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.

  • Article
  • Published:

Distinct editing functions of natural HLA-DM allotypes impact antigen presentation and CD4+ T cell activation

Cellular & Molecular Immunology volume 17, pages 133–142 (2020)Cite this article

Subjects

Abstract

Classical human leukocyte antigen (HLA) molecules of the major histocompatibility class II (MHCII) complex present peptides for the development, surveillance and activation of CD4+ T cells. The nonclassical MHCII-like protein HLA-DM (DM) catalyzes the exchange and loading of peptides onto MHCII molecules, thereby shaping MHCII immunopeptidomes. Natural variations of DM in both chains of the protein (DMA and DMB) have been hypothesized to impact peptide presentation, but no evidence for altered function has been reported. Here we define the presence of DM allotypes in human populations covered by the 1000 Genomes Project and probe their activity. The functional properties of several allotypes are investigated and show strong enhancement of peptide-induced T cell activation for a particular combination of DMA and DMB. Biochemical evidence suggests a broader pH activity profile for the new variant relative to that of the most commonly expressed DM allotype. Immunopeptidome analysis indicates that the compartmental activity of the new DM heterodimer extends beyond the late endosome and suggests that the natural variation of DM has profound effects on adaptive immunity when antigens bypass the canonical processing pathway.

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
Buy now

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Blum, J. S., Wearsch, P. A. & Cresswell, P. Pathways of antigen processing. Annu. Rev. Immunol. 31, 443–473 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Mellins, E. et al. Defective processing and presentation of exogenous antigens in mutants with normal HLA class II genes. Nature 343, 71–74 (1990).

    Article  CAS  PubMed  Google Scholar 

  3. Sloan, V. S. et al. Mediation by HLA-DM of dissociation of peptides from HLA-DR. Nature 375, 802–806 (1995).

    Article  CAS  PubMed  Google Scholar 

  4. Grotenbreg, G. M. et al. Empty class II major histocompatibility complex created by peptide photolysis establishes the role of DM in peptide association. J. Biol. Chem. 282, 21425–21436 (2007).

    Article  CAS  PubMed  Google Scholar 

  5. Wieczorek, M. et al. MHC class II complexes sample intermediate states along the peptide exchange pathway. Nat. Commun. 7, 13224 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Wieczorek M, Tolba ET, Stich J, Álvaro-Benito M, Stolzenberg S, Noe F, Freund C. Conformational plasticity of MHC proteins. Frontiers Immunol. 8, 292 (2017).

  7. Guce, A. I. et al. HLA-DO acts as a substrate mimic to inhibit HLA-DM by a competitive mechanism. Nat. Struct. Mol. Biol. 20, 90–98 (2013).

    Article  CAS  PubMed  Google Scholar 

  8. Unanue, E. R., Turk, V. & Neefjes, J. Variations in MHC class II antigen processing and presentation in health and disease. Annu. Rev. Immunol. 34, 265–300 (2016).

    Article  CAS  PubMed  Google Scholar 

  9. Lindner, R. & Unanue, E. R. Distinct antigen MHC class II complexes generated by separate processing pathways. EMBO J. 15, 6910–6920 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Amria, S. et al. HLA‐DM negatively regulates HLA-DR4-restricted collagen pathogenic peptide presentation and T cell recognition. Eur. J. Immunol. 38, 1961–1970 (2008).

    Article  CAS  PubMed  Google Scholar 

  11. Hou, T. et al. An insertion mutant in DQA1*0501 restores susceptibility to HLA-DM: implications for disease associations. J. Immunol. 187, 2442–2452 (2011).

    Article  CAS  PubMed  Google Scholar 

  12. Mohan, J. F., Petzold, S. J. & Unanue, E. R. Register shifting of an insulin peptide-MHC complex allows diabetogenic T cells to escape thymic deletion. J. Exp. Med. 208, 2375–2383 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kremer, A. N. et al. Endogenous HLA class II epitopes that are immunogenic in vivo show distinct behavior toward HLA-DM and its natural inhibitor HLA-DO. Blood 120, 3246–3255 (2012).

    Article  CAS  PubMed  Google Scholar 

  14. Rosskopf, S. et al. Creation of an engineered APC system to explore and optimize the presentation of immunodominant peptides of major allergens. Sci. Rep. 6, 31580 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Álvaro-Benito, M., Morrison, E., Wieczorek, M., Sticht, J. & Freund, C. Human leukocyte antigen-DM polymorphisms in autoimmune diseases. Open Biol. 6, 160165 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  16. Pierre, P. et al. HLA-DM is localized to conventional and unconventional MHC class II–containing endocytic compartments. Immunity 4, 229–239 (1996).

    Article  CAS  PubMed  Google Scholar 

  17. Arndt, S. O. et al. Functional HLA‐DM on the surface of B cells and immature dendritic cells. EMBO J. 19, 1241–1251 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Álvaro-Benito, M., Wieczorek, M., Sticht, J., Kipar, C. & Freund, C. HLA-DMA polymorphisms differentially affect MHC class II peptide loading. J. Immunol. 194, 803–816 (2014).

