Characterization of human αβTCR repertoire and discovery of D-D fusion in TCRβ chains

Protein and Cell

Volumn 5, Issue 8, 2014, Pages 603-615

  Liu, Peipei ^a,b   Liu, Di ^a   Yang, Xi ^a,b   Gao, Jing ^a,b   Chen, Yan ^a   Xiao, Xue ^a   Liu, Fei ^a   Zou, Jing ^a   Wu, Jun ^a   Ma, Juncai ^a   Zhao, Fangqing ^d   Zhou, Xuyu ^a,b   Gao, George F ^a,b,c,d   Zhu, Baoli ^a,b  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

^d INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

CDR3; D D fusion; next generation sequencing; TCR repertoire; V J pairing; V J usage

Indexed keywords

ALPHA BETA T LYMPHOCYTE RECEPTOR; T LYMPHOCYTE RECEPTOR; T LYMPHOCYTE RECEPTOR BETA CHAIN; UNCLASSIFIED DRUG; COMPLEMENTARITY DETERMINING REGION; IMMUNOGLOBULIN STRUCTURE; IMMUNOGLOBULIN VARIABLE REGION; LYMPHOCYTE ANTIGEN RECEPTOR; PRIMER DNA;

AMINO ACID SEQUENCE; ARTICLE; FEMALE; GENE AMPLIFICATION; GENE LIBRARY; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN; MALE; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PERIPHERAL BLOOD MONONUCLEAR CELL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; ULTRASOUND; CHEMISTRY; COMPLEMENTARITY DETERMINING REGION; GENETIC VARIABILITY; GENETICS; HIGH THROUGHPUT SEQUENCING; IMMUNOGLOBULIN STRUCTURE; IMMUNOGLOBULIN VARIABLE REGION; T LYMPHOCYTE RECEPTOR GENE;

COMPLEMENTARITY DETERMINING REGIONS; DNA PRIMERS; FEMALE; GENE REARRANGEMENT, BETA-CHAIN T-CELL ANTIGEN RECEPTOR; GENE REARRANGEMENT, DELTA-CHAIN T-CELL ANTIGEN RECEPTOR; GENES, T-CELL RECEPTOR BETA; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMMUNOGLOBULIN JOINING REGION; IMMUNOGLOBULIN VARIABLE REGION; MALE; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA;

EID: 84925883542     PISSN: 1674800X     EISSN: 16748018     Source Type: Journal    
DOI: 10.1007/s13238-014-0060-1     Document Type: Article

References (46)

