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T cell receptor cross-reactivity expanded by dramatic peptide–MHC adaptability

Nature Chemical Biologyvolume 14pages934942 (2018) | Download Citation


T cell receptor cross-reactivity allows a fixed T cell repertoire to respond to a much larger universe of potential antigens. Recent work has emphasized the importance of peptide structural and chemical homology, as opposed to sequence similarity, in T cell receptor cross-reactivity. Surprisingly, though, T cell receptors can also cross-react between ligands with little physiochemical commonalities. Studying the clinically relevant receptor DMF5, we demonstrate that cross-recognition of such divergent antigens can occur through mechanisms that involve heretofore unanticipated rearrangements in the peptide and presenting MHC protein, including binding-induced peptide register shifts and extensions from MHC peptide binding grooves. Moreover, cross-reactivity can proceed even when such dramatic rearrangements do not translate into structural or chemical molecular mimicry. Beyond demonstrating new principles of T cell receptor cross-reactivity, our results have implications for efforts to predict and control T cell specificity and cross-reactivity and highlight challenges associated with predicting T cell reactivities.

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Data availability

Crystallographic data sets are available in the PDB repository under ascension codes 6AMT (MMWDRGLGMM/HLA-A2), 6AMU (DMF5-MMWDRGLGMM/HLA-A2), and 6AM5 (DMF5-SMLGIGIVPV/HLA-A2). Other data are available from the corresponding author upon request.

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  1. 1.

    Wucherpfennig, K. W. et al. Polyspecificity of T cell and B cell receptor recognition. Semin. Immunol. 19, 216–224 (2007).

  2. 2.

    Mason, D. A very high level of crossreactivity is an essential feature of the T-cell receptor. Immunol. Today 19, 395–404 (1998).

  3. 3.

    Sewell, A. K. Why must T cells be cross-reactive? Nat. Rev. Immunol. 12, 669–677 (2012).

  4. 4.

    Wooldridge, L. et al. A single autoimmune T cell receptor recognizes more than a million different peptides. J. Biol. Chem. 287, 1168–1177 (2012).

  5. 5.

    Singh, N. K. et al. Emerging concepts in TCR specificity: rationalizing and (maybe) predicting outcomes. J. Immunol. 199, 2203–2213 (2017).

  6. 6.

    Maynard, J. et al. Structure of an autoimmune T cell receptor complexed with class II peptide- MHC: insights into MHC bias and antigen specificity. Immunity 22, 81–92 (2005).

  7. 7.

    Linette, G. P. et al. Cardiovascular toxicity and titin cross-reactivity of affinity-enhanced T cells in myeloma and melanoma. Blood 122, 863–871 (2013).

  8. 8.

    Adams, J. J. et al. Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity. Nat. Immunol. 17, 87–94 (2016).

  9. 9.

    Birnbaum, Michael E. et al. Deconstructing the peptide-MHC specificity of T cell recognition. Cell 157, 1073–1087 (2014).

  10. 10.

    Cole, D. K. et al. Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity. J. Clin. Invest. 126, 2191–2204 (2016).

  11. 11.

    Hausmann, S. et al. Peptide recognition by two HLA-A2/Tax11-19-specific T cell clones in relationship to their MHC/peptide/TCR crystal structures. J. Immunol. 162, 5389–5397 (1999).

  12. 12.

    Garboczi, D. N. et al. Structure of the complex between human T-cell receptor, viral peptide and HLA-A2. Nature 384, 134–141 (1996).

  13. 13.

    Borbulevych, O. Y., Piepenbrink, K. H. & Baker, B. M. Conformational melding permits a conserved binding geometry in TCR recognition of foreign and self molecular mimics. J. Immunol. 186, 2950–2958 (2011).

  14. 14.

    Borbulevych, O. Y. et al. T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility. Immunity 31, 885–896 (2009).

  15. 15.