    Article  PubMed  CAS  Google Scholar 

  19. Denzin, L. K. et al. Neutralizing antibody responses to viral infections are linked to the non-classical MHC class II gene H2-Ob. Immunity 47, 310–322.e7 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Robinson, J. et al. The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Res. 43, D423–D431 (2015).

    Article  CAS  PubMed  Google Scholar 

  22. Gibbs, R. A. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015).

    Article  CAS  Google Scholar 

  23. Pos, W. et al. Crystal structure of the HLA-DM–HLA-DR1 complex defines mechanisms for rapid peptide selection. Cell 151, 1557–1568 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Barrett, J. C., Fry, B., Maller, J. & Daly, M. J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265 (2005).

    Article  CAS  PubMed  Google Scholar 

  25. Weber, D. A., Dao, C. T., Jun, J., Wigal, J. L. & Jensen, P. E. Transmembrane domain-mediated colocalization of HLA-DM and HLA-DR is required for optimal HLA-DM catalytic activity. J. Immunol. 167, 5167–5174 (2001).

    Article  CAS  PubMed  Google Scholar 

  26. Denzin, L. K., Robbins, N. F., Carboy-Newcomb, C. & Cresswell, P. Assembly and intracellular transport of HLA-DM and correction of the class II antigen-processing defect in T2 cells. Immunity 1, 595–606 (1994).

    Article  CAS  PubMed  Google Scholar 

  27. Álvaro-Benito, M., Morrison, E., Abualrous, E. T., Kuropka, B. & Freund, C. Quantification of HLA-DM-dependent major histocompatibility complex of class II immunopeptidomes by the peptide landscape antigenic epitope alignment utility. Front. Immunol. 9, 872 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Ramachandra, L., Kovats, S., Eastman, S. & Rudensky, A. Y. Variation in HLA-DM expression influences conversion of MHC class II alpha beta:class II-associated invariant chain peptide complexes to mature peptide-bound class II alpha beta dimers in a normal B cell line. J. Immunol. 156, 2196–2204 (1996).

    CAS  PubMed  Google Scholar 

  29. Cox, J. & Mann, M. 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. BMC Bioinformatics 13(Suppl 16), S12 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Feng, M. L. et al. Analysis of HLA-DM polymorphisms in the Chinese Han population. Tissue Antigens 79, 157–164 (2012).

    Article  CAS  PubMed  Google Scholar 

  31. Hughes, A. L. & Nei, M. Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection. Proc. Natl Acad. Sci. USA 86, 958–962 (1989).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Hughes, A. L., Hughes, M. K., Howell, C. Y. & Nei, M. Natural selection at the class II major histocompatibility complex loci of mammals. Philos. Trans. R. Soc. Lond. B Biol. Sci. 346, 359–366 (1994).

    Article  CAS  PubMed  Google Scholar 

  33. Denzin, L. K. & Cresswell, P. HLA-DM induces clip dissociation from MHC class II αβ dimers and facilitates peptide loading. Cell 82, 155–165 (1995).

    Article  CAS  PubMed  Google Scholar 

  34. Pu, Z., Lovitch, S. B., Bikoff, E. K. & Unanue, E. R. T cells distinguish MHC-peptide complexes formed in separate vesicles and edited by H2-DM. Immunity 20, 467–476 (2004).

    Article  CAS  PubMed  Google Scholar 

  35. Stadinski, B. D. et al. Diabetogenic T cells recognize insulin bound to IAg7 in an unexpected, weakly binding register. Proc. Natl Acad. Sci. USA 107, 10978–10983 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Fremont, D. H., Crawford, F., Marrack, P., Hendrickson, W. A. & Kappler, J. Crystal structure of mouse H2-M. Immunity 9, 385–393 (1998).

    Article  CAS  PubMed  Google Scholar 

  37. Busch, R., Reich, Z., Zaller, D. M., Sloan, V. & Mellins, E. D. Secondary structure composition and pH-dependent conformational changes of soluble recombinant HLA-DM. J. Biol. Chem. 273, 27557–27564 (1998).

    Article  CAS  PubMed  Google Scholar 

  38. Pashine, A. et al. Interaction of HLA-DR with an acidic face of HLA-DM disrupts sequence-dependent interactions with peptides. Immunity 19, 183–192 (2003).

    Article  CAS  PubMed  Google Scholar 

  39. Nicholson, M. J. et al. Small molecules that enhance the catalytic efficiency of HLA-DM. J. Immunol. 176, 4208–4220 (2006).

