Vincent's University Hospital, Dublin, Ireland

    Oliver Fitzgerald & Brian Kirby

  16. Department of Biopathology, Centre of Excellence for Genomic risk Assessment in Multifactorial and Complex Diseases, School of Medicine, University of Rome Tor Vergata, Rome, Italy

    Emiliano Giardina & Giuseppe Novelli

  17. Department of Dermatology, Medical University of Graz, Graz, Austria

    Angelika Hofer, Wolfgang Salmhofer & Wolfgang Weger

  18. Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany

    Ulrike Hüffmeier & André Reis

  19. Department of Clinical Medicine, Trinity College Dublin, Our Lady's Children's Hospital Crumlin, Dublin, Ireland

    Alan D Irvine

  20. Centre for Gastroenterology, Bart's and the London School of Medicine and Dentistry, London, UK

    Janusz Jankowski

  21. Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Jesús Lascorz

  22. Department of Dermatology, Western Infirmary, Glasgow, UK

    Joyce Leman & A David Burden

  23. Department of Medicine, Dermatology Unit, Karolinska Institutet, Stockholm, Sweden

    Lotus Mallbris, Mona Ståhle & Katarina Wolk

  24. Clinical Neurosciences, St. George's University of London, London, UK

    Hugh S Markus

  25. Division of Molecular Medicine, Epithelial Genetics Group, Colleges of Life Sciences and Medicine, Dentistry and Nursing, University of Dundee, Dundee, UK

    W H Irwin McLean

  26. Department of Clinical Medicine, Trinity College Dublin, St. James's Hospital, Dublin, Ireland

    Ross McManus & Anthony W Ryan

  27. Institute of Molecular Medicine, Trinity College Dublin, St. James's Hospital, Dublin, Ireland

    Ross McManus & Anthony W Ryan

  28. Department of Dermatology, University of Göttingen, Göttingen, Germany

    Rotraut Mössner

  29. Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden

    Åsa T Naluai & Lena Samuelsson

  30. Biomedical Research Institute, Ninewells Hospital and Medical School, Dundee, UK

    Colin N A Palmer

  31. Department of Clinic and Medical Therapy, La Sapienza University of Rome, Unit of Rheumatology, Rome, Italy

    Carlo Perricone

  32. Social, Genetic and Developmental Psychiatry Centre, King's College London Institute of Psychiatry, Denmark Hill, London, UK.,

    Robert Plomin

  33. Dermatology Service, Hospital del Mar-Institut Municipal d'Assisténcia Sanitári (IMAS), Barcelona, Spain

    Ramon M Pujol

  34. University of Cambridge Department of Clinical Neurosciences, Addenbrooke's Hospital, Cambridge, UK

    Stephen J Sawcer & Adrian Hayday

  35. St. John's Institute of Dermatology, King's College London, London, UK

    Catherine H Smith & Jonathan N Barker

  36. Department of Dermatology, University of Münster, Münster, Germany

    Heiko Traupe

  37. Glaucoma Research Unit, Moorfields Eye Hospital NHS Foundation Trust, London, UK

    Ananth C Viswanathan

  38. Department of Genetics, University College London Institute of Ophthalmology, London, UK

    Ananth C Viswanathan

  39. Dermatological Sciences, Salford Royal NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK

    Richard B Warren, Helen S Young & Christopher E M Griffiths

  40. Department of Molecular Neuroscience, Institute of Neurology, Queen Square, London, UK

    Nicholas Wood

  41. Division of Immunology, Infection and Inflammatory Disease, King's College London, London, UK

    Adrian Hayday

  42. Immuno Surveillance Laboratory, London Research Institute, London, UK

    Adrian Hayday

  43. Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden

    Juha Kere

  44. Science for Life Laboratory, Stockholm, Sweden

    Juha Kere

  45. Folkhälsan Institute of Genetics, Helsinki, Finland

    Juha Kere

  46. Department of Medical Genetics, University of Helsinki, Finland

    Juha Kere

  47. Department of Social Medicine, Medical Research Council Centre for Causal Analyses in Translational Epidemiology, University of Bristol, Bristol, UK

    David M Evans

  48. Diamantina Institute of Cancer, Immunology and Metabolic Medicine, Princess Alexandra Hospital, University of Queensland, Brisbane, Queensland, Australia

    David M Evans & Matthew A Brown

Consortia

Genetic Analysis of Psoriasis Consortium & the Wellcome Trust Case Control Consortium 2

