Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

An IRF8-binding promoter variant and AIRE control CHRNA1 promiscuous expression in thymus

Abstract

Promiscuous expression of tissue-restricted auto-antigens in the thymus imposes T-cell tolerance and provides protection from autoimmune diseases1,2,3. Promiscuous expression of a set of self-antigens occurs in medullary thymic epithelial cells4,5 and is partly controlled by the autoimmune regulator (AIRE), a nuclear protein for which loss-of-function mutations cause the type 1 autoimmune polyendocrine syndrome6,7. However, additional factors must be involved in the regulation of this promiscuous expression. Here we describe a mechanism controlling thymic transcription of a prototypic tissue-restricted human auto-antigen gene, CHRNA1. This gene encodes the α-subunit of the muscle acetylcholine receptor, which is the main target of pathogenic auto-antibodies in autoimmune myasthenia gravis8,9. On re-sequencing the CHRNA1 gene, we identified a functional bi-allelic variant in the promoter that is associated with early onset of disease in two independent human populations (France and United Kingdom). We show that this variant prevents binding of interferon regulatory factor 8 (IRF8) and abrogates CHRNA1 promoter activity in thymic epithelial cells in vitro. Notably, both the CHRNA1 promoter variant and AIRE modulate CHRNA1 messenger RNA levels in human medullary thymic epithelial cells ex vivo and also in a transactivation assay. These findings reveal a critical function of AIRE and the interferon signalling pathway in regulating quantitative expression of this auto-antigen in the thymus, suggesting that together they set the threshold for self-tolerance versus autoimmunity.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Purchase on Springer Link

Instant access to full article PDF

Prices may be subject to local taxes which are calculated during checkout

Figure 1: rs16862847 allele variation affects IRF8 binding.
Figure 2: Characterization of IRF8-dependent CHRNA1 transcriptional activity in the TEC line.
Figure 3: Effect of rs16862847 and AIRE on CHRNA1 expression levels in mTECs.

Similar content being viewed by others

References

  1. Mathis, D. & Benoist, C. Back to central tolerance. Immunity 20, 509–516 (2004)

    Article  CAS  Google Scholar 

  2. Liston, A., Lesage, S., Gray, D. H., Boyd, R. L. & Goodnow, C. C. Genetic lesions in T-cell tolerance and thresholds for autoimmunity. Immunol. Rev. 204, 87–101 (2005)

    Article  CAS  Google Scholar 

  3. Kyewski, B. & Klein, L. A central role for central tolerance. Annu. Rev. Immunol. 24, 571–606 (2006)

    Article  CAS  Google Scholar 

  4. Anderson, M. S. et al. Projection of an immunological self shadow within the thymus by the Aire protein. Science 298, 1395–1401 (2002)

    Article  ADS  CAS  Google Scholar 

  5. Derbinski, J. et al. Promiscuous gene expression in thymic epithelial cells is regulated at multiple levels. J. Exp. Med. 202, 33–45 (2005)

    Article  CAS  Google Scholar 

  6. Nagamine, K. et al. Positional cloning of the APECED gene. Nature Genet. 17, 393–398 (1997)

    Article  CAS  Google Scholar 

  7. The Finnish-German APECED Consortium. An autoimmune disease, APECED, caused by mutations in a novel gene featuring two PHD-type zinc-finger domains. Nature Genet. 17, 399–403 (1997)

  8. Drachman, D. B. Myasthenia gravis. N. Engl. J. Med. 330, 1797–1810 (1994)

    Article  CAS  Google Scholar 

  9. Vincent, A. Unravelling the pathogenesis of myasthenia gravis. Nature Rev. Immunol. 2, 797–804 (2002)

    Article  CAS  Google Scholar 

  10. Tamura, T., Thotakura, P., Tanaka, T. S., Ko, M. S. & Ozato, K. Identification of target genes and a unique cis element regulated by IRF-8 in developing macrophages. Blood 106, 1938–1947 (2005)

    Article  CAS  Google Scholar 

  11. Barnes, B., Lubyova, B. & Pitha, P. M. On the role of IRF in host defense. J. Interferon Cytokine Res. 22, 59–71 (2002)

    Article  CAS  Google Scholar 

  12. Lohoff, M. & Mak, T. W. Roles of interferon-regulatory factors in T-helper-cell differentiation. Nature Rev. Immunol. 5, 125–135 (2005)

    Article  CAS  Google Scholar 

  13. Holtschke, T. et al. Immunodeficiency and chronic myelogenous leukemia-like syndrome in mice with a targeted mutation of the ICSBP gene. Cell 87, 307–317 (1996)

    Article  CAS  Google Scholar 

  14. Pagani, F. et al. A new type of mutation causes a splicing defect in ATM. Nature Genet. 30, 426–429 (2002)

    Article  CAS  Google Scholar 

  15. Fernandez, E. et al. Establishment and characterization of cloned human thymic epithelial cell lines. Analysis of adhesion molecule expression and cytokine production. Blood 83, 3245–3254 (1994)

    CAS  PubMed  Google Scholar 

  16. Kyewski, B. & Derbinski, J. Self-representation in the thymus: an extended view. Nature Rev. Immunol. 4, 688–698 (2004)

    Article  CAS  Google Scholar 

  17. Sillanpaa, N. et al. Autoimmune regulator induced changes in the gene expression profile of human monocyte-dendritic cell-lineage. Mol. Immunol. 41, 1185–1198 (2004)