    Frankild, S., de Boer, R. J., Lund, O., Nielsen, M. & Kesmir, C. Amino acid similarity accounts for T cell cross-reactivity and for ‘holes’ in the T cell repertoire. PLoS One 3, e1831 (2008).

  16. 16.

    Rubio-Godoy, V. et al. Positional scanning-synthetic peptide library-based analysis of self- and pathogen-derived peptide cross-reactivity with tumor-reactive melan-A-specific CTL. J. Immunol. 169, 5696–5707 (2002).

  17. 17.

    Dutoit, V. et al. Degeneracy of antigen recognition as the molecular basis for the high frequency of naive A2/melan-A peptide multimer+ CD8+ T cells in humans. J. Exp. Med. 196, 207–216 (2002).

  18. 18.

    Brehm, M. A. et al. T cell immunodominance and maintenance of memory regulated by unexpectedly cross-reactive pathogens. Nat. Immunol. 3, 627 (2002).

  19. 19.

    Clute, S. C. et al. Broad cross-reactive TCR repertoires recognizing dissimilar Epstein-Barr and influenza A virus epitopes. J. Immunol. 185, 6753–6764 (2010).

  20. 20.

    Miles, J. J., McCluskey, J., Rossjohn, J. & Gras, S. Understanding the complexity and malleability of T-cell recognition. Immunol. Cell Biol. 93, 433–441 (2015).

  21. 21.

    Armstrong, K. M., Piepenbrink, K. H. & Baker, B. M. Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes. Biochem. J. 415, 183–196 (2008).

  22. 22.

    Johnson, L. A. et al. Gene transfer of tumor-reactive TCR confers both high avidity and tumor reactivity to nonreactive peripheral blood mononuclear cells and tumor-infiltrating lymphocytes. J. Immunol. 177, 6548–6559 (2006).

  23. 23.

    Johnson, L. A. et al. Gene therapy with human and mouse T-cell receptors mediates cancer regression and targets normal tissues expressing cognate antigen. Blood 114, 535–546 (2009).

  24. 24.

    Chodon, T. et al. Adoptive Transfer of MART-1 T-cell receptor transgenic lymphocytes and dendritic cell vaccination in patients with metastatic melanoma. Clin. Cancer Res. 20, 2457–2465 (2014).

  25. 25.

    Borbulevych, O. Y., Santhanagopolan, S. M., Hossain, M. & Baker, B. M. TCRs used in cancer gene therapy cross-react with MART-1/melan-A tumor antigens via distinct mechanisms. J. Immunol. 187, 2453–2463 (2011).

  26. 26.

    Ayres, C. M., Scott, D. R., Corcelli, S. A. & Baker, B. M. Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity. Sci. Rep. 6, 25070 (2016).

  27. 27.

    Gee, M. H. et al. Antigen Identification for Orphan T cell receptors expressed on tumor-infiltrating lymphocytes. Cell 172, 549–563.e516 (2018).

  28. 28.

    Riley, T. P. et al. A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces. Protein Eng. Des. Sel. 29, 595–606 (2016).

  29. 29.

    Riley, T. P., Singh, N. K., Pierce, B. G., Weng, Z. & Baker, B. M. in Computational Design of Ligand Binding Proteins. (ed. Stoddard, L. B.) 319–340 (Springer New York, New York, NY, 2016).

  30. 30.

    Sliz, P. et al. Crystal structures of two closely related but antigenically distinct HLA- A2/melanocyte-melanoma tumor-antigen peptide complexes. J. Immunol. 167, 3276–3284 (2001).

  31. 31.

    Borbulevych, O. Y. et al. Structures of MART-126/27-35 peptide/HLA-A2 complexes reveal a remarkable disconnect between antigen structural homology and T cell recognition. J. Mol. Biol. 372, 1123–1136 (2007).

  32. 32.

    Macdonald, W. A. et al. T cell allorecognition via molecular mimicry. Immunity 31, 897–908 (2009).