1. Arstila TP, Casrouge A, Baron V, Even J, Kanellopoulos J, Kourilsky P (1999) A direct estimate of the human alphabeta T cell receptor diversity. Science 286:958–961
2. Bank I, Book M, Cohen L, Kneller A, Rosental E, Pras M, Bassat IB, Ben-Nun A (1992) Expansion of a unique subpopulation of cytotoxic T cells that express a C alpha V delta 1 T-cell receptor gene in a patient with severe persistent neutropenia. Blood 80:3157–3163
3. Bank I, Cohen L, Kneller A, de Rosbo NK, Book M, Ben-Nun A (2003) Aberrant T-Cell Receptor Signalling of Interferon-γ- and Tumour Necrosis Factor-α-Producing Cytotoxic CD8+Vδ1/Vβ16 T Cells in a Patient with Chronic Neutropenia. Scand J Immunol 58:89–98
4. Bassing CH, Swat W, Alt FW (2002) The mechanism and regulation of chromosomal V(D)J recombination. Cell 109(Suppl):S45–S55
5. Borgulya P, Kishi H, Uematsu Y, von Boehmer H (1992) Exclusion and inclusion of alpha and beta T cell receptor alleles. Cell 69:529–537
6. Castelli C, Mazzocchi A, Salvi S, Anichini A, Sensi M (1992) Use of the V delta 1 variable region in the functional T-cell receptor alpha chain of a WT31+ cytotoxic T lymphocyte clone which specifically recognizes HLA-A2 molecule. Scand J Immunol 35:487–494
7. Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA (2009) Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res 19:1817–1824
8. Fuschiotti P, Pasqual N, Hierle V, Borel E, London J, Marche PN, Jouvin-Marche E (2007) Analysis of the TCR alpha-chain rearrangement profile in human T lymphocytes. Mol Immunol 44:3380–3388
9. Genolet R, Stevenson BJ, Farinelli L, Osteras M, Luescher IF (2012) Highly diverse TCRalpha chain repertoire of pre-immune CD8(+) T cells reveals new insights in gene recombination. EMBO J 31:1666–1678
10. Gorski J, Yassai M, Zhu X, Kissela B, Kissella B, Keever C, Flomenberg N (1994) Circulating T cell repertoire complexity in normal individuals and bone marrow recipients analyzed by CDR3 size spectratyping. Correlation with immune status. J Immunol 152:5109–5119
11. Hempel WM, Stanhope-Baker P, Mathieu N, Huang F, Schlissel MS, Ferrier P (1998) Enhancer control of V(D)Jrecombination at the TCRβ locus: differential effects on DNA cleavage and joining. Genes & Development 12:2305–2317
12. Huang C, Kanagawa O (2001) Ordered and coordinated rearrangement of the TCR alpha locus: role of secondary rearrangement in thymic selection. J Immunol 166:2597–2601
13. Klarenbeek PL, Tak PP, van Schaik BD, Zwinderman AH, Jakobs ME, Zhang Z, van Kampen AH, van Lier RA, Baas F, de Vries N (2010) Human T-cell memory consists mainly of unexpanded clones. Immunol Lett 133:42–48
14. Klarenbeek PL, Remmerswaal EB, ten Berge IJ, Doorenspleet ME, van Schaik BD, Esveldt RE, Koch SD, ten Brinke A, van Kampen AH, Bemelman FJ et al (2012) 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
15. Krangel MS (2009) Mechanics of T cell receptor gene rearrangement. Curr Opin Immunol 21:133–139
16. Larimore K, McCormick MW, Robins HS, Greenberg PD (2012) Shaping of human germline IgH repertoires revealed by deep sequencing. J Immunol 189:3221–3230
17. Lefranc MP (2001) Nomenclature of the human T cell receptor genes. Curr Protoc Immunol Appendix 1, Appendix 1O
18. Lefranc MP (2011) From IMGT-ONTOLOGY CLASSIFICATION Axiom to IMGT standardized gene and allele nomenclature: for immunoglobulins (IG) and T cell receptors (TR). Cold Spring Harb Protoc 2011:627–632
19. Lefranc MP, Rabbitts TH (1990) Genetic organization of the human T-cell receptor gamma and delta loci. Res Immunol 141:565–577
20. Li H, Ye C, Ji G, Wu X, Xiang Z, Li Y, Cao Y, Liu X, Douek DC, Price DA et al (2012) Recombinatorial biases and convergent recombination determine interindividual TCRbeta sharing in murine thymocytes. J Immunol 189:2404–2413
21. Loh EY, Cwirla S, Serafini AT, Phillips JH, Lanier LL (1988) Human T-cell-receptor delta chain: genomic organization, diversity, and expression in populations of cells. Proc Natl Acad Sci USA 85:9714–9718
22. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402
23. Meek KD, Hasemann CA, Capra JD (1989) Novel rearrangements at the immunoglobulin D locus. Inversions and fusions add to IgH somatic diversity. J Exp Med 170:39–57
24. Miossec C (1990) Further analysis of the T cell receptor gamma/delta+ peripheral lymphocyte subset. The V delta 1 gene segment is expressed with either C alpha or C delta. J Exp Med 171:1171–1188
