CDR3α drives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection

Autoři: Larisa Kamga aff001;  Anna Gil aff002;  Inyoung Song aff002;  Robin Brody aff001;  Dario Ghersi aff003;  Nuray Aslan aff002;  Lawrence J. Stern aff002;  Liisa K. Selin aff002;  Katherine Luzuriaga aff001
Působiště autorů: Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America aff001;  Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America aff002;  School of Interdisciplinary Informatics, University of Nebraska at Omaha, Nebraska, United States of America aff003
Vyšlo v časopise: CDR3α drives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection. PLoS Pathog 15(11): e32767. doi:10.1371/journal.ppat.1008122
Kategorie: Research Article
doi: 10.1371/journal.ppat.1008122


The T cell receptor (TCR) repertoire is an essential component of the CD8 T-cell immune response. Here, we seek to investigate factors that drive selection of TCR repertoires specific to the HLA-A2-restricted immunodominant epitope BRLF1109-117 (YVLDHLIVV) over the course of primary Epstein Barr virus (EBV) infection. Using single-cell paired TCRαβ sequencing of tetramer sorted CD8 T cells ex vivo, we show at the clonal level that recognition of the HLA-A2-restricted BRLF1 (YVL-BR, BRLF-1109) epitope is mainly driven by the TCRα chain. For the first time, we identify a CDR3α (complementarity determining region 3 α) motif, KDTDKL, resulting from an obligate AV8.1-AJ34 pairing that was shared by all four individuals studied. This observation coupled with the fact that this public AV8.1-KDTDKL-AJ34 TCR pairs with multiple different TCRβ chains within the same donor (median 4; range: 1–9), suggests that there are some unique structural features of the interaction between the YVL-BR/MHC and the AV8.1-KDTDKL-AJ34 TCR that leads to this high level of selection. Newly developed TCR motif algorithms identified a lysine at position 1 of the CDR3α motif that is highly conserved and likely important for antigen recognition. Crystal structure analysis of the YVL-BR/HLA-A2 complex revealed that the MHC-bound peptide bulges at position 4, exposing a negatively charged aspartic acid that may interact with the positively charged lysine of CDR3α. TCR cloning and site-directed mutagenesis of the CDR3α lysine ablated YVL-BR-tetramer staining and substantially reduced CD69 upregulation on TCR mutant-transduced cells following antigen-specific stimulation. Reduced activation of T cells expressing this CDR3 motif was also observed following exposure to mutated (D4A) peptide. In summary, we show that a highly public TCR repertoire to an immunodominant epitope of a common human virus is almost completely selected on the basis of CDR3α and provide a likely structural basis for the selection. These studies emphasize the importance of examining TCRα, as well as TCRβ, in understanding the CD8 T cell receptor repertoire.

Klíčová slova:

Cell staining – Crystal structure – Cytotoxic T cells – Sequence analysis – Sequence motif analysis – T cell receptors – T cells


1. Bollard CM, Gottschalk S, Torrano V, Diouf O, Ku S, Hazrat Y, et al. Sustained complete responses in patients with lymphoma receiving autologous cytotoxic T lymphocytes targeting Epstein-Barr virus latent membrane proteins. J Clin Oncol. 2014;32(8):798–808. doi: 10.1200/JCO.2013.51.5304 24344220; PubMed Central PMCID: PMC3940538.

2. Bollard CM, Rooney CM, Heslop HE. T-cell therapy in the treatment of post-transplant lymphoproliferative disease. Nat Rev Clin Oncol. 2012;9(9):510–9. doi: 10.1038/nrclinonc.2012.111 22801669; PubMed Central PMCID: PMC3743122.

3. Keymeulen B, Vandemeulebroucke E, Ziegler AG, Mathieu C, Kaufman L, Hale G, et al. Insulin needs after CD3-antibody therapy in new-onset type 1 diabetes. N Engl J Med. 2005;352(25):2598–608. Epub 2005/06/24. doi: 10.1056/NEJMoa043980 15972866.

4. Loren AW, Porter DL, Stadtmauer EA, Tsai DE. Post-transplant lymphoproliferative disorder: a review. Bone Marrow Transplant. 2003;31(3):145–55. Epub 2003/03/07. doi: 10.1038/sj.bmt.1703806 12621474.

