Abstract

Susceptibility and protection against human autoimmune diseases, including type I diabetes, multiple sclerosis, and Goodpasture disease, is associated with particular human leukocyte antigen (HLA) alleles. However, the mechanisms underpinning such HLA-mediated effects on self-tolerance remain unclear. Here we investigate the molecular mechanism of Goodpasture disease, an HLA-linked autoimmune renal disorder characterized by an immunodominant CD4+ T-cell self-epitope derived from the α3 chain of type IV collagen (α3135–145)1,2,3,4. While HLA-DR15 confers a markedly increased disease risk, the protective HLA-DR1 allele is dominantly protective in trans with HLA-DR15 (ref. 2). We show that autoreactive α3135–145-specific T cells expand in patients with Goodpasture disease and, in α3135–145-immunized HLA-DR15 transgenic mice, α3135–145-specific T cells infiltrate the kidney and mice develop Goodpasture disease. HLA-DR15 and HLA-DR1 exhibit distinct peptide repertoires and binding preferences and present the α3135–145 epitope in different binding registers. HLA-DR15-α3135–145 tetramer+ T cells in HLA-DR15 transgenic mice exhibit a conventional T-cell phenotype (Tconv) that secretes pro-inflammatory cytokines. In contrast, HLA-DR1-α3135–145 tetramer+ T cells in HLA-DR1 and HLA-DR15/DR1 transgenic mice are predominantly CD4+Foxp3+ regulatory T cells (Treg cells) expressing tolerogenic cytokines. HLA-DR1-induced Treg cells confer resistance to disease in HLA-DR15/DR1 transgenic mice. HLA-DR15+ and HLA-DR1+ healthy human donors display altered α3135–145-specific T-cell antigen receptor usage, HLA-DR15-α3135–145 tetramer+ Foxp3 Tconv and HLA-DR1-α3135–145 tetramer+ Foxp3+CD25hiCD127lo Treg dominant phenotypes. Moreover, patients with Goodpasture disease display a clonally expanded α3135–145-specific CD4+ T-cell repertoire. Accordingly, we provide a mechanistic basis for the dominantly protective effect of HLA in autoimmune disease, whereby HLA polymorphism shapes the relative abundance of self-epitope specific Treg cells that leads to protection or causation of autoimmunity.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

References

  1. 1.

    , , & Alport’s syndrome, Goodpasture’s syndrome, and type IV collagen. N. Engl. J. Med. 348, 2543–2556 (2003)

  2. 2.

    & The HLA complex in Goodpasture’s disease: a model for analyzing susceptibility to autoimmunity. Kidney Int. 56, 1638–1653 (1999)

  3. 3.

    et al. The fine specificity and cytokine profile of T-helper cells responsive to the α3 chain of type IV collagen in Goodpasture’s disease. J. Am. Soc. Nephrol. 14, 2801–2812 (2003)

  4. 4.

    et al. The HLA-DRB1*15:01-restricted Goodpasture’s T cell epitope induces GN. J. Am. Soc. Nephrol. 24, 419–431 (2013)

  5. 5.

    et al. Regulation by CD25+ lymphocytes of autoantigen-specific T-cell responses in Goodpasture’s (anti-GBM) disease. Kidney Int. 64, 1685–1694 (2003)

  6. 6.

    , & Identification of a motif for HLA-DR1 binding peptides using M13 display libraries. J. Exp. Med. 176, 1007–1013 (1992)

  7. 7.

    et al. Ligand motifs of HLA-DRB5*0101 and DRB1*1501 molecules delineated from self-peptides. J. Immunol. 153, 1665–1673 (1994)

  8. 8.

    et al. HLA-DR15-derived self-peptides are involved in increased autologous T cell proliferation in multiple sclerosis. Brain 136, 1783–1798 (2013)

  9. 9.

    et al. The dendritic cell major histocompatibility complex II (MHC II) peptidome derives from a variety of processing pathways and includes peptides with a broad spectrum of HLA-DM sensitivity. J. Biol. Chem. 291, 5576–5595 (2016)

  10. 10.

    , , , & A systems approach to understand antigen presentation and the immune response. Methods Mol. Biol. 1394, 189–209 (2016)

  11. 11.

    et al. A molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis. J. Exp. Med. 210, 2569–2582 (2013)

  12. 12.

    et al. Immune self-reactivity triggered by drug-modified HLA-peptide repertoire. Nature 486, 554–558 (2012)

  13. 13.

