αβ T cell receptors as predictors of health and disease

Cellular and Molecular Immunology

Volumn 12, Issue 4, 2015, Pages 391-399

  Attaf, Meriem ^a   Huseby, Eric ^b   Sewell, Andrew K ^a  

^a CARDIFF UNIVERSITY SCHOOL OF MEDICINE   (United Kingdom)

^b UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

Deep sequencing; T cell receptor (TCR); TCR bias; TCR clonotype; TCR diversity; TCR repertoire

Indexed keywords

AMINOPEPTIDASE I; IMMUNOGLOBULIN HEAVY CHAIN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; PROTEIN ERAP1; T LYMPHOCYTE RECEPTOR ALPHA CHAIN; T LYMPHOCYTE RECEPTOR BETA CHAIN; UNCLASSIFIED DRUG; ANTIGEN; BIOLOGICAL MARKER; HISTOCOMPATIBILITY ANTIGEN; LYMPHOCYTE ANTIGEN RECEPTOR;

ACUTE LYMPHOBLASTIC LEUKEMIA; ANTIGEN PRESENTATION; ARTHRITIS; ARTICLE; AUTOIMMUNE DISEASE; AUTOIMMUNITY; CD8+ T LYMPHOCYTE; CELL EXPANSION; CELL SUBPOPULATION; CORD BLOOD STEM CELL TRANSPLANTATION; DISEASE MARKER; DNA METHYLATION; GENE FREQUENCY; GENE LOCUS; HAPLOTYPE; HERPES SIMPLEX VIRUS 1; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; IMMUNE RESPONSE; LYMPHATIC LEUKEMIA; LYMPHOCYTE; MONOZYGOTIC TWINS; MULTIPLE SCLEROSIS; NONHUMAN; PHENOTYPE; SIBLING; T LYMPHOCYTE; THYMOCYTE; VIRUS LOAD; VIRUS REPLICATION; ANIMAL; IMMUNOLOGY; PATHOLOGY; THYMUS;

ANIMALS; ANTIGENS; BIOMARKERS; HISTOCOMPATIBILITY ANTIGENS; HUMANS; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA; T-LYMPHOCYTES; THYMUS GLAND;

EID: 84936066884     PISSN: 16727681     EISSN: 20420226     Source Type: Journal    
DOI: 10.1038/cmi.2014.134     Document Type: Article

References (59)