    Article  CAS  Google Scholar 

  18. Pitkanen, J. et al. Cooperative activation of transcription by autoimmune regulator AIRE and CBP. Biochem. Biophys. Res. Commun. 333, 944–953 (2005)

    Article  CAS  Google Scholar 

  19. Vafiadis, P. et al. Insulin expression in human thymus is modulated by INS VNTR alleles at the IDDM2 locus. Nature Genet. 15, 289–292 (1997)

    Article  CAS  Google Scholar 

  20. Pugliese, A. et al. The insulin gene is transcribed in the human thymus and transcription levels correlated with allelic variation at the INS VNTR-IDDM2 susceptibility locus for type 1 diabetes. Nature Genet. 15, 293–297 (1997)

    Article  CAS  Google Scholar 

  21. Sabater, L. et al. Insulin alleles and autoimmune regulator (AIRE) gene expression both influence insulin expression in the thymus. J. Autoimmun. 25, 312–318 (2005)

    Article  CAS  Google Scholar 

  22. Taubert, R., Schwendemann, J. & Kyewski, B. Highly variable expression of tissue-restricted self-antigens in human thymus: implications for self-tolerance and autoimmunity. Eur. J. Immunol. 37, 838–848 (2007)

    Article  CAS  Google Scholar 

  23. Chentoufi, A. A. & Polychronakos, C. Insulin expression levels in the thymus modulate insulin-specific autoreactive T-cell tolerance: the mechanism by which the IDDM2 locus may predispose to diabetes. Diabetes 51, 1383–1390 (2002)

    Article  CAS  Google Scholar 

  24. Thebault-Baumont, K. et al. Acceleration of type 1 diabetes mellitus in proinsulin 2-deficient NOD mice. J. Clin. Invest. 111, 851–857 (2003)

    Article  CAS  Google Scholar 

  25. Liston, A. et al. Gene dosage–limiting role of Aire in thymic expression, clonal deletion, and organ-specific autoimmunity. J. Exp. Med. 200, 1015–1026 (2004)

    Article  CAS  Google Scholar 

  26. Ewing, B., Hillier, L., Wendl, M. C. & Green, P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185 (1998)

    Article  CAS  Google Scholar 

  27. Carlson, C. S. et al. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet. 74, 106–120 (2004)

    Article  CAS  Google Scholar 

  28. Gotter, J., Brors, B., Hergenhahn, M. & Kyewski, B. Medullary epithelial cells of the human thymus express a highly diverse selection of tissue-specific genes colocalized in chromosomal clusters. J. Exp. Med. 199, 155–166 (2004)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This study was funded by INSERM (Institut National de la Santé et de la Recherche Médicale) and the Association Française contre les Myopathies. M.G. was supported by a fellowship of the Fondation pour la Recherche Médicale in Oxford and of the European Molecular Biology Organization in Trieste. R.T. and B.K. have been supported by the DKFZ, the Sonderforschungsbereich 405 and EU-Thymaide; F.E.B. and F.P. by the Associazione Italiana Ricerca Cancro. D.B., N.W. and A.V. thank the UK MRC, Muscular Dystrophy Campaign and the Myasthenia Gravis Association for support. We thank the participating patients. We thank J. Newsom-Davis for clinical samples and expertise; S. Krumeich and G. Picarda for technical assistance; W. Savino for providing us with an aliquot of the TEC line; A. Harris for advice on EMSA; M. Lathrop for advice on genetic data analysis; P. Peterson for the gift of the AIRE expression plasmid; S. Hagl and members of the Department of Cardiac Surgery for providing human thymic tissue; K. Hexel and M. Scheuermann for cell sorting; G. Moldenhauer for providing monoclonal antibodies; and A. Kopp-Schneider for statistical analysis.

Author Contributions M.G. did the genomic experiments, EMSAs, made the reporter constructs, carried out transfections, RNAi and ChIP, analysed the data, and wrote the manuscript; R.T. carried out the experiments related to thymic gene expression; C.V. did genotyping and edited the manuscript; X.K. analysed the genetic data and edited the manuscript; M.L.-S. provided expertise to M.G. on gene cloning and proofread the manuscript; F.P. and F.E.B. provided expertise on RNA splicing analysis to M.G., when he was in Trieste, and proofread the manuscript; B.E., C.T. and P.G. recruited the French patients; A.V. and N.W. helped plan the project, provided access to the UK cohort and edited the manuscript; D.B. helped devise the experiments related to EMSAs and luciferase reporter constructs, supervised M.G. when he was in Oxford, and edited the manuscript; B.K. devised and supervised experiments related to promiscuous gene expression and wrote the manuscript; H.-J.G. coordinated the project, analysed the data and wrote the manuscript.

Newly identified SNPs (listed with an asterisk in Supplementary Table 1; accession numbers also listed) have been deposited in dbSNP.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Henri-Jean Garchon.

Ethics declarations

Competing interests

Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Tables 1-4 and Supplementary Figures 1-8 with Legends, Supplementary Discussion and additional references. (PDF 2885 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Giraud, M., Taubert, R., Vandiedonck, C. et al. An IRF8-binding promoter variant and AIRE control CHRNA1 promiscuous expression in thymus. Nature 448, 934–937 (2007). https://doi.org/10.1038/nature06066

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature06066

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing