Abstract
The aim of this work was to assess whether each T-cell receptor (TCR) BV segment generates a random pattern of junctional diversity or if, alternatively, biased patterns of V-D-J rearrangements limit the number of available TCR specificities. Detailed molecular analysis of T-cell receptors expressed by lymphocytes was obtained by generating a large number of junctional regions sequences from TCRBV3, TCRBV4, TCRBV5S1, TCRBV12, TCRBV13S2, TCRBV17, TCRBV20, and TCRBV22 variable genes. The > 800 sequences analyzed have allowed the characterization of the recombination frequencies of each germline-encoded V,D, and J segments, as well as of the magnitude of exonucleolytic nibbling and of the number of N nucleotides inserted for each group of TCRB segments. The data obtained indicate that the extent of junctional diversity varies considerably depending on the TCRBV gene implicated in the recombination event, due to the occurrence of skewed patterns of J and D region usage. Furthermore, our results show that “illegitimate” rearrangements occur with unexpectedly high incidence, specifically at the level of TCRBD to TCRBJ joining. These findings provide additional information for a more accurate estimation of the size of the TCRBV repertoire and for understanding the well-established biased pattern of TCRBV expression in humans.
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Acha-Orbea, H., Shakhov, A. N., Scarpellino, L., Kolb, E., Muller, V., Vessaz-Shaw, A., Fuchs, R., Blochlinger, K., Rollini, P., Billotte, J., Sarafidou, M., MacDonald, H. R., and Diggelmann, H. Clonal deletion of Vβ14-bearing T cells in mice transgenic for mammary tumour virus. Nature 350: 207–211, 1991
Aster, J. C. and Sklar, J. Interallelic V(D)J trans-rearrangement within the \ T cell receptor gene is infrequent and occurs preferentially during attempted Dβ to Jβ joining. J Exp Med 175: 1773–1782, 1992
Blackman, M., Kappler, J., and Marrack, P. The role of the cell receptor in positive and negative selection of developing T cells. Science 248: 1335–1341, 1990
Candéias, S., Waltzinger, C., Benoist, C., and Mathis, D. The Vβ17+ T cell repertoire: skewed Jβ usage after thymic selection; dissimilar CDR3s in CD4+ versus CD8+cells. J Exp Med 174: 989–1000, 1991
Chien, Y.-H., Gascoigne, N. R. J., Kavaler, J., Lee, N. E., and Davis, M. M. Somatic recombination in a murine T-cell receptor gene. Nature 309: 322–326, 1984
Choi, Y., Kotzin, B., Herron, L., Callahan, J., Marrack, P., and Kappler, J. Interaction of Staphylococcus aureus toxin “super-antigens” with human cells. Proc Natl Acad Sci USA 86: 8941–8945, 1989
Chomczynski, P. and Sacchi, N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162: 156–159, 1987
Clothia, C., Boswell, D. R., and Lesk, A. M. The outline structure of the T-cell αβ receptor. EMBO J 7: 3745–3755, 1988
Concannon, P., Pickering, L. A., Kung, P., and Hood, L. Diversity and structure of human T-cell receptor \-chain variable region genes. Proc Natl Acad Sci USA 83: 6598–6602, 1986
Cuisinier, A. M., Fumoux, F., Moinier, D., Boubli, L., Guigou, V., Milili, M., Schiff, C., Fougereau, M., and Tonnelle, C. Rapid expansion of human immunoglobulins repertoire (V H, VK and V λ) expressed in early fetal bone marrow. New Biol 2: 689–799, 1990
Davis, M. M. Molecular genetics of the T-cell receptor β chain. Annu Rev Immunol 3: 537–560, 1985
Davis, M. M. T cell antigen receptor genes. In B. D. Hames and D. M. Glover (eds.): Molecular Immunology, pp. 61–79, IRL Press, Washington DC, 1988
Davis, M. M. and Bjorkman, P. J. T-cell antigen receptor genes and T-cell recognition. Nature 334: 395–402, 1988