1. Alam SM, Davies GM, Lin CM, Zal T, Nasholds W, Jameson SC, et al. Qualitative and quantitative differences in T cell receptor binding of agonist and antagonist ligands. Immunity 1999; 10: 227-237
2. Almeida A, Rocha B, Freitas AA, Tanchot C. Homeostasis of T cell numbers: from thymus production to peripheral compartmentalization and the indexation of regulatory T cells. Sem Immunol 2005; 17: 239-249
3. Kappler J, Kubo R, Haskins K, Hannum C, Marrack P, Pigeon M, et al. The major histocompatibility complex-restricted antigen receptor on T cells in mouse and man: identification of constant and variable peptides. Cell 1983; 35: 295-302
4. Raulet DH. The structure, function and molecular genetics of the cd T cell receptor. Annu Rev Immunol 1989; 7: 175-207
5. Chothia C, Boswell DR, Lesk AM. The outline structure of the T cell ab receptor. EMBO J 1988; 7: 3745
6. Yui MA, Rothenberg EV. Developmental gene networks: a triathlon on the course to T cell identity. Nat Rev Immunol 2014; 14: 529-545
7. Shinkai Y, Rathbun G, Lam KP, Oltz EM, Stewart V, Mendelsohn M, et al. RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement. Cell 1992; 68: 855-867
8. Corneo B, Moshous D, Güngör T, Wulffraat N, Philippet P, Le Deist FL, et al. Identical mutations in RAG1 or RAG2 genes leading to defective V(D)J recombinase activity can cause either T-B-severe combined immune deficiency or Omenn syndrome. Blood 2001; 97: 2772-2776
9. Villa A, Sobacchi C, Notarangelo LD, Bozzi F, Abinun M, Abrahamsen TG, et al. V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. Blood 2001; 97: 81-88
10. Aleman K, Noordzij JG, de Groot R, van Drogen JJ, Hartwig NG. Reviewing Omenn syndrome. Eur J Pediatr 2001; 160: 718-725
11. Davis MM, Bjorkman PJ. T cell antigen receptor genes and T cell recognition. Nature 1988; 334: 395-402
12. Sewell AK. Why must T cells be crossreactive? Nat Rev Immunol 2012; 12: 669-677
13. Casrouge A, Beaudoing E, Dalle S, Pannetier C, Kanellopoulos J, Kourilsky P. Size estimate of the alpha beta TCR repertoire of naive mouse splenocytes. J Immunol 2000; 164: 5782-5787
14. Arstila T, Casrouge A, Baron V, Even J, Kanellopoulos J, Kourilsky P. A direct estimate of the human ab T cell receptor diversity. Science 1999; 286: 958-961
15. Yancopoulos GD, Alt FW. Developmentally controlled and tissuespecific expression of unrearranged VH gene segments. Cell 1985; 40: 271-281
16. Ebert A, Medvedovic J, Tagoh H, Schwickert TA, Busslinger M. Control of antigen receptor diversity through spatial regulation of V(D)J recombination. Cold Spring Harb Symp Quant Biol 2013; 78: 11-21
17. Krangel MS, McMurry MT, Hernandez-Munain C, Zhong XP, Carabana J. Accessibility control of T cell receptor gene rearrangement in developing thymocytes. The TCR alpha/delta locus. Immunol Res 2000; 22: 127-135
18. Mathieu N, Hempel WM, Spicuglia S, Verthuy C, Ferrier P. Chromatin remodelling by the T cell receptors (TCR)-b gene enhancer during early T cell development: implications for the control of TCR-b locus recombination. J Exp Med 2000; 192: 625-636
19. Choi NM, Loguercio S, Verma-Gaur J, Degner SC, Torkamani A, Su AI, et al. Deep sequencing of the murine IgH repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies. J Immunol 2013; 191: 2393-2402
20. Genolet R, Stevenson BJ, Farinelli, østerås M, Luescher IF. Highly diverse TCRa chain repertoire of pre-immune CD81 T cells reveals new insights in gene recombination. EMBO J 2012; 31: 1666-1678
21. Li H, Ye C, Ji G, Wu X, Xiang Z, Li Y, et al. Recombinatorial biases and convergent recombination determine interindividual TCRb sharing in murine thymocytes. J Immunol 2012; 189: 2404-2413
22. Furmanski AL, Ferreira C, Bartok I, Dimakou S, Rice J, Stevenson FK, et al. Public T cell receptor beta-chains are not advantaged during positive selection. J Immunol 2008; 180: 1029-1039
23. van Laethem F, Tikhonova AN, Singer A. MHC restriction is imposed on a diverse T cell receptor repertoire by CD4 and CD8 co-receptors during thymic selection. Trends Immunol 2012; 33: 437-441
24. Goldrath AW, Bevan MJ. Selecting and maintaining and diverse T cell repertoire. Nature 1999; 402: 255-262
25. Nikolich-Zugich J, Bevan MJ. Role of self-peptides in positively selecting the T cell repertoire. Nature 1990; 344: 65
26. Anderson G, Partington KM, Jenkinson EJ. Differential effects of peptide diversity and stromal cell type in positive and negative selection in the thymus. J Immunol 1998; 161: 6599-6603
27. Bevan MJ. In thymic selection, peptide diversity gives and takes away. Immunity 1997; 7: 175-178
28. Dyall R, Messaoudi I, Janetzki S, Nikolich-Zugich J. MHC polymorphism can enrich the T cell repertoire of the species by shifts in intrathymic selection. J Immunol 2000; 164: 1695-1698
29. Messaoudi I, Guevara Patino A, Dyall R, LeMaoult J, Nikolich-Zugich J. Direct link between mhc polymorphism, T cell avidity, and diversity in immune defense. Science 2002; 298: 1797-1800
30. Ashton-Rickardt P, van Kaer L, Schumacher TN, Ploegh HL, Tonegawa S. Peptide contributes to the specificity of positive selection of CD81 T cells in the thymus. Cell 1993; 73: 1041
31. Hogquist KA, Gavin MA, Bevan MJ. Positive selection of CD81 T cells induced by major histocompatibility complex binding peptides in fetal thymic organ culture. J Exp Med 1994; 177: 1469-1473