    , , & Structural basis for the binding of an immunodominant peptide from myelin basic protein in different registers by two HLA-DR2 proteins. J. Mol. Biol. 304, 177–188 (2000)

  14. 14.

    , , & IL-23, not IL-12, directs autoimmunity to the Goodpasture antigen. J. Am. Soc. Nephrol. 20, 980–989 (2009)

  15. 15.

    & Genetic protection from the inflammatory disease type 1 diabetes in humans and animal models. Immunity 15, 387–395 (2001)

  16. 16.

    et al. Functional epistasis on a common MHC haplotype associated with multiple sclerosis. Nature 443, 574–577 (2006)

  17. 17.

    et al. HLA-DQ-associated predisposition to and dominant HLA-DR-associated protection against rheumatoid arthritis. Hum. Immunol. 60, 152–158 (1999)

  18. 18.

    et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439, 851–855 (2006)

  19. 19.

    et al. Biased T cell receptor usage directed against human leukocyte antigen DQ8-restricted gliadin peptides is associated with celiac disease. Immunity 37, 611–621 (2012)

  20. 20.

    et al. T-cell receptor recognition of HLA-DQ2-gliadin complexes associated with celiac disease. Nature Struct. Mol. Biol. 21, 480–488 (2014)

  21. 21.

    , , , & The isolation and purification of biologically active recombinant and native autoantigens for the study of autoimmune disease. J. Immunol. Methods 308, 167–178 (2006)

  22. 22.

    et al. The Goodpasture autoantigen. Mapping the major conformational epitope(s) of alpha3(IV) collagen to residues 17–31 and 127–141 of the NC1 domain. J. Biol. Chem. 274, 11267–11274 (1999)

  23. 23.

    et al. Healthy individuals have Goodpasture autoantigen-reactive T cells. J. Am. Soc. Nephrol. 19, 396–404 (2008)

  24. 24.

    et al. Paired analysis of TCRα and TCRβ chains at the single-cell level in mice. J. Clin. Invest. 121, 288–295 (2011)

  25. 25.

    , , , & T cell receptor αβ diversity inversely correlates with pathogen-specific antibody levels in human cytomegalovirus infection. Sci. Transl. Med. 4, 128ra42 (2012)

  26. 26.

    et al. IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res. 37, D1006–D1012 (2009)

  27. 27.

    et al. Constitutive and inflammatory immunopeptidome of pancreatic β-cells. Diabetes 61, 3018–3025 (2012)

  28. 28.

    et al. The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol. Cell. Proteomics 6, 1638–1655 (2007)

  29. 29.

    , , , & A comprehensive analysis of constitutive naturally processed and presented HLA-C*04:01 (Cw4)-specific peptides. Tissue Antigens 83, 174–179 (2014)

  30. 30.

    et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 44 (D1), D447–D456 (2016)

  31. 31.

    et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009)

  32. 32.

    , , , & Improved visualization of protein consensus sequences by iceLogo. Nature Methods 6, 786–787 (2009)

  33. 33.

    et al. MX1: a bending-magnet crystallography beamline serving both chemical and macromolecular crystallography communities at the Australian Synchrotron. J. Synchrotron Radiat. 22, 187–190 (2015)

  34. 34.

    et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D 67, 235–242 (2011)

  35. 35.

    et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)

  36. 36.

    , , & Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010)

  37. 37.

    et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

Download references

Acknowledgements

We thank the staff of the Australian Synchrotron (beamline MX1 and MX2) for assistance with data collection and donors of the Australian Bone Marrow Donor Registry for blood samples. This study was supported by grants from the National Health and Medical Research Council of Australia (NHMRC), 1048575 and 1079648 to A.R.K., 334067 to A.R.K. and S.R.H., and 1071916 to N.L.L.G. N.L.L.G. is supported by a Sylvia and Charles Viertel Senior Medical Research Fellowship. A.W.P. is supported by an NHMRC Senior Research Fellowship. J.R. is supported by an Australian Research Council Laureate Fellowship.

Author information

Author notes

    • Katherine A. Watson

    Present address: Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.

    • Joshua D. Ooi
    •  & Jan Petersen

    These authors contributed equally to this work.

    • Hugh H. Reid
    • , Jamie Rossjohn
    •  & A. Richard Kitching

    These authors jointly supervised this work.