  33. 33.

    McMurtrey, C. et al. Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove. eLife 5, e12556 (2016).

  34. 34.

    Blevins, S. J. et al. How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire. Proc. Natl. Acad. Sci. USA 113, E1276–E1285 (2016).

  35. 35.

    Smith, K. J. et al. An altered position of the α2 helix of MHC class I is revealed by the crystal structure of HLA-B*3501. Immunity 4, 203–213 (1996).

  36. 36.

    Motozono, C. et al. Distortion of the major histocompatibility complex class I binding groove to accommodate an insulin-derived 10-mer peptide. J. Biol. Chem. 290, 18924–18933 (2015).

  37. 37.

    Collins, E. J., Garboczi, D. N. & Wiley, D. C. Three-dimensional structure of a peptide extending from one end of a class I MHC binding site. Nature 371, 626–629 (1994).

  38. 38.

    Sidney, J., Peters, B., Frahm, N., Brander, C. & Sette, A. HLA class I supertypes: a revised and updated classification. BMC. Immunol. 9, 1 (2008).

  39. 39.

    Mohammed, F. et al. Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self. Nat. Immunol. 9, 1236 (2008).

  40. 40.

    Pellicci, D. G. et al. Recognition of β-linked self glycolipids mediated by natural killer T cell antigen receptors. Nat. Immunol. 12, 827 (2011).

  41. 41.

    Jones, L. L., Colf, L. A., Stone, J. D., Garcia, K. C. & Kranz, D. M. Distinct CDR3 Conformations in TCRs determine the level of cross-reactivity for diverse antigens, but not the docking orientation. J. Immunol. 181, 6255–6264 (2008).

  42. 42.

    Colf, L. A. et al. How a single T cell receptor recognizes both self and foreign MHC. Cell 129, 135–146 (2007).

  43. 43.

    Rossjohn, J. et al. T cell antigen receptor recognition of antigen-presenting molecules. Annu. Rev. Immunol. 33, 169–200 (2015).

  44. 44.

    Reiser, J. B. et al. A T cell receptor CDR3beta loop undergoes conformational changes of unprecedented magnitude upon binding to a peptide/MHC class I complex. Immunity 16, 345–354 (2002).

  45. 45.

    Stewart-Jones, G. B., McMichael, A. J., Bell, J. I., Stuart, D. I. & Jones, E. Y. A structural basis for immunodominant human T cell receptor recognition. Nat. Immunol. 4, 657–663 (2003).

  46. 46.

    Rudolph, M. G., Stanfield, R. L. & Wilson, I. A. How TCRs bind MHCs, peptides, and coreceptors. Annu. Rev. Immunol. 24, 419–466 (2006).

  47. 47.

    Bovay, A. et al. T cell receptor alpha variable 12-2 bias in the immunodominant response to Yellow fever virus. Eur. J. Immunol. 48, 258–272 (2018).

  48. 48.

    Cole, D. K. et al. Germline-governed recognition of a cancer epitope by an immunodominant human T-cell receptor. J. Biol. Chem. 284, 27281–27289 (2009).

  49. 49.

    Van Braeckel-Budimir, N. et al. A T cell receptor locus harbors a malaria-specific immune response gene. Immunity 47, 835–847.e834 (2017).

  50. 50.

    Das, R. & Baker, D. Macromolecular modeling with rosetta. Annu. Rev. Biochem. 77, 363–382 (2008).

  51. 51.

    Kortemme, T. & Baker, D. A simple physical model for binding energy hot spots in protein- protein complexes. Proc. Natl. Acad. Sci. USA 99, 14116–14121 (2002).

  52. 52.

    Davis-Harrison, R. L., Armstrong, K. M. & Baker, B. M. Two different T cell receptors use different thermodynamic strategies to recognize the same peptide/MHC ligand. J. Mol. Biol. 346, 533–550 (2005).

  53. 53.

