Article | Published:

Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope

Nature Structural & Molecular Biology volume 24, pages 395406 (2017) | Download Citation

Abstract

A keystone of antiviral immunity is CD8+ T cell recognition of viral peptides bound to MHC-I proteins. The recognition modes of individual T cell receptors (TCRs) have been studied in some detail, but the role of TCR variation in providing a robust response to viral antigens is unclear. The influenza M1 epitope is an immunodominant target of CD8+ T cells that help to control influenza in HLA-A2+ individuals. Here we show that CD8+ T cells use many distinct TCRs to recognize HLA-A2–M1, which enables the use of different structural solutions to the problem of specifically recognizing a relatively featureless peptide antigen. The vast majority of responding TCRs target a small cleft between HLA-A2 and the bound M1 peptide. These broad repertoires lead to plasticity in antigen recognition and protection against T cell clonal loss and viral escape.

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

Referenced accessions

Protein Data Bank

References

  1. 1.

    & T cell mediated immunity to influenza: mechanisms of viral control. Trends Immunol. 35, 396–402 (2014).

  2. 2.

    , , , & T cell-mediated protection against lethal 2009 pandemic H1N1 influenza virus infection in a mouse model. J. Virol. 85, 448–455 (2011).

  3. 3.

    et al. The design and proof of concept for a CD8+ T cell-based vaccine inducing cross-subtype protection against influenza A virus. Immunol. Cell Biol. 91, 96–104 (2013).

  4. 4.

    , , & Identification of viral molecules recognized by influenza-specific human cytotoxic T lymphocytes. J. Exp. Med. 165, 408–416 (1987).

  5. 5.

    , , , & Cytotoxic T lymphocytes recognize a fragment of influenza virus matrix protein in association with HLA-A2. Nature 326, 881–882 (1987).

  6. 6.

    et al. Immunomic analysis of the repertoire of T-cell specificities for influenza A virus in humans. J. Virol. 82, 12241–12251 (2008).

  7. 7.

    et al. Physical detection of influenza A epitopes identifies a stealth subset on human lung epithelium evading natural CD8 immunity. Proc. Natl. Acad. Sci. USA 112, 2151–2156 (2015).

  8. 8.

    et al. Extensive conservation of alpha and beta chains of the human T-cell antigen receptor recognizing HLA-A2 and influenza A matrix peptide. Proc. Natl. Acad. Sci. USA 88, 8987–8990 (1991).

  9. 9.

    et al. Human HLA-A0201-restricted cytotoxic T lymphocyte recognition of influenza A is dominated by T cells bearing the Vβ17 gene segment. J. Exp. Med. 181, 79–91 (1995).

  10. 10.

    et al. Complex T cell memory repertoires participate in recall responses at extremes of antigenic load. J. Immunol. 177, 2006–2014 (2006).

  11. 11.

    , , , & A class I MHC-restricted recall response to a viral peptide is highly polyclonal despite stringent CDR3 selection: implications for establishing memory T cell repertoires in “real-world” conditions. J. Immunol. 160, 2842–2852 (1998).

  12. 12.

    et al. Multiple glycines in TCR α-chains determine clonally diverse nature of human T cell memory to influenza A virus. J. Immunol. 181, 7407–7419 (2008).

  13. 13.

    , , , & A structural basis for immunodominant human T cell receptor recognition. Nat. Immunol. 4, 657–663 (2003).

  14. 14.

    et al. The structural dynamics and energetics of an immunodominant T cell receptor are programmed by its Vβ domain. Immunity 28, 171–182 (2008).

  15. 15.

    , , & Structural determinants of T-cell receptor bias in immunity. Nat. Rev. Immunol. 6, 883–894 (2006).

  16. 16.

    et al. Molecular basis of a dominant T cell response to an HIV reverse transcriptase 8-mer epitope presented by the protective allele HLA-B*51:01. J. Immunol. 192, 3428–3434 (2014).

  17. 17.

    et al. Superimposed epitopes restricted by the same HLA molecule drive distinct HIV-specific CD8+ T cell repertoires. J. Immunol. 193, 77–84 (2014).

  18. 18.

    et al. Lack of prominent peptide-major histocompatibility complex features limits repertoire diversity in virus-specific CD8+ T cell populations. Nat. Immunol. 6, 382–389 (2005).

  19. 19.

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

  20. 20.

    , , , & Direct link between MHC polymorphism, T cell avidity, and diversity in immune defense. Science 298, 1797–1800 (2002).

  21. 21.

    et al. Age-associated decline in T cell repertoire diversity leads to holes in the repertoire and impaired immunity to influenza virus. J. Exp. Med. 205, 711–723 (2008).

  22. 22.

    et al. T cell receptor recognition motifs govern immune escape patterns in acute SIV infection. Immunity 21, 793–803 (2004).

  23. 23.

    et al. GagCM9-specific CD8+ T cells expressing limited public TCR clonotypes do not suppress SIV replication in vivo. PLoS One 6, e23515 (2011).