5. Luzuriaga K, Sullivan JL. Infectious mononucleosis. N Engl J Med. 2010;362(21):1993–2000. doi: 362/21/1993 [pii];doi: 10.1056/NEJMcp1001116 20505178

6. Catalina MD, Sullivan JL, Bak KR, Luzuriaga K. Differential evolution and stability of epitope-specific CD8(+) T cell responses in EBV infection. J Immunol. 2001;167(8):4450–7. doi: 10.4049/jimmunol.167.8.4450 11591771.

7. Taylor GS, Long HM, Brooks JM, Rickinson AB, Hislop AD. The immunology of Epstein-Barr virus-induced disease. Annu Rev Immunol. 2015;33:787–821. Epub 2015/02/24. doi: 10.1146/annurev-immunol-032414-112326 25706097.

8. Yanagi Y, Yoshikai Y, Leggett K, Clark SP, Aleksander I, Mak TW. A human T cell-specific cDNA clone encodes a protein having extensive homology to immunoglobulin chains. Nature. 1984;308(5955):145–9. doi: 10.1038/308145a0 6336315.

9. Zinkernagel RM, Doherty PC. Restriction of in vitro T cell-mediated cytotoxicity in lymphocytic choriomeningitis within a syngeneic or semiallogeneic system. Nature. 1974;248(5450):701–2. doi: 10.1038/248701a0 4133807.

10. Hedrick SM, Cohen DI, Nielsen EA, Davis MM. Isolation of cDNA clones encoding T cell-specific membrane-associated proteins. Nature. 1984;308(5955):149–53. doi: 10.1038/308149a0 6199676.

11. La Gruta NL, Gras S, Daley SR, Thomas PG, Rossjohn J. Understanding the drivers of MHC restriction of T cell receptors. Nat Rev Immunol. 2018;18(7):467–78. doi: 10.1038/s41577-018-0007-5 29636542.

12. Attaf M, Sewell AK. Disease etiology and diagnosis by TCR repertoire analysis goes viral. Eur J Immunol. 2016;46(11):2516–9. doi: 10.1002/eji.201646649 27813075.

13. Furman D, Jojic V, Sharma S, Shen-Orr SS, Angel CJ, Onengut-Gumuscu S, et al. Cytomegalovirus infection enhances the immune response to influenza. Science translational medicine. 2015;7(281):281ra43. Epub 2015/04/04. doi: 10.1126/scitranslmed.aaa2293 25834109; PubMed Central PMCID: PMC4505610.

14. Kloverpris HN, McGregor R, McLaren JE, Ladell K, Harndahl M, Stryhn A, et al. CD8+ TCR Bias and Immunodominance in HIV-1 Infection. Journal of immunology (Baltimore, Md: 1950). 2015;194(11):5329–45. Epub 2015/04/26. doi: 10.4049/jimmunol.1400854 25911754; PubMed Central PMCID: PMC4433859.

15. Miles JJ, Douek DC, Price DA. Bias in the alphabeta T-cell repertoire: implications for disease pathogenesis and vaccination. Immunol Cell Biol. 2011;89(3):375–87. Epub 2011/02/09. doi: 10.1038/icb.2010.139 21301479.

16. Watkin L, Gil A, Mishra R, Aslan N, Ghersi D, Luzuriaga K, et al. Unique influenza A cross-reactive memory CD8 T-cell receptor repertoire has a potential to protect against EBV seroconversion. J Allergy Clin Immunol. 2017;140(4):1206–10. doi: 10.1016/j.jaci.2017.05.037 28629751

17. Aslan N, Watkin LB, Gil A, Mishra R, Clark FG, Welsh RM, et al. Severity of Acute Infectious Mononucleosis Correlates with Cross-Reactive Influenza CD8 T-Cell Receptor Repertoires. MBio. 2017;8(6). doi: 10.1128/mBio.01841-17 29208744; PubMed Central PMCID: PMC5717389.

18. Siu G, Clark SP, Yoshikai Y, Malissen M, Yanagi Y, Strauss E, et al. The human T cell antigen receptor is encoded by variable, diversity, and joining gene segments that rearrange to generate a complete V gene. Cell. 1984;37(2):393–401. doi: 10.1016/0092-8674(84)90369-6 6202421.

19. Nikolich-Zugich J, Slifka MK, Messaoudi I. The many important facets of T-cell repertoire diversity. Nat Rev Immunol. 2004;4(2):123–32. doi: 10.1038/nri1292 15040585.