25. Miossec C, Caignard A, Ferradini L, Roman-Roman S, Faure F, Michalaki H, Triebel F, Hercend T (1991) Molecular characterization of human T cell receptor alpha chains including a V delta 1-encoded variable segment. Eur J Immunol 21:1061–1064
26. Murphy KM, Travers P, Walport M (2007) Janeway’s Immunobiology. UK, Garland Science, London
27. Neller MA, Burrows JM, Rist MJ, Miles JJ, Burrows SR (2013) High frequency of herpesvirus-specific clonotypes in the human T cell repertoire can remain stable over decades with minimal turnover. J Virol 87:697–700
28. Nikolich-Zugich J, Slifka MK, Messaoudi I (2004) The many important facets of T-cell repertoire diversity. Nat Rev Immunol 4:123–132
29. Olaru A, Petrie HT, Livak F (2005) Beyond the 12/23 rule of VDJ recombination independent of the Rag proteins. J Immunol 174:6220–6226
30. Ozawa T, Kishi H, Muraguchi A (2006) Amplification and analysis of cDNA generated from a single cell by 5′-RACE: application to isolation of antibody heavy and light chain variable gene sequences from single B cells. Biotechniques 40:469–478
31. Padovan E, Casorati G, Dellabona P, Meyer S, Brockhaus M, Lanzavecchia A (1993) Expression of two T cell receptor alpha chains: dual receptor T cells. Science 262:422–424
32. Pannetier C, Cochet M, Darche S, Casrouge A, Zoller M, Kourilsky P (1993) The Sizes of the Cdr3 Hypervariable Regions of the Murine T-Cell Receptor Beta-Chains Vary as a Function of the Recombined Germ-Line Segments. Proc Natl Acad Sci USA 90:4319–4323
33. Pasqual N, Gallagher M, Aude-Garcia C, Loiodice M, Thuderoz F, Demongeot J, Ceredig R, Marche PN, Jouvin-Marche E (2002) Quantitative and Qualitative Changes in V-J Rearrangements During Mouse Thymocytes Differentiation: Implication For a Limited T Cell Receptor Chain Repertoire. J Exp Med 196:1163–1174
34. Quigley MF, Greenaway HY, Venturi V, Lindsay R, Quinn KM, Seder RA, Douek DC, Davenport MP, Price DA (2010) Convergent recombination shapes the clonotypic landscape of the naive T-cell repertoire. Proc Natl Acad Sci U S A 107:19414–19419
35. Robins HS, Campregher PV, Srivastava SK, Wacher A, Turtle CJ, Kahsai O, Riddell SR, Warren EH, Carlson CS (2009) Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood 114:4099–4107
36. Robins HS, Srivastava SK, Campregher PV, Turtle CJ, Andriesen J, Riddell SR, Carlson CS, Warren EH (2010) Overlap and effective size of the human CD8+ T cell receptor repertoire. Sci Transl Med 2, 47ra64
37. Roth ME, Holman PO, Kranz DM (1991) Nonrandom use of J alpha gene segments. Influence of V alpha and J alpha gene location. J Immunol 147:1075–1081
38. Ryu CJ, Haines BB, Draganov DD, Kang YH, Whitehurst CE, Schmidt T, Hong HJ, Chen J (2003) The T cell receptor beta enhancer promotes access and pairing of Dbeta and Jbeta gene segments during V(D)J recombination. Proc Natl Acad Sci USA 100:13465–13470
39. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145
40. Sherwood AM, Desmarais C, Livingston RJ, Andriesen J, Haussler M, Carlson CS, Robins H (2011). Deep sequencing of the human TCRgamma and TCRbeta repertoires suggests that TCRbeta rearranges after alphabeta and gammadelta T cell commitment. Sci Transl Med 3, 90ra61
41. Takihara Y, Tkachuk D, Michalopoulos E, Champagne E, Reimann J, Minden M, Mak TW (1988) Sequence and organization of the diversity, joining, and constant region genes of the human T-cell delta-chain locus. Proc Natl Acad Sci U S A 85:6097–6101
42. Ueno T, Tomiyama H, Fujiwara M, Oka S, Takiguchi M (2003) HLA class I-restricted recognition of an HIV-derived epitope peptide by a human T cell receptor alpha chain having a Vdelta1 variable segment. Eur J Immunol 33:2910–2916
43. Venturi V, Quigley MF, Greenaway HY, Ng PC, Ende ZS, McIntosh T, Asher TE, Almeida JR, Levy S, Price DA et al (2011) A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J Immunol 186:4285–4294
44. Wang C, Sanders CM, Yang Q, Schroeder HW Jr, Wang E, Babrzadeh F, Gharizadeh B, Myers RM, Hudson JR Jr, Davis RW et al (2010) High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc Natl Acad Sci U S A 107:1518–1523
45. Warren RL, Freeman JD, Zeng T, Choe G, Munro S, Moore R, Webb JR, Holt RA (2011) Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res 21:790–797
46. Yousfi Monod M, Giudicelli V, Chaume D, Lefranc MP (2004) 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(Suppl 1):i379–i385