TCR Analyses

T-cell receptor CDR3 analysis: Molecular fingerprinting of the T-cell receptor repertoire
  • Markus J. Maeurer


T-cells play a crucial role in immune surveillance against transformed cells and intracellular infections; they are involved in auto-immune reactions. They recognize their targets, i.e. MHC / peptide complexes, trough the T-cell receptor. TCR usage determines the molecular interaction of the immune system with biologically relevant MHC/peptide molecules. The TCR coding genes (variable, diversity and junctional) determine the molecular composition of the TCR alpha and beta heterodimer. The random association of the VDJ genes constitutes the complementarity determining region 3 (CDR3) responsible for antigen recognition and TCR specificity. The molecular composition of a T-cell population can be objectively defined by measuring the CDR3 region. Qualitative and quantitative comparisons of the TCR composition in different anatomic compartments, or longitudinally over time, allow to asses the entire TCR repertoire. This methodology can be supplemented with functional T-cell based assays and aids to objectively describe any alteration in the T-cell pool. TCR CDR3 analysis is useful in immunomonitoring, e.g. examining patients after BMT or solid organ transplantation, patients with HAART therapy, or patients receiving molecularly defined vaccines.

Key words



  1. 1.
    LeFranc M.L., Lefranc G. The T cell receptor FactsBook. 2001 Academic Press, San Diego, San Francisco, New York, Boston, London, Sydney, Tokyo.Google Scholar
  2. 2.
    Nemazee D. Receptor selection in B and T lymphocytes. Annu Rev Immunol 2000;18:19.PubMedCrossRefGoogle Scholar
  3. 3.
    Brandt V.L., Roth D.B. A recombinase diversified: new functions of the RAG proteins. Curr Opin Immunol 2002;14:224.PubMedCrossRefGoogle Scholar
  4. 4.
    Pannetier C., Even J., Kourilsky P. T-cell repertoire diversity and clonal expansions in normal and clinical samples. Immunol Today 1995;16:176.PubMedCrossRefGoogle Scholar
  5. 5.
    Arstila T.P., Casrouge A., Baron V., Even J., Kanellopoulos J., Kourilsky P. A direct estimate of the human alphabeta T cell receptor diversity. Science 1999;286:958.PubMedCrossRefGoogle Scholar
  6. 6.
    Davodeau F., Peyrat M.A., Romagne F., et al. Dual T cell receptor beta chain expression on human T lymphocytes. J Exp Med 1995;181:1391.PubMedCrossRefGoogle Scholar
  7. 7.
    Sant’Angelo D. B., Cresswell P., Janeway C.A. Jr., Denzin L.K. Maintenance of TCR clonality in T cells expressing genes for two TCR heterodimers. Proc Natl Acad Sci U S A 2001;98:6824.PubMedCrossRefGoogle Scholar
  8. 8.
    Pilch H., Hohn H., Freitag K., et al. Improved assessment of T-cell receptor (TCR) VB repertoire in clinical specimens: combination of TCR-CDR3 spectratyping with flow cytometry-based TCR VB frequency analysis. Clin Diagn Lab Immunol 2002;9:257.PubMedCrossRefGoogle Scholar
  9. 9.
    Degauque N., Schadendorf D., Brouard S., et al. Blood T-cell Vbeta transcriptome in melanoma patients. Int J Cancer 2004;110:721.PubMedCrossRefGoogle Scholar
  10. 10.
    Lennon G.P., Sillibourne J.E., Furrie E., Doherty M.J., Kay R.A. Antigen triggering selectively increases TCRBV gene transcription. J Immunol 2000;165:2020.PubMedGoogle Scholar
  11. 11.
    Liu H., Rhodes M., Wiest D.L., Vignali D.A. On the dynamics of TCR:CD3 complex cell surface expression and downmodulation. Immunity 2000;13:665.PubMedCrossRefGoogle Scholar
  12. 12.
    Puisieux I., Even J., Pannetier C., Jotereau F., Favrot M., Kourilsky P. Oligoclonality of tumor-infiltrating lymphocytes from human melanomas. J Immunol 1994;153:2807.PubMedGoogle Scholar
  13. 13.
    Genevee C., Diu A., Nierat J., et al. An experimentally validated panel of subfamilyspecific oligonucleotide primers (V alpha 1-w29/V beta 1-w24) for the study of human T cell receptor variable V gene segment usage by polymerase chain reaction. Eur J Immunol 1992;22:1261.PubMedCrossRefGoogle Scholar
  14. 14.
    Sebille F., Gagne K., Guillet M., et al. Direct recognition of foreign MHC determinants by naive T cells mobilizes specific Vbeta families without skewing of the complementarity-determining region 3 length distribution. J Immunol 2001;167:3082.PubMedGoogle Scholar
  15. 15.