20. Dash P, Fiore-Gartland AJ, Hertz T, Wang GC, Sharma S, Souquette A, et al. Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature. 2017;547(7661):89–93. doi: 10.1038/nature22383 28636592; PubMed Central PMCID: PMC5616171.

21. Glanville J, Huang H, Nau A, Hatton O, Wagar LE, Rubelt F, et al. Identifying specificity groups in the T cell receptor repertoire. Nature. 2017;547(7661):94–8. doi: 10.1038/nature22976 28636589; PubMed Central PMCID: PMC5794212.

22. Abdel-Hakeem MS, Boisvert M, Bruneau J, Soudeyns H, Shoukry NH. Selective expansion of high functional avidity memory CD8 T cell clonotypes during hepatitis C virus reinfection and clearance. PLoS Pathog. 2017;13(2):e1006191. doi: 10.1371/journal.ppat.1006191 28146579; PubMed Central PMCID: PMC5305272.

23. Chen G, Yang X, Ko A, Sun X, Gao M, Zhang Y, et al. Sequence and Structural Analyses Reveal Distinct and Highly Diverse Human CD8+ TCR Repertoires to Immunodominant Viral Antigens. Cell Rep. 2017;19(3):569–83. doi: 10.1016/j.celrep.2017.03.072 28423320; PubMed Central PMCID: PMC5472051.

24. Klarenbeek PL, Remmerswaal EB, ten Berge IJ, Doorenspleet ME, van Schaik BD, Esveldt RE, 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. 2012;8(9):e1002889. doi: 10.1371/journal.ppat.1002889 23028307; PubMed Central PMCID: PMC3460621.

25. Sant S, Grzelak L, Wang Z, Pizzolla A, Koutsakos M, Crowe J, et al. Single-Cell Approach to Influenza-Specific CD8(+) T Cell Receptor Repertoires Across Different Age Groups, Tissues, and Following Influenza Virus Infection. Front Immunol. 2018;9:1453. doi: 10.3389/fimmu.2018.01453 29997621; PubMed Central PMCID: PMC6030351.

26. Song I, Gil A, Mishra R, Ghersi D, Selin LK, Stern LJ. Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope. Nat Struct Mol Biol. 2017;24(4):395–406. doi: 10.1038/nsmb.3383 28250417; PubMed Central PMCID: PMC5383516.

27. Watkin LB, Mishra R, Gil A, Aslan N, Ghersi D, Luzuriaga K, et al. Unique influenza A cross-reactive memory CD8 T-cell receptor repertoire has a potential to protect against EBV seroconversion. J Allergy Clin Immunol. 2017;140(4):1206–10. Epub 2017/06/21. doi: 10.1016/j.jaci.2017.05.037 28629751; PubMed Central PMCID: PMC5669360.

28. Bradley P, Thomas PG. Using T Cell Receptor Repertoires to Understand the Principles of Adaptive Immune Recognition. Annu Rev Immunol. 2019. Epub 2019/01/31. doi: 10.1146/annurev-immunol-042718-041757 30699000.

29. Padovan E, Casorati G, Dellabona P, Meyer S, Brockhaus M, Lanzavecchia A. Expression of two T cell receptor alpha chains: dual receptor T cells. Science. 1993;262(5132):422–4. Epub 1993/10/15. doi: 10.1126/science.8211163 8211163.

30. Naumov YN, Naumova EN, Yassai MB, Kota K, Welsh RM, Selin LK. Multiple glycines in TCR alpha-chains determine clonally diverse nature of human T cell memory to influenza A virus. J Immunol. 2008;181(10):7407–19. doi: 181/10/7407 [pii]. doi: 10.4049/jimmunol.181.10.7407 18981164

31. Annels NE, Callan MF, Tan L, Rickinson AB. Changing patterns of dominant TCR usage with maturation of an EBV-specific cytotoxic T cell response. J Immunol. 2000;165(9):4831–41. doi: 10.4049/jimmunol.165.9.4831 11046006.

32. Callan MF, Fazou C, Yang H, Rostron T, Poon K, Hatton C, et al. CD8(+) T-cell selection, function, and death in the primary immune response in vivo. J Clin Invest. 2000;106(10):1251–61. doi: 10.1172/JCI10590 11086026; PubMed Central PMCID: PMC381436.