    Article  CAS  PubMed  Google Scholar 

  40. Zhou, Z. & Jensen, P. E. Structural characteristics of HLA-DQ that may impact DM editing and susceptibility to type-1 diabetes. Front. Immunol. 4, 262 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Zhou, Z. et al. Type 1 diabetes associated HLA-DQ2 and DQ8 molecules are relatively resistant to HLA-DM mediated release of invariant chain-derived CLIP peptides. Eur. J. Immunol. 46, 834–845 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. van Lith, M., McEwen-Smith, R. M. & Benham, A. M. H. L. A.-D. P. HLA-DQ, and HLA-DR have different requirements for invariant chain and HLA-DM. J. Biol. Chem. 285, 40800–40808 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Garcia, K. C. & Adams, E. J. How the T cell receptor sees antigen—a structural view. Cell 122, 333–336 (2005).

    Article  CAS  PubMed  Google Scholar 

  44. Fissolo, N. et al. Naturally presented peptides on major histocompatibility complex I and II molecules eluted from central nervous system of multiple sclerosis patients. Mol. Cell Proteomics 8, 2090–2101 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Heyder, T. et al. Approach for identifying human leukocyte antigen (HLA)-DR bound peptides from scarce clinical samples. Mol. Cell Proteomics 15, 3017–3029 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Weber, K., Bartsch, U., Stocking, C. & Fehse, B. A multicolor panel of novel lentiviral "gene ontology" (LeGO) vectors for functional gene analysis. Mol. Ther. 16, 698–706 (2008).

    Article  CAS  PubMed  Google Scholar 

  47. Bacher, P. et al. Antigen-reactive T cell enrichment for direct, high-resolution analysis of the human naive and memory Th cell repertoire. J. Immunol. 190, 3967–3976 (2013).

    Article  CAS  PubMed  Google Scholar 

  48. Webb, B. & Sali, A. Comparative protein structure modeling using MODELLER. Curr. Protoc. Bioinformatics 54, 5.6.1–5.6.37 (2016).

    Article  Google Scholar 

  49. Olsson, M. H. M., Søndergaard, C. R., Rostkowski, M. & Jensen, J. H. PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J. Chem. Theory Comput. 7, 525–537 (2011).

    Article  CAS  PubMed  Google Scholar 

  50. Pronk, S. et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845–854 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Case, D. A. et al. The Amber biomolecular simulation programs. J. Comput. Chem. 26, 1668–1688 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).

    Article  CAS  PubMed  Google Scholar 

  53. Vizcaíno, J. A. et al. update of the PRIDE database and its related tools. Nucleic Acids Res. 2016, D447–D456 (2016).

    Article  CAS  Google Scholar 

  54. Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016).

    Article  CAS  PubMed  Google Scholar 

  55. Andreatta, M. et al. Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification. Immunogenetics 67, 641–650 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Álvaro-Benito M, Morrison E, Abualrous ET, Kuropka B, Freund C. Quantification of HLA-DM-dependent major histocompatibility complex of class II immunopeptidomes by the peptide landscape antigenic epitope alignment utility. Front Immunol. 9:872 (2018).

Download references

Acknowledgements

We thank Peter Cresswell for providing the cell lines used in this study. We also would like to thank the group of Petra Knaus for the S2 working space and David H. Canaday for the 9AF6 T cell hybridoma. For mass spectrometry, we would like to acknowledge the assistance of the Core Facility BioSupraMol supported by the Deutsche Forschungsgemeinschaft (DFG). C.F. is thankful for funding by the DFG (FR-1325/17–1, SFB958 (project Z03) and TRR186 (projects A05, A11)). M.A.-B. is thankful for funding from the Freie Universität Berlin Forschungskommision.

Author information

Authors and Affiliations

  1. Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany

    Miguel Álvaro-Benito, Eliot Morrison, Marie Urbicht, Marek Wieczorek & Christian Freund

  2. Institut für Immunologie, Department of Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany

    Friederike Ebner

  3. Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany

    Esam T. Abualrous

Authors
  1. Miguel Álvaro-Benito
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Eliot Morrison
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Friederike Ebner
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Esam T. Abualrous
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Marie Urbicht
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Marek Wieczorek
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Christian Freund
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

M.A.-B. designed and performed the research. E.M. contributed to the MS experiments and bioinformatics analysis. E.T.A. analyzed the influence of pH on DM structure in silico. M.U. and M.W. performed the biochemical experiments. F.E. contributed to the antigen presentation assays. C.F. initiated and supervised the project. M.A.-B. wrote the paper with support from E.M. and major input from C.F.

Corresponding authors

Correspondence to Miguel Álvaro-Benito or Christian Freund.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

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

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Álvaro-Benito, M., Morrison, E., Ebner, F. et al. Distinct editing functions of natural HLA-DM allotypes impact antigen presentation and CD4+ T cell activation. Cell Mol Immunol 17, 133–142 (2020). https://doi.org/10.1038/s41423-018-0181-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41423-018-0181-1

Keywords

This article is cited by

Search

Advanced search

Quick links