    Guillet M., Brouard S., Gagne K., et al. Different qualitative and quantitative regulation of V beta TCR transcripts during early acute allograft rejection and tolerance induction. J Immunol 2002;168:5088.PubMedGoogle Scholar
  16. 16.
    Gorochov G., Neumann A.U., Kereveur A., et al. Perturbation of CD4+ and CD8+ Tcell repertoires during progression to AIDS and regulation of the CD4+ repertoire during antiviral therapy. Nat Med 1998;4:215.PubMedCrossRefGoogle Scholar
  17. 17.
    Guillet M., Sebille F., Soulillou J. TCR usage in naive and committed alloreactive cells: implications for the understanding of TCR biases in transplantation. Curr Opin Immunol 2001;13:566.PubMedCrossRefGoogle Scholar
  18. 18.
    Morley J.K., Batliwalla F.M., Hingorani R., Gregersen P.K. Oligoclonal CD8+ T cells are preferentially expanded in the CD57+ subset. J Immunol 1995;154:6182.PubMedGoogle Scholar
  19. 19.
    Prevost-Blonde, A., Lengagne R., Letourneur F., Pannetier C., Gomard E., Guillet J.G. In vivo longitudinal analysis of a dominant TCR repertoire selected in human response to influenza virus. Virology 1997;233:93.CrossRefGoogle Scholar
  20. 20.
    Maini M.K., Gudgeon N., Wedderburn L.R., Rickinson A.B., Beverley P.C. Clonal expansions in acute EBV infection are detectable in the CD8 and not the CD4 subset and persist with a variable CD45 phenotype. J Immunol 2000;165:5729.PubMedGoogle Scholar
  21. 21.
    Bitmansour A.D., Waldrop S.L., Pitcher C.J., et al. Clonotypic structure of the human CD4+ memory T cell response to cytomegalovirus. J Immunol 2001;167:1151.PubMedGoogle Scholar
  22. 22.
    Naumov Y.N., Hogan K. T., Naumova E. N., Pagel J. T., Gorski J. 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 1998;160:2842.PubMedGoogle Scholar
  23. 23.
    Maeurer M.J., Martin D.M., Storkus W.J., Lotze M.T. TCR usage in CTLs recognizing melanoma/melanocyte antigens. Immunol Today 1995;16:603.PubMedCrossRefGoogle Scholar
  24. 24.
    Dietrich P.Y., Le Gal F.A., Dutoit V., et al. Prevalent role of TCR alpha-chain in the selection of the preimmune repertoire specific for a human tumor-associated self-antigen. J Immunol 2003;170:5103.PubMedGoogle Scholar
  25. 25.
    Hofbauer M., Wiesener S., Babbe H., et al. Clonal tracking of autoaggressive T cells in polymyositis by combining laser microdissection, single-cell PCR, and CDR3-spectratype analysis. Proc Natl Acad Sci U S A 2003;100:4090.PubMedCrossRefGoogle Scholar
  26. 26.
    Demoulins T., Mouthon F., Clayette P., Bequet D., Gachelin G., Dormont D. The same TCR (N)Dbeta(N)Jbeta junctional region is associated with several different vbeta13 subtypes in a multiple sclerosis patient at the onset of the disease. Neurobiol Dis 2003;14:470.PubMedCrossRefGoogle Scholar
  27. 27.
    Kim G., Kohyama K., Tanuma N., Matsumoto Y. Diagnosis and assessment of preclinical and clinical autoimmune encephalomyelitis using peripheral blood lymphocyte TCR. Eur J Immunol 1998;28:2751.PubMedCrossRefGoogle Scholar
  28. 28.
    Jager E., Maeurer M., Hohn H., et al. Clonal expansion of Melan A-specific cytotoxic T lymphocytes in a melanoma patient responding to continued immunization with melanoma-associated peptides. Int J Cancer 2000;86:538.PubMedCrossRefGoogle Scholar
  29. 29.
    Hohn H., Pilch H., Gunzel S., et al. Human papillomavirus type 33 E7 peptides presented by HLA-DR*0402 to tumor-infiltrating T cells in cervical cancer. J Virol 2000;74:6632.PubMedCrossRefGoogle Scholar
  30. 30.
    Gallard A., Foucras G., Coureau C., Guery J.C. Tracking T cell clonotypes in complex T lymphocyte populations by real-time quantitative PCR using fluorogenic complementarity-determining region-3-specific probes. J Immunol Methods 2002;270:269.PubMedGoogle Scholar
  31. 31.
    Coulie P.G., Karanikas V., Colau D., et al. A monoclonal cytolytic T-lymphocyte response observed in a melanoma patient vaccinated with a tumor-specific antigenic peptide encoded by gene MAGE-3. Proc Natl Acad Sci U S A 2001;98:10290.PubMedCrossRefGoogle Scholar
  32. 32.
    Sarzotti M., Patel D.D., Li X., et al. T cell repertoire development in humans with SCID after nonablative allogeneic marrow transplantation. J Immunol 2003;170:2711.PubMedGoogle Scholar
  33. 33.