33. Miles JJ, Bulek AM, Cole DK, Gostick E, Schauenburg AJ, Dolton G, et al. Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection. PLoS Pathog. 2010;6(11):e1001198. doi: 10.1371/journal.ppat.1001198 21124993; PubMed Central PMCID: PMC2987824.

34. Genolet R, Stevenson BJ, Farinelli L, Osteras M, Luescher IF. Highly diverse TCRalpha chain repertoire of pre-immune CD8(+) T cells reveals new insights in gene recombination. EMBO J. 2012;31(21):4247–8. Epub 2012/11/07. doi: 10.1038/emboj.2012.277 23128857; PubMed Central PMCID: PMC3492736.

35. Howie B, Sherwood AM, Berkebile AD, Berka J, Emerson RO, Williamson DW, et al. High-throughput pairing of T cell receptor alpha and beta sequences. Sci Transl Med. 2015;7(301):301ra131. Epub 2015/08/21. doi: 10.1126/scitranslmed.aac5624 26290413.

36. Ndifon W, Gal H, Shifrut E, Aharoni R, Yissachar N, Waysbort N, et al. Chromatin conformation governs T-cell receptor Jbeta gene segment usage. Proc Natl Acad Sci U S A. 2012;109(39):15865–70. Epub 2012/09/18. doi: 10.1073/pnas.1203916109 22984176; PubMed Central PMCID: PMC3465372.

37. Ruggiero E, Nicolay JP, Fronza R, Arens A, Paruzynski A, Nowrouzi A, et al. High-resolution analysis of the human T-cell receptor repertoire. Nat Commun. 2015;6:8081. Epub 2015/09/02. doi: 10.1038/ncomms9081 26324409; PubMed Central PMCID: PMC4569693.

38. Watkin LB, Gil A, Mishra R, Aslan N, Ghersi D, Luzuriaga K, et al. Potential of influenza A memory CD8+ T-cells to protect against Epstein Barr virus (EBV) seroconversion. Journal of Allergy and Clinical Immunology. 2017;140(4):1206–10. doi: 10.1016/j.jaci.2017.05.037 28629751

39. Cornberg M, Clute SC, Watkin LB, Saccoccio FM, Kim SK, Naumov YN, et al. CD8 T cell cross-reactivity networks mediate heterologous immunity in human EBV and murine vaccinia virus infections. J Immunol. 2010;184(6):2825–38. doi: jimmunol.0902168 [pii];doi: 10.4049/jimmunol.0902168 20164414

40. Clute SC, Watkin LB, Cornberg M, Naumov YN, Sullivan JL, Luzuriaga K, et al. Cross-reactive influenza virus-specific CD8+ T cells contribute to lymphoproliferation in Epstein-Barr virus-associated infectious mononucleosis. J Clin Invest. 2005;115(12):3602–12. doi: 10.1172/JCI25078 16308574

41. Venturi V, Price DA, Douek DC, Davenport MP. The molecular basis for public T-cell responses? Nat Rev Immunol. 2008;8(3):231–8. doi: 10.1038/nri2260 18301425.

42. Bovay A, Zoete V, Dolton G, Bulek AM, Cole DK, Rizkallah PJ, et al. T cell receptor alpha variable 12–2 bias in the immunodominant response to Yellow fever virus. Eur J Immunol. 2018;48(2):258–72. Epub 2017/10/05. doi: 10.1002/eji.201747082 28975614; PubMed Central PMCID: PMC5887915.

43. Tynan FE, Burrows SR, Buckle AM, Clements CS, Borg NA, Miles JJ, et al. T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I-bound peptide. Nat Immunol. 2005;6(11):1114–22. Epub 2005/09/28. doi: 10.1038/ni1257 16186824.

44. Tynan FE, Borg NA, Miles JJ, Beddoe T, El-Hassen D, Silins SL, et al. High resolution structures of highly bulged viral epitopes bound to major histocompatibility complex class I. Implications for T-cell receptor engagement and T-cell immunodominance. J Biol Chem. 2005;280(25):23900–9. Epub 2005/04/26. doi: 10.1074/jbc.M503060200 15849183.