  24. 24.

    , & Sequence analysis of T-cell repertoires in health and disease. Genome Med. 5, 98 (2013).

  25. 25.

    et al. Deep sequencing of antiviral T-cell responses to HCMV and EBV in humans reveals a stable repertoire that is maintained for many years. PLoS Pathog. 8, e1002889 (2012).

  26. 26.

    et al. Abundant cytomegalovirus (CMV) reactive clonotypes in the CD8+ T cell receptor alpha repertoire following allogeneic transplantation. Clin. Exp. Immunol. 184, 389–402 (2016).

  27. 27.

    et al. A structural basis for varied αβ TCR usage against an immunodominant EBV antigen restricted to a HLA-B8 molecule. J. Immunol. 188, 311–321 (2012).

  28. 28.

    et al. Highly divergent T-cell receptor binding modes underlie specific recognition of a bulged viral peptide bound to a human leukocyte antigen class I molecule. J. Biol. Chem. 288, 15442–15454 (2013).

  29. 29.

    et al. Structural basis for clonal diversity of the public T cell response to a dominant human cytomegalovirus epitope. J. Biol. Chem. 290, 29106–29119 (2015).

  30. 30.

    et al. Cross-reactive influenza virus-specific CD8+ T cells contribute to lymphoproliferation in Epstein-Barr virus-associated infectious mononucleosis. J. Clin. Invest. 115, 3602–3612 (2005).

  31. 31.

    , , & Precursor frequency and competition dictate the HLA-A2-restricted CD8+ T cell responses to influenza A infection and vaccination in HLA-A2.1 transgenic mice. J. Immunol. 187, 1895–1902 (2011).

  32. 32.

    , , & Narrowing of human influenza A virus-specific T cell receptor α and β repertoires with increasing age. J. Virol. 89, 4102–4116 (2015).

  33. 33.

    The problem of plain vanilla peptides. Nat. Immunol. 4, 649–650 (2003).

  34. 34.

    , , , & Structural and biophysical determinants of αβ T-cell antigen recognition. Immunology 135, 9–18 (2012).

  35. 35.

    et al. A structural voyage toward an understanding of the MHC-I-restricted immune response: lessons learned and much to be learned. Immunol. Rev. 250, 61–81 (2012).

  36. 36.

    , , , & A correlation between TCR Vα docking on MHC and CD8 dependence: implications for T cell selection. Immunity 19, 595–606 (2003).

  37. 37.

    et al. T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I-bound peptide. Nat. Immunol. 6, 1114–1122 (2005).

  38. 38.

    & The role of naive T cell precursor frequency and recruitment in dictating immune response magnitude. J. Immunol. 188, 4135–4140 (2012).

  39. 39.

    et al. Naive CD8+ T-cell precursors display structured TCR repertoires and composite antigen-driven selection dynamics. Immunol. Cell Biol. 93, 625–633 (2015).

  40. 40.

    , , & Sizing up the key determinants of the CD8+ T cell response. Nat. Rev. Immunol. 15, 705–716 (2015).

  41. 41.

    et al. Complex T-cell receptor repertoire dynamics underlie the CD8+ T-cell response to HIV-1. J. Virol. 89, 110–119 (2015).

  42. 42.

    et al. CD8+ TCR repertoire formation is guided primarily by the peptide component of the antigenic complex. J. Immunol. 190, 931–939 (2013).

  43. 43.

    , , , & The immunodominant influenza A virus M158-66 cytotoxic T lymphocyte epitope exhibits degenerate class I major histocompatibility complex restriction in humans. J. Virol. 88, 10613–10623 (2014).

  44. 44.

    et al. T-cell receptor specificity maintained by altered thermodynamics. J. Biol. Chem. 288, 18766–18775 (2013).

  45. 45.

    et al. Naive T cell repertoire skewing in HLA-A2 individuals by a specialized rearrangement mechanism results in public memory clonotypes. J. Immunol. 186, 2970–2977 (2011).

  46. 46.

    , , & The molecular basis for public T-cell responses? Nat. Rev. Immunol. 8, 231–238 (2008).

  47. 47.

    et al. Crossreactive T cells spotlight the germline rules for αβ T cell-receptor interactions with MHC molecules. Immunity 28, 324–334 (2008).

  48. 48.

    et al. Heterologous immunity: immunopathology, autoimmunity and protection during viral infections. Autoimmunity 44, 328–347 (2011).

  49. 49.

    et al. Memory of mice and men: CD8+ T-cell cross-reactivity and heterologous immunity. Immunol. Rev. 211, 164–181 (2006).

  50. 50.

    , , & Regulatory T cells resist virus infection-induced apoptosis. J. Virol. 89, 2112–2120 (2015).

  51. 51.

    , , & A small jab—a big effect: nonspecific immunomodulation by vaccines. Trends Immunol. 34, 431–439 (2013).