    Kou Z.C., Puhr J.S., Wu S.S., Goodenow M.M., Sleasman J.W. Combination antiretroviral therapy results in a rapid increase in T cell receptor variable region beta repertoire diversity within CD45RA CD8 T cells in human immunodeficiency virus-infected children. J Infect Dis 2003;187:385.PubMedCrossRefGoogle Scholar
  34. 34.
    Imamura M., Tsutsumi Y., Miura Y., Toubai T., Tanaka J. Immune reconstitution and tolerance after allogeneic hematopoietic stem cell transplantation. Hematology 2003;8:19.PubMedCrossRefGoogle Scholar
  35. 35.
    Michalek J., Collins R.H., Durrani H.P., et al. Definitive separation of graft-versus-leukemia-and graft-versus-host-specific CD4+ T cells by virtue of their receptor beta loci sequences. Proc Natl Acad Sci U S A 2003;100:1180.PubMedCrossRefGoogle Scholar
  36. 36.
    Tsutsumi Y., Tanaka J., Miura Y., et al. Molecular analysis of T-cell repertoire in patients with graft-versus-host disease after allogeneic stem cell transplantation. Leuk Lymphoma 2004;45:481.PubMedCrossRefGoogle Scholar
  37. 37.
    Silins S.L., Cross S.M., Krauer K.G., Moss D.J., Schmidt C.W., Misko I.S. A functional link for major TCR expansions in healthy adults caused by persistent Epstein-Barr virus infection. J Clin Invest 1998;102:1551.PubMedCrossRefGoogle Scholar
  38. 38.
    Jager E., Jager D., Knuth A. Antigen-specific immunotherapy and cancer vaccines. Int J Cancer 2003;106:817.PubMedCrossRefGoogle Scholar
  39. 39.
    Kolowos W., Herrmann M., Ponner B.B., et al. Detection of restricted junctional diversity of peripheral T cells in SLE patients by spectratyping. Lupus 1997;6:701.PubMedCrossRefGoogle Scholar
  40. 40.
    Alam A., Lambert N., Lule J., et al. Persistence of dominant T cell clones in synovial tissues during rheumatoid arthritis. J Immunol 1996;156:3480.PubMedGoogle Scholar
  41. 41.
    Gulwani-Akolkar B., Akolkar P.N., Minassian A., et al. Selective expansion of specific T cell receptors in the inflamed colon of Crohn’s disease. J Clin Invest 1996;98:1344.PubMedCrossRefGoogle Scholar
  42. 42.
    Laplaud D.A., Ruiz C., Wiertlewski S., et al. Blood T-cell receptor beta chain transcriptome in multiple sclerosis. Characterization of the T cells with altered CDR3 length distribution. Brain 2004;127:981.PubMedCrossRefGoogle Scholar
  43. 43.
    Hong J., Zang Y.C., Li S., Rivera V.M., Zhang J.Z. Ex vivo detection of myelin basic protein-reactive T cells in multiple sclerosis and controls using specific TCR oligonucleotide probes. Eur J Immunol 2004;34:870.PubMedCrossRefGoogle Scholar
  44. 44.
    Koga M., Yuki N., Tsukada Y., Hirata K., Matsumoto Y. CDR3 spectratyping analysis of the T cell receptor repertoire in Guillain-Barre and Fisher syndromes. J Neuroimmunol 2003;141:112.PubMedCrossRefGoogle Scholar
  45. 45.
    Borgato L., Puccetti A., Beri R., et al. The T cell receptor repertoire in psoriatic synovitis is restricted and T lymphocytes expressing the same TCR are present in joint and skin lesions. J Rheumatol 2002;29:1914.PubMedGoogle Scholar
  46. 46.
    Saito M., Higuchi I., Saito A., et al. Molecular analysis of T cell clonotypes in muscle-infiltrating lymphocytes from patients with human T lymphotropic virus type 1 polymyositis. J Infect Dis 2002;186:1231.PubMedCrossRefGoogle Scholar
  47. 47.
    Killian M.S., Monteiro J., Matud J., et al. Persistent alterations in the T-cell repertoires of HIV-1-infected and at-risk uninfected men. Aids 2004;18:161.PubMedCrossRefGoogle Scholar
  48. 48.
    O’shea U., Wyatt J.I., Howdle P.D. Analysis of T cell receptor beta chain CDR3 size using RNA extracted from formalin fixed paraffin wax embedded tissue. J Clin Pathol 1997;50:811.PubMedCrossRefGoogle Scholar
  49. 49.
    Wilson J.D., Cranage M., Cook N., Leech S., McMichael A.J., Callan M.F. Evidence for the persistence of monoclonal expansions of CD8+ T cells following primary simian immunodeficiency virus infection. Eur J Immunol 1998;28:1172.PubMedCrossRefGoogle Scholar
  50. 50.
    Nilges K., Hohn H., Pilch H., et al. Human papillomavirus type 16 E7 peptide-directed CD8+ T cells from patients with cervical cancer are cross-reactive with the coronavirus NS2 protein. J Virol 2003;77:5464.PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2005

Authors and Affiliations

  • Markus J. Maeurer
    • 1
  1. 1.Microbiology and Tumor Biology Center (MTC), Clinical ImmunologyKarolinska Institute, SMISilnaSweden

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