Dyson, P. J., Knight, A. M., Fairchild, S., Simpson, E., and Tomonari, K. Genes encoding ligands for deletion of Vβ11 T cells consegregate with mammary tumour virus genomes. Nature 349: 531–532, 1991
Ferradini, L., Roman-Roman, S., Azocar, J., Michalaki, H., Triebel, F., and Hercend, T. Studies on the human T cell receptor α/β variable region genes II. Identification of four additional Vβ subfamilies. Eur J Immunol 21: 935–942, 1991
Gascoigne, N. R. J., Chien, Y.-H., Becker, D. M., Kavaler, J., and Davis, M. M. Genomic organization and sequence of T-cell receptor β-chain constant and joining region genes. Nature 310: 387–391, 1994
Hinds-Frey, K., Nishikata, H., Litman, R. T., and Litman, G. W. Somatic variation precedes extensive diversification of germline sequences and combinatorial joining in the evolution of immunoglobulin heavy chain diversity. J Exp Med 178: 815–824, 1993
Hochtl, J., Muller, C. R., and Zachau, H. G. Recombined flanks of the variable and joining segments of immunoglobulin genes. Proc Natl Acad Sci USA 79: 1383–1387, 1982
Ikuta, K., Ogura, T., Shimizu, A., and Honjo, T. Low frequency of somatic mutation in β-chain variable region genes of human T-cell receptors. Proc Natl Acad Sci USA 82: 7701–7705, 1985
Jeong, H. D. and Teale, J. M. comparison of the fetal and adult functional repertoire by analysis of VH family expression. J Exp Med 168: 417–435, 1988
Kappler, J. W., Rohehm, N., and Marrack, P. T cell tolerance by clonal elimination in the thymus. Cell 49: 273–280, 1987
Kimura, N., Toyonaga, B., Yoshikai, Y., Triebel, F., Debre, P., Minden, M. D., and Mak, T. W. Sequences and diversity of the human T cell receptor β chain variable region. J Exp Med 164: 739–750, 1986
Kimura, N., Toyonaga, B., Yoshikai, Y., Du, R.-P., and Mak, T. W. Sequences and repertoire of human T cell receptor α and β chain variable region genes in thymocytes. Eur J Immunol 17: 375–383, 1987
Kronenberg, M., Siu, G., Hood, L., and Shastri, N. The molecular genetics of the T-cell antigen receptor and T-cell antigen recognition. Annu Rev Immunol 4: 529–547, 1986
Lai, E., Wilson, R. K., and Hood, L. E. Physical maps of the mouse and human immunoglobulin-like loci. Adv Immunol 46: 1–58, 1989
Lewis, S., Gifford, A., and Baltimore, D. Joining of Vk to Jk gene segments in a retroviral vector introduced into lymphoid cells. Nature 308: 425–428, 1984
Lipkowitz, S., Stern, M.-H., and Kirsch, I. R. Hybrid T cell receptor genes formed by interlocus recombination in normal and ataxia-telangiectasia lymphocytes. J Exp Med 172: 409–418, 1990
Malissen, M., Minard, K., Mjolsness, S., Kronenberg, M., Goverman, J., Hunkapiller, T., Prystowsky, M. B., Yoshikai, Y., Fitch, F., Mak, T. W. and Hood, L. Mouse T-cell antigen receptor: structure and organization of constant and joining gene segments encoding the β polypeptide. Cell 37: 1101–1110, 1984
Malissen, M., McCoy, C., Blanc, D., Trucy, J., Devaux, C., Schmitt-Verhulst, A.-M., Fitch, F., Hood, L., and Malissen, B. Direct evidence for chromosomal inversion during T-cell receptor β-gene rearrangements. Nature 319: 28–33, 1986
Marolleau, J.-P., Fondell, J. D., Malissen, M., Trucy, J., Barbier, E., Marcu, K. B., Cazenave, P.-A., and Primi, D. The joining of germline Vα to Jα genes replaces the preexisting Vα-Jβ complexes in a T cell receptor, α, β positive T cell line. Cell 55: 291–300, 1988
Marrack, P., and Kappler, J. The T cell receptor, Science 238: 1073–1079, 1987
Pannetier, C., Cochet, M., Darche, S., Casrouge, A., Zoller, M., and Kourilsky, P. The sizes of the CDR3 hypervariable regions of the murine T-cell receptor β chains vary as a function of the recombined germ-line segments. Proc Natl Acad Sci USA 90: 4319–4323, 1993