    Hellman, L. M. et al. Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide-MHC complexes. J. Immunol. Methods 432, 95–101 (2016).

  54. 54.

    Morgan, C. S., Holton, J. M., Olafson, B. D., Bjorkman, P. J. & Mayo, S. L. Circular dichroism determination of class I MHC-peptide equilibrium dissociation constants. Protein Sci. 6, 1771–1773 (1997).

  55. 55.

    Blevins, S. J. & Baker, B. M. Using global analysis to extend the accuracy and precision of binding measurements with T cell receptors and their peptide/MHC ligands. Front. Mol. Biosci. 4, 1–9 (2017).

  56. 56.

    Piepenbrink, K. H., Gloor, B. E., Armstrong, K. M. & Baker, B. M. Methods for quantifying T cell receptor binding affinities and thermodynamics. Methods Enzymol. 466, 359–381 (2009).

  57. 57.

    Spear, T. T. et al. Hepatitis C virus-cross-reactive TCR gene-modified T cells: a model for immunotherapy against diseases with genomic instability. J. Leukoc. Biol. 100, 545–557 (2016).

  58. 58.

    Cole, D. J. et al. Characterization of the functional specificity of a cloned T-cell receptor heterodimer recognizing the MART-1 melanoma antigen. Cancer Res. 55, 748–752 (1995).

  59. 59.

    Bevington, P. R. & Robinson, D. K. Data Reduction and Error Analysis for the Physical Sciences, Edn. 2nd. (McGraw-Hill, New York, NY, 1992).

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Authors were supported by NIH grants GM118166 and AI29543 (B.M.B.); CA154778 and CA153789 (M.I.N.); and AI103867 (K.C.G.); and American Cancer Society grant IRG-14-195-01 (L.M.H.). T.P.R. and J.A.A. were supported by fellowships from the Indiana CTSI, funded in part by NIH grants TR001107 and TR001108. M.H.G. was supported by a Stanford Graduate Research Fellowship and NIH grant CA216926. J.L.M. was supported by NIH grant CA175127. K.C.G. is supported by the Howard Hughes Medical Institute and the Parker Institute for Cancer Immunotherapy.

Author information


  1. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA

    • Timothy P. Riley
    • , Lance M. Hellman
    •  & Brian M. Baker
  2. Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA

    • Timothy P. Riley
    • , Lance M. Hellman
    •  & Brian M. Baker
  3. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA

    • Marvin H. Gee
    • , Juan L. Mendoza
    • , Jesus A. Alonso
    •  & K. Christopher Garcia
  4. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA

    • Marvin H. Gee
    • , Juan L. Mendoza
    • , Jesus A. Alonso
    •  & K. Christopher Garcia
  5. Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA

    • Kendra C. Foley
    •  & Michael I. Nishimura
  6. Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA

    • Craig W. Vander Kooi


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Modeling, crystallographic, and TCR binding experiments were performed by T.P.R., L.M.H., and J.A.A. C.W.V.K assisted with crystallographic data collection and analysis. Thermal stability experiments were performed by T.P.R. and L.M.H. Functional experiments were performed by L.M.H. with assistance from K.C.F. in T cell transduction. Data analysis was performed by T.P.R., L.M.H., M.H.G., J.L.M., J.A.A., and C.W.V.K. The manuscript was drafted and edited by T.P.R., M.H.G., J.L.M., and B.M.B. The project was conceptualized by T.P.R., K.C.G., and B.M.B. Personnel were supervised by M.I.N., K.C.G., and B.M.B.

Competing interests

T.P.R. is employed by a new startup company that uses structural information to explore and modulate TCR specificity. B.M.B. is on the board of this company.

Corresponding author

Correspondence to Brian M. Baker.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Tables 1–4, Supplementary Figures 1–4

  2. Reporting Summary

  3. Supplementary Video 1

    Animation shown the transition of the MMWDRGLGMM/HLA-A2 complex from TCR-free to TCR-bound

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