  52. 52.

    et al. Molecular basis for universal HLA-A*0201-restricted CD8+ T-cell immunity against influenza viruses. Proc. Natl. Acad. Sci. USA 113, 4440–4445 (2016).

  53. 53.

    , , & Linking T-cell receptor sequence to functional phenotype at the single-cell level. Nat. Biotechnol. 32, 684–692 (2014).

  54. 54.

    et al. Diversity index of mucosal resident T lymphocyte repertoire predicts clinical prognosis in gastric cancer. OncoImmunology 4, e1001230 (2015).

  55. 55.

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

  56. 56.

    et al. Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells. Blood 114, 4099–4107 (2009).

  57. 57.

    et al. Using synthetic templates to design an unbiased multiplex PCR assay. Nat. Commun. 4, 2680 (2013).

  58. 58.

    et al. Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms. Eur. J. Immunol. 42, 3073–3083 (2012).

  59. 59.

    , , , & Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding. Sci. Rep. 5, 14629 (2015).

  60. 60.

    , , & IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 20, i379–i385 (2004).

  61. 61.

    , & IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res. 36, W503–W508 (2008).

  62. 62.

    et al. Correction of multi-gene deficiency in vivo using a single 'self-cleaving' 2A peptide-based retroviral vector. Nat. Biotechnol. 22, 589–594 (2004).

  63. 63.

    et al. A single TCR α-chain with dominant peptide recognition in the allorestricted HER2/neu-specific T cell repertoire. J. Immunol. 184, 1617–1629 (2010).

  64. 64.

    , & HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides. Proc. Natl. Acad. Sci. USA 89, 3429–3433 (1992).

  65. 65.

    & Impaired assembly and transport of HLA-A and -B antigens in a mutant TxB cell hybrid. EMBO J. 5, 943–949 (1986).

  66. 66.

    et al. Stable, soluble T-cell receptor molecules for crystallization and therapeutics. Protein Eng. 16, 707–711 (2003).

  67. 67.

    et al. Production of soluble αβ T-cell receptor heterodimers suitable for biophysical analysis of ligand binding. Protein Sci. 8, 2418–2423 (1999).

  68. 68.

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

  69. 69.

    Scaling and assessment of data quality. Acta Crystallogr. D Biol. Crystallogr. 62, 72–82 (2006).

  70. 70.

    , , , & iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta Crystallogr. D Biol. Crystallogr. 67, 271–281 (2011).

  71. 71.

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

  72. 72.

    et al. Collaboration gets the most out of software. eLife 2, e01456 (2013).

  73. 73.

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

  74. 74.

    & Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

Download references

Acknowledgements

This work was supported by the NIH (grants AI038996 (to L.J.S.), AI49320 (to L.K.S.), and AI109858 (to L.J.S. and L.K.S.)) and the Nebraska Research Initiative (grant to D.G.). This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. Use of the Lilly Research Laboratories Collaborative Access Team (LRL-CAT) beamline at Sector 31 of the Advanced Photon Source was provided by Eli Lilly Company, which operates the facility. We thank J. Birtley and Z. Maben for assistance with crystallization, freezing, and shipping of crystals; P. Trehn for advice on model analysis; W. Uckert (Max Delbruck Center, Berlin, Germany) for TCRα/β Jurkat J76 cells transfected with human CD8α; and P. Thomas for technical advice on single-cell PCR.

Author information

Author notes

    • Liisa K Selin
    •  & Lawrence J Stern

    These authors contributed equally to this work.

Affiliations

  1. Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

    • InYoung Song
    • , Anna Gil
    • , Rabinarayan Mishra
    • , Liisa K Selin
    •  & Lawrence J Stern
  2. Graduate Program in Immunology and Microbiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

    • InYoung Song
    • , Liisa K Selin
    •  & Lawrence J Stern
  3. School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, Nebraska, USA.

    • Dario Ghersi
  4. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

    • Lawrence J Stern

Authors

  1. Search for InYoung Song in:

  2. Search for Anna Gil in:

  3. Search for Rabinarayan Mishra in:

  4. Search for Dario Ghersi in:

  5. Search for Liisa K Selin in:

  6. Search for Lawrence J Stern in:

Contributions

I.Y.S. conceived the project, designed the experimental approach, performed single-cell sequencing experiments, characterized TCR transfectants, determined crystal structures, and wrote the manuscript. A.G. performed NGS analyses, performed single-cell sequencing experiments, and edited the manuscript. R.M. performed NGS analyses and edited the manuscript. D.G. performed NGS analyses and edited the manuscript. L.K.S. conceived the project, designed the experimental approach, supervised TCR sequencing analyses, and wrote the manuscript. L.J.S. conceived the project, designed the experimental approach, supervised cellular and molecular studies, and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Liisa K Selin or Lawrence J Stern.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–6, Supplementary Table 1 and Supplementary Note 1.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nsmb.3383