45. Gil A, Yassai MB, Naumov YN, Selin LK. Narrowing of human influenza A virus-specific T cell receptor alpha and beta repertoires with increasing age. J Virol. 2015;89(8):4102–16. doi: JVI.03020-14 [pii];doi: 10.1128/JVI.03020-14 25609818

46. Ishizuka J, Stewart-Jones GB, van der Merwe A, Bell JI, McMichael AJ, Jones EY. The structural dynamics and energetics of an immunodominant T cell receptor are programmed by its Vbeta domain. Immunity. 2008;28(2):171–82. Epub 2008/02/16. doi: 10.1016/j.immuni.2007.12.018 18275829.

47. DeWitt WS, Smith A, Schoch G, Hansen JA, Matsen FA, Bradley P. Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity. Elife. 2018;7. doi: 10.7554/eLife.38358 30152754.

48. Emerson RO, DeWitt WS, Vignali M, Gravley J, Hu JK, Osborne EJ, et al. Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire. Nat Genet. 2017;49(5):659–65. doi: 10.1038/ng.3822 28369038.

49. Attaf M, Huseby E, Sewell AK. alphabeta T cell receptors as predictors of health and disease. Cell Mol Immunol. 2015;12(4):391–9. doi: 10.1038/cmi.2014.134 25619506; PubMed Central PMCID: PMC4496535.

50. Luzuriaga K, McManus M, Catalina M, Mayack S, Sharkey M, Stevenson M, et al. Early therapy of vertical human immunodeficiency virus type 1 (HIV-1) infection: control of viral replication and absence of persistent HIV-1-specific immune responses. J Virol. 2000;74(15):6984–91. doi: 10.1128/jvi.74.15.6984-6991.2000 10888637; PubMed Central PMCID: PMC112215.

51. Wang GC, Dash P, McCullers JA, Doherty PC, Thomas PG. T cell receptor alphabeta diversity inversely correlates with pathogen-specific antibody levels in human cytomegalovirus infection. Sci Transl Med. 2012;4(128):128ra42. doi: 10.1126/scitranslmed.3003647 22491952; PubMed Central PMCID: PMC3593633.

52. Lefranc MP. IMGT, the international ImMunoGeneTics database. Nucleic Acids Res. 2003;31(1):307–10. doi: 10.1093/nar/gkg085 12520009; PubMed Central PMCID: PMC165532.

53. Precopio ML, Sullivan JL, Willard C, Somasundaran M, Luzuriaga K. Differential kinetics and specificity of EBV-specific CD4+ and CD8+ T cells during primary infection. J Immunol. 2003;170(5):2590–8. doi: 10.4049/jimmunol.170.5.2590 12594286.

54. Liang X, Weigand LU, Schuster IG, Eppinger E, van der Griendt JC, Schub A, et al. A single TCR alpha-chain with dominant peptide recognition in the allorestricted HER2/neu-specific T cell repertoire. J Immunol. 2010;184(3):1617–29. Epub 2010/01/01. doi: 10.4049/jimmunol.0902155 20042572.

55. Garboczi DN, Hung DT, Wiley DC. HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides. Proceedings of the National Academy of Sciences of the United States of America. 1992;89(8):3429–33. doi: 10.1073/pnas.89.8.3429 1565634; PubMed Central PMCID: PMC48881.

56. Powell HR, Battye TGG, Kontogiannis L, Johnson O, Leslie AGW. Integrating macromolecular X-ray diffraction data with the graphical user interface iMosflm. Nature protocols. 2017;12(7):1310–25. doi: 10.1038/nprot.2017.037 28569763; PubMed Central PMCID: PMC5562275.

57. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. Journal of applied crystallography. 2007;40(Pt 4):658–74. doi: 10.1107/S0021889807021206 19461840; PubMed Central PMCID: PMC2483472.

58. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, et al. Overview of the CCP4 suite and current developments. Acta crystallographica Section D, Biological crystallography. 2011;67(Pt 4):235–42. doi: 10.1107/S0907444910045749 21460441; PubMed Central PMCID: PMC3069738.

59. Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta crystallographica Section D, Biological crystallography. 2010;66(Pt 4):486–501. doi: 10.1107/S0907444910007493 20383002; PubMed Central PMCID: PMC2852313.

60. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta crystallographica Section D, Biological crystallography. 2010;66(Pt 2):213–21. doi: 10.1107/S0907444909052925 20124702; PubMed Central PMCID: PMC2815670.

61. Karplus PA, Diederichs K. Linking crystallographic model and data quality. Science. 2012;336(6084):1030–3. doi: 10.1126/science.1218231 22628654; PubMed Central PMCID: PMC3457925.

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