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Cell-specific protein phenotypes for the autoimmune locus IL2RA using a genotype-selectable human bioresource

Nature Genetics volume 41, pages 1011–1015 (2009)Cite this article

Abstract

Genome-wide association studies (GWAS) have identified over 300 regions associated with more than 70 common diseases1. However, identifying causal genes within an associated region remains a major challenge1,2. One approach to resolving causal genes is through the dissection of gene-phenotype correlations. Here we use polychromatic flow cytometry to show that differences in surface expression of the human interleukin-2 (IL-2) receptor alpha (IL2RA, or CD25) protein are restricted to particular immune cell types and correlate with several haplotypes in the IL2RA region that have previously been associated with two autoimmune diseases, type 1 diabetes (T1D) and multiple sclerosis2,3,4. We confirm our strongest gene-phenotype correlation at the RNA level by allele-specific expression (ASE). We also define key parameters for the design and implementation of post-GWAS gene-phenotype investigations and demonstrate the usefulness of a large bioresource of genotype-selectable normal donors from whom fresh, primary cells can be analyzed.

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Figure 1: The four common IL2RA (CD25) haplotypes and summary of the subject statistics by haplotype group.
Figure 2: Gating strategy for CD4+ T-cell subsets.
Figure 3: IL2RA genotype and CD4+ T-cell phenotype correlations.
Figure 4: IL-2 secretion by stimulated CD69+ CD4+ T-cell subsets.

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Acknowledgements

We gratefully acknowledge the participation of all Cambridge BioResource subjects. We thank R. Bailey, P. Clarke, H. Stevens, S. Duley, D. Harrison, M. Maisuria, T. Mistry and N. Taylor for DNA sample preparation and D. Smyth for genotype double scoring. We thank J. Casey, W. Herring, K. Hodge, H. Lloyd-Jones, R. Walker and M. Wiesner for donor coordination and blood sample obtainment and J. Clark for help with immunostaining. We thank T. Attwood for his contribution to sample management. We thank the other members of the Cambridge BioResource Management Committee: D. Dunger, S. O'Rahilly, D. Savage, J. Sambrook, A. Calder, W. Marslen-Wilson, K. Chatterjee and C. Saunders. We acknowledge use of the DNA from the British 1958 Birth Cohort collection, funded by the Medical Research Council and Wellcome Trust. We thank the Avon Longitudinal Study of Parents and Children laboratory in Bristol and the British 1958 Birth Cohort team, including S. Ring, R. Jones, M. Pembrey, W. McArdle, D. Strachan and P. Burton, for preparing and providing the control DNA samples. We also thank the Wellcome Trust, the Juvenile Diabetes Research Foundation (JDRF) International and the National Institute for Health Research Cambridge Biomedical Research Centre for funding. This work was also supported by a National Institutes of Health (USA) grant P01 AI39671 and a grant from the JDRF UK Centre for Diabetes Genes, Autoimmunity and Prevention (D-GAP; 4-2007-1003). The Cambridge Institute for Medical Research is the recipient of a Wellcome Trust Strategic Award (079895). L.S.W. is a Juvenile Diabetes Research Foundation/Wellcome Trust Principal Research Fellow.

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Authors and Affiliations

  1. Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK

    Calliope A Dendrou, Vincent Plagnol, Erik Fung, Jennie H M Yang, Kate Downes, Jason D Cooper, Sarah Nutland, Gillian Coleman, Matthew Himsworth, Matthew Hardy, Oliver Burren, Barry Healy, Neil M Walker, John A Todd & Linda S Wicker

  2. Department of Haematology, University of Cambridge and NHS Blood and Transplant Cambridge, Long Road, Cambridge, UK

    Kerstin Koch & Willem H Ouwehand

  3. Human Genetics Department, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

    Willem H Ouwehand

  4. Respiratory Medicine Division, Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's and Papworth Hospitals, Cambridge, UK

    John R Bradley

  5. Medical Research Council Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Hills Road, Cambridge, UK

    Nicholas J Wareham

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  1. Calliope A Dendrou
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Contributions

C.A.D. contributed to the conception, design and coordination of the study, performed and analyzed all experiments except those involving monocytes and the allele-specific expression assays, and drafted the manuscript. V.P. contributed to the design of the study, statistical analysis of immunophenotyping data and graphical displays. E.F. contributed to the conception and design of the study and performed the monocyte activation experiments. J.H.M.Y. contributed to PBMC manipulation and stimulations and performed the allele-specific expression assays. K.D. and J.D.C. contributed to the genetic data analysis. G.C. and M. Himsworth contributed to blood sample preparation. M. Hardy performed the genotyping and K.D. contributed to genotype double scoring. S.N. coordinated collection of the blood samples for this study. N.M.W. contributed to the coordination of the study. S.N., K.K., W.H.O., J.R.B., N.J.W. and J.A.T. are members of the Cambridge BioResource (CBR) Management Committee who had a primary role in the creation and management of the CBR. N.M.W., O.B. and B.H. managed the data. J.A.T. and L.S.W. participated in the conception, design and coordination of the study, data analysis and drafting of the manuscript.

Corresponding author

Correspondence to Linda S Wicker.

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Dendrou, C., Plagnol, V., Fung, E. et al. Cell-specific protein phenotypes for the autoimmune locus IL2RA using a genotype-selectable human bioresource. Nat Genet 41, 1011–1015 (2009). https://doi.org/10.1038/ng.434

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