32. Reeves E, Edwards CJ, Elliott T, James E. Naturally occurring ERAP1 haplotypes encode functionally distinct alleles with fine substrate specificity. J Immunol 2011; 191: 35-43
33. Nitta T, Murata S, Sasaki K, Fujii H, Ripen A, Ishimaru N, et al. Thymoproteasome shapes immunocompetent repertoire of CD81 T cells. Immunity 2010; 32: 29-40
34. Xing Y, Jameson SC, Hogquist KA. Thymoproteasome subunit-b5T generates peptide-MHC complexes specialized for positive selection. Proc Natl Acad Sci USA 2013; 110: 6979-6984
35. Blackman M, Woodland DL. The narrowing of the CD8 T cell repertoire in old age. Curr Opin Immunol 2011; 23: 537-542
36. Rudd BD, Venturi V, Davenport MP, Nikolich-Zugich J. Evolution of the antigen-specific CD81 TCR repertoire across the life span: evidence of clonal homogenization of the old TCR repertoire. J Immunol 2011; 186: 2056-2064
37. Qi Q, Liu Y, Cheng Y, Glanville J, Zhang D, Lee JY, et al. Diversity and clonal selection in the human T cell repertoire. Proc Natl Acad Sci USA 2014; 111: 13139-13144
38. Robins HS, Srivastava SK, Campregher PV, Turtle CJ, Andriesen J, Riddell SR, et al. Overlap and effective size of the human CD81 T cell receptor repertoire. Sci Transl Med 2010; 2: 47ra64
39. 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: e1001198
40. Price DA, Asher TE, Wilson NA, Nason MC, Brenchley JM, Metzler IS, et al. Public clonotype usage identifies protective Gag-specific CD81 T cell responses in SIV infection. J Exp Med 2009; 206: 923-936
41. Chen H, Ndhlovu ZM, Liu D, Porter LC, Fang JW, Darko S, et al. TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1infection. Nat Immunol 2012; 13: 691-702
42. Clemente MJ, Przychodzen B, Jerez A, Dienes BE, Afable MG, Husseinzadeh H, et al. Deep sequencing of the T cell receptor repertoire in CD81 T-large granular lymphocyte leukemia identifies signature landscapes. Blood 2013; 122: 4077-4085
43. Wu Q, Pesenacker AM, Stansfield A, King D, Barge D, Poster HE, et al. Immunological characteristics and T cell receptor clonal diversity in children with systemic juvenile idiopathic arthritis undergoing T celldepleted autologous stem cell transplantation. Immunology 142: 227-236
44. von Boehmer H, Teh HS, Kisielow P. The thymus selects the useful, neglects the useless and destroys the harmful. Immunol Today 1989; 10: 57-61
45. Maeda T, Sumida T, Kurasawa K, Tomioka H, Itoh I, Yoshida S, et al. Tlymphocyte-receptor repertoire of infiltrating T lymphocytes into NOD mouse pancreas. Diabetes 1991; 40: 1580-1585
46. Osman GE, Toda M, Kanagawa O, Hood L. Characterization of the T cell receptor repertoire causing collagen arthritis in mice. J Exp Med 1993; 172: 387-395
47. Ferreira C, Palmer D, Blake K, Garden OA, Dyson J. Reduced regulatory T cell diversity in NOD mice is linked to early events in the thymus. J Immunol 2014; 192: 4145-4152
48. Föhse L, Suffner J, Suhre K, Wahl B, Lindner C, Lee CW, et al. High TCR diversity ensures optimal function and homeostasis of Foxp31 regulatory T cells. Eur J Immunol 2011; 41: 3101-3113
49. Gulwani-Akolkar B, Posnett DN, Janson CH, Grunewald J, Wigzell H, Akolkar P, et al. T cell receptor V-segment frequencies in peripheral blood T cells correlate with human leukocyte antigen type. J Exp Med 1991; 174: 1139-1146
50. Davey MP, Meyer MM, Bakke AC. T cell receptor Vb gene expression in monozygotic twins, discordance in CD8subset and in disease states. J Immunol 1994; 152: 315-321
51. Yu XG, Lichterfeld M, Williams KL, Martinez-Picado J, Walker BD. Random T cell receptor recruitment in human immunodeficiency virus type 1 (HIV-1)-specific CD81 T cells from genetically identical twins infected with the same HIV-1 strain. J Virol 2007; 81: 12666-12669
52. Fozza C, Contini S, Corda G, Virdis P, Galleu A, Bonfigli S, et al. T cell receptor repertoire analysis in monozygotic twins concordant and discordant for type 1 diabetes. Immunobiology 2012; 217: 920-925
53. Somma P, Ristori G, Battistini L, Cannoni S, Borsellino G, Diamantini A, et al. Characterization of CD81 T cell repertoire in identical twins discordant and concordant for multiple sclerosis. J Leukoc Biol 2007; 81: 696-710
54. Utz U, Biddison WE, MacFarland HF, McFarlin DE, Flerlage M, Martin R. Skewed T cell receptor repertoire in genetically identical twins correlates with multiple sclerosis. Nature 1993; 364: 243-247
55. Lossius A, Johansen JN, Vardtal F, Robins H, Jurate S, Holmøy T, et al. High-throughput sequencing of TCR repertoires in multiple sclerosis reveal intrathecal enrichment of EBV-reactive CD81 T cells. Eur J Immunol 2014; 44: 3439-3452
56. Skowera A, Ladell K, McLaren JE, Dolton G, Matthews KK, Gostick E, et al. b-cell-specific CD8 T cell phenotype in type 1 diabetes reflects chronic autoantigen exposure. Diabetes 2014; in press
57. Zyvagin IV, Pogorelyy MV, Ivanova ME, Komech EA, Shugay M, Bolotin DA, et al. Distinctive properties of identical twins TCR repertoires revealed by high-throughput sequencing. Proc Natl Acad Sci USA 2014; 111: 5980-5985
58. Rossjohn J, Gras S, Miles JJ, Turner SJ, Godfrey DI, McCluskey J. T cell antigen receptor recognition of antigen-presenting molecules. Annu Rev Immunol 2014; 33: in press
59. Allam A, Kabelitz D. TCR trans rearrangements: biological significance in antigen recognition versus the role as lymphoma marker. J Immunol 2006; 176: 5707-5712