Affiliations

  1. Centre for Inflammatory Diseases, Monash University Department of Medicine, Monash Medical Centre, Clayton, Victoria 3168, Australia

    • Joshua D. Ooi
    • , Megan Huynh
    • , Zoe J. Willett
    • , Peter J. Eggenhuizen
    • , Poh Y. Gan
    • , Maliha A. Alikhan
    • , Stephen R. Holdsworth
    •  & A. Richard Kitching
  2. Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia

    • Jan Petersen
    • , Yu H. Tan
    • , Sri H. Ramarathinam
    • , Khai L. Loh
    • , Nadine L. Dudek
    • , Anthony W. Purcell
    • , Nicole L. La Gruta
    • , Hugh H. Reid
    •  & Jamie Rossjohn
  3. Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia

    • Jan Petersen
    • , Hugh H. Reid
    •  & Jamie Rossjohn
  4. Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3010, Australia

    • Katherine A. Watson
    •  & Nicole L. La Gruta
  5. Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia 30602, USA

    • Andreas Handel
  6. Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA

    • Billy G. Hudson
  7. Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK

    • Lars Fugger
  8. Department of Nephrology, Austin Health, Heidelberg, Victoria 3084, Australia

    • David A. Power
  9. Department of Medicine, University of Melbourne, Melbourne, Victoria 3010, Australia

    • David A. Power
    •  & Stephen G. Holt
  10. Department of Nephrology, The Royal Melbourne Hospital, Parkville, Victoria 3050, Australia

    • Stephen G. Holt
  11. Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia 5000, Australia

    • P. Toby Coates
  12. Department of Medicine, Viborg Regional Hospital, Viborg 8800, Denmark

    • Jon W. Gregersen
  13. Department of Nephrology, Monash Health, Clayton, Victoria 3168, Australia

    • Stephen R. Holdsworth
    •  & A. Richard Kitching
  14. Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK

    • Jamie Rossjohn
  15. NHMRC Centre for Personalised Immunology, Monash University, Clayton, Victoria 3168, Australia

    • A. Richard Kitching
  16. Department of Pediatric Nephrology, Monash Health, Victoria 3168, Australia

    • A. Richard Kitching

Authors

  1. Search for Joshua D. Ooi in:

  2. Search for Jan Petersen in:

  3. Search for Yu H. Tan in:

  4. Search for Megan Huynh in:

  5. Search for Zoe J. Willett in:

  6. Search for Sri H. Ramarathinam in:

  7. Search for Peter J. Eggenhuizen in:

  8. Search for Khai L. Loh in:

  9. Search for Katherine A. Watson in:

  10. Search for Poh Y. Gan in:

  11. Search for Maliha A. Alikhan in:

  12. Search for Nadine L. Dudek in:

  13. Search for Andreas Handel in:

  14. Search for Billy G. Hudson in:

  15. Search for Lars Fugger in:

  16. Search for David A. Power in:

  17. Search for Stephen G. Holt in:

  18. Search for P. Toby Coates in:

  19. Search for Jon W. Gregersen in:

  20. Search for Anthony W. Purcell in:

  21. Search for Stephen R. Holdsworth in:

  22. Search for Nicole L. La Gruta in:

  23. Search for Hugh H. Reid in:

  24. Search for Jamie Rossjohn in:

  25. Search for A. Richard Kitching in:

Contributions

J.D.O., J.P., H.H.R, J.R. and A.R.K. initiated and designed the research and wrote the manuscript. J.D.O., J.P., Y.H.T., M.H., Z.J.W., N.L.D., P.J.E., K.L.L, K.A.W., P.Y.G., M.A.A., S.H.R. and H.H.R. performed experiments. D.A.P., S.G.H., P.T.C. and J.W.G. provided blood samples and clinicopathological information from patients with Goodpasture disease. A.H., B.G.H., L.F., A.W.P., S.R.H. and N.L.L.G. provided intellectual input and technical support. J.D.O. and J.P. are joint first authors. H.H.R., J.R. and A.R.K. are the co-corresponding and co-senior authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Hugh H. Reid or Jamie Rossjohn or A. Richard Kitching.

Reviewer Information Nature thanks H.-G. Rammensee, D. Wraith and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Data

    This file contains peptide repertoires eluted from human BLCLs IHW09013 (DR15+/DR51+) and IHW09004 (HLA-DR1+).

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature22329

Further reading

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.

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