  • Amy Strange
  • , Francesca Capon
  • , Chris C A Spencer
  • , Jo Knight
  • , Michael E Weale
  • , Michael H Allen
  • , Anne Barton
  • , Gavin Band
  • , Céline Bellenguez
  • , Judith G M Bergboer
  • , Jenefer M Blackwell
  • , Elvira Bramon
  • , Suzannah J Bumpstead
  • , Juan P Casas
  • , Michael J Cork
  • , Aiden Corvin
  • , Panos Deloukas
  • , Alexander Dilthey
  • , Audrey Duncanson
  • , Sarah Edkins
  • , Xavier Estivill
  • , Oliver Fitzgerald
  • , Colin Freeman
  • , Emiliano Giardina
  • , Emma Gray
  • , Angelika Hofer
  • , Ulrike Hüffmeier
  • , Sarah E Hunt
  • , Alan D Irvine
  • , Janusz Jankowski
  • , Brian Kirby
  • , Cordelia Langford
  • , Jesús Lascorz
  • , Joyce Leman
  • , Stephen Leslie
  • , Lotus Mallbris
  • , Hugh S Markus
  • , Christopher G Mathew
  • , W H Irwin McLean
  • , Ross McManus
  • , Rotraut Mössner
  • , Loukas Moutsianas
  • , Åsa T Naluai
  • , Frank O Nestle
  • , Giuseppe Novelli
  • , Alexandros Onoufriadis
  • , Colin N A Palmer
  • , Carlo Perricone
  • , Matti Pirinen
  • , Robert Plomin
  • , Simon C Potter
  • , Ramon M Pujol
  • , Anna Rautanen
  • , Eva Riveira-Munoz
  • , Anthony W Ryan
  • , Wolfgang Salmhofer
  • , Lena Samuelsson
  • , Stephen J Sawcer
  • , Joost Schalkwijk
  • , Catherine H Smith
  • , Mona Ståhle
  • , Zhan Su
  • , Rachid Tazi-Ahnini
  • , Heiko Traupe
  • , Ananth C Viswanathan
  • , Richard B Warren
  • , Wolfgang Weger
  • , Katarina Wolk
  • , Nicholas Wood
  • , Jane Worthington
  • , Helen S Young
  • , Patrick L J M Zeeuwen
  • , Adrian Hayday
  • , A David Burden
  • , Christopher E M Griffiths
  • , Juha Kere
  • , André Reis
  • , Gilean McVean
  • , David M Evans
  • , Matthew A Brown
  • , Jonathan N Barker
  • , Leena Peltonen
  • , Peter Donnelly
  •  & Richard C Trembath

Contributions

F.C., A.D.B., C.E.M.G., J. Kere, A. Reis, J.N.B. and R.C.T. oversaw cohort collection for both the discovery and the replication datasets. The WTCCC2 DNA, genotyping, data quality control and informatics group (S.J.B., P. Deloukas, S.E., E. Gray, S.E.H., C.L. and S.C.P.) executed GWAS sample handling, genotyping and quality control. Members of the WTCCC2 analysis group (C.C.A.S., A.S., G.B., C.B., C.F., M.P., Z.S. and P. Donnelly), J. Knight and M.E.W. performed statistical analyses. A. Dilthey, S.L., L. Moutsianas and G.M. performed HLA imputation and analyses. D.M.E. and M.A.B. provided advice on similarities of association to another autoimmune disease. A.S., F.C., C.C.A.S., J. Knight, M.E.W., A. Hayday, J.N.B., P. Donnelly and R.C.T. contributed to writing the manuscript. The WTCCC2 Management Committee (P. Donnelly (chair), J.M.B., E.B., J.P.C., A. Duncanson, J.J., H.S.M., C.G.M., C.N.A.P., R.P., S.J.S., A. Rautanen, A.C.V., N.W., M.A.B., L.P. and R.C.T.) monitored the execution of the GWAS. The GAP Consortium (R.C.T. (chair), M.H.A., A.B., J.G.M.B., M.J.C., A.C., X.E., O.F., E. Giardina, A. Hofer, U.H., A.D.I., B.K., J. Lascorz, J. Leman, L. Mallbris, W.H.I.M., R. McManus, R. Mössner, Å.T.N., F.O.N., G.N., A.O., C.P., R.M.P., E.R.M., A.W.R., W.S., L.S., J.S., C.H.S., M.S., R.T.A., H.T., R.B.W., W.W., K.W., J.W., H.S.Y. and P.L.J.M.Z.) contributed to sample collection. All authors reviewed the final manuscript.

Corresponding authors

Correspondence to Peter Donnelly or Richard C Trembath.

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The author declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–9, Supplementary Figures 1–4 and Supplementary Note. (PDF 6704 kb)

Supplementary Table 9

Other SNPs with GWAS p-value less than 10-4 (XLS 37 kb)

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Genetic Analysis of Psoriasis Consortium & the Wellcome Trust Case Control Consortium 2. A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat Genet 42, 985–990 (2010). https://doi.org/10.1038/ng.694

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