Rosenberg, W. M. C., Moss, P. A. H., and Bell, J. I. Variation in human T cell receptor Vβ and Jβ repertoire: analysis using anchor polymerase chain reaction. Eur J Immunol 22: 541–549, 1992
Sanger, F., Nicklen, S., and Coulson, A. R. DNA sequencing with chain-terminating inhibitor. Proc Natl Acad Sci USA 74: 5463–5467, 1987
Schroeder, H. W., Walter, M. A., Hofker, M. H., Ebens, A., Van Dijk, K. W., Liao, L. C., Cox, D. W., Milner, E. C. B., and Perlmutter, R. M. Physical linkage of a human immunoglobulin heavy chain variable region gene segment to diversity and joining region elements. Proc Natl Acad Sci USA 85: 8196–8200, 1988
Schroeder, H. W., and Wang, J. Y. Preferential utilization of conserved immunoglobulin heavy chain variable gene segments during fetal life. Proc Natl Acad Sci USA 87: 6146–6150, 1990
Selsing, E. and Storb, U. Mapping of immunoglobulin variable region genes: relationship to the “deletion” model of immunoglobulin gene rearrangement. Nucleic Acids Res 9: 5725–5735, 1989
Siu, G., Clark, S. P., Yoshikai, Y., Malissen, M., Yanagi, Y., Strauss, E., Mak, T. W., and Hood, L. The human T-cell antigen receptor is encoded by variable, diversity and joining gene segments that rearrange to generate a complete V gene. Cell 37: 393–401, 1984a
Siu, G., Kronenberg, M., Strauss, E., Haars, R., Mak, T. M., and Hood, L. The structure, rearrangement and expression of Dβ gene segments of the murine T-cell antigen receptor. Nature 311: 344–350, 1984b
Toyonaga, B. and Mak, T. W. Genes of the T-cell antigen receptor in normal and malignant T cells. Annu Rev Immunol 5: 585–620, 1987
Tycko, B., Palmer, J. D., and Sklar, J. T cell receptor gene trans-rearrangements: chimeric ψ-Σ genes in normal lymphoid tissues. Science 245: 1242–1246, 1989
Van Dijk, K. W., Milner, L. A., Sasso, E. H., and Milner, E. C. B. Chromosomal organization of heavy chain variable region gene segments comprising the human fetal antibody repertoire. Proc Natl Acad Sci USA 89: 10430–10434, 1992
Van Ness, B. G., Coleclough, C., Perry, R. P., and Weigert, M. DNA between variable and joining gene segments of immunoglobulin K light chain is frequently retained in cells that rearrange in the K locus. Proc Natl Acad Sci USA 79: 262–266, 1982
Weiss, A. Structure and function of the T cell antigen receptor. J Clin Invest 86: 1015–1022, 1990
WHO-IUIS Nomenclature Sub-Committee on TCR Designation. Nomenclature for T-cell receptor (TCR) gene segments of the immune system. Bull WHO 71: 113–115, 1993
Wilson, R. K., Lai, E., Concannon, P., Barth, R. K., and Hood, L. E. Structure, organization and polymorphism of murine and human T-cell α and β receptor gene families. Immunol Rev 101: 149–172, 1988
Woodland, D. L., Happ, M. P., Gollob, K. J., and Palmer, E. An endogenous retrovirus mediating deletion of αβ T cells? Nature 349: 529–530, 1991
Yancopoulos, G. D., Malynn, B. A., and Alt, F. W. Developmentally regulated and strain-specific expression of murine V H gene families. J Exp Med : 589–603, 1988
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The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession number DS 19973
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Roldan, E.Q., Sottini, A., Bettinardi, A. et al. Different TCRBV genes generate biased patterns of V-D-J diversity in human T cells. Immunogenetics 41, 91–100 (1995). https://doi.org/10.1007/BF00182318
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DOI: https://doi.org/10.1007/BF00182318