Comprehensive analysis of the T-cell receptor beta chain gene in rhesus monkey by high throughput sequencing

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Li, Zhoufang ^a   Liu, Guangjie ^b   Tong, Yin ^a   Zhang, Meng ^a   Xu, Ying ^c   Qin, Li ^b   Wang, Zhanhui ^c   Chen, Xiaoping ^b   He, Jiankui ^a  

^a SOUTHERN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH   (China)

^c SOUTHERN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARITY DETERMINING REGION; LYMPHOCYTE ANTIGEN RECEPTOR;

ANIMAL; COMPLEMENTARITY DETERMINING REGION; DNA SEQUENCE; GENETICS; MULTIPLEX POLYMERASE CHAIN REACTION; RHESUS MONKEY;

ANIMALS; COMPLEMENTARITY DETERMINING REGIONS; MACACA MULATTA; MULTIPLEX POLYMERASE CHAIN REACTION; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA; SEQUENCE ANALYSIS, DNA;

EID: 84929179993     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep10092     Document Type: Article

References (57)

1. Arif, S. et al. Autoreactive T cell responses show proinflammatory polarization in diabetes but a regulatory phenotype in health. The Journal of clinical investigation 113, 451-463, doi:10.1172/JCI19585 (2004).
2. Freeman, J. D., Warren, R. L., Webb, J. R., Nelson, B. H. & Holt, R. A. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome research 19, 1817-1824, doi:10.1101/gr.092924.109 (2009).
3. Levinson, G., Hughes, A. L. & Letvin, N. L. Sequence and diversity of rhesus monkey T-cell receptor beta chain genes. Immunogenetics 35, 75-88 (1992).
4. Jaeger, E. E., Bontrop, R. E. & Lanchbury, J. S. Structure, diversity, and evolution of the T-cell receptor VB gene repertoire in primates. Immunogenetics 40, 184-191 (1994).
5. Allen, T. M., Lanchbury, J. S., Hughes, A. L. & Watkins, D. I. The T-cell receptor beta chain-encoding gene repertoire of a New World primate species, the cotton-top tamarin. Immunogenetics 45, 151-160 (1996).
6. Uccelli, A. et al. Characterization of the TCRB chain repertoire in the New World monkey Callithrix jacchus. Journal of immunology 158, 1201-1207 (1997).
7. Currier, J. R., Stevenson, K. S. & Robinson, M. A. Molecular cloning and sequencing of cDNA encoding eight new rhesus macaque TCRBV gene families. Immunogenetics 51, 387-391 (2000).
8. Meyer-Olson, D. et al. Analysis of the TCR beta variable gene repertoire in chimpanzees: identification of functional homologs to human pseudogenes. Journal of immunology 170, 4161-4169 (2003).
9. Moncada, C. A. et al. The T-cell receptor in primates: identifying and sequencing new owl monkey TRBV gene sub-groups. Immunogenetics 57, 42-52, doi:10.1007/s00251-004-0758-y (2005).
10. Weinstein, J. A., Jiang, N., White, R. A., 3rd, Fisher, D. S. & Quake, S. R. High-throughput sequencing of the zebrafish antibody repertoire. Science 324, 807-810, doi:10.1126/science.1170020 (2009).
11. Wang, C. et al. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proceedings of the National Academy of Sciences of the United States of America 107, 1518-1523, doi:10.1073/ pnas.0913939107 (2010).
12. Robins, H. S. et al. Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood 114, 4099-4107, doi:10.1182/blood-2009-04-217604 (2009).
13. Ademokun, A. et al. Vaccination-induced changes in human B-cell repertoire and pneumococcal IgM and IgA antibody at different ages. Aging cell 10, 922-930, doi:10.1111/j.1474-9726.2011.00732.x (2011).
14. Wu, Y. C., Kipling, D. & Dunn-Walters, D. K. Age-Related Changes in Human Peripheral Blood IGH Repertoire Following Vaccination. Frontiers in immunology 3, 193, doi:10.3389/fimmu.2012.00193 (2012).
15. Jiang, N. et al. Lineage structure of the human antibody repertoire in response to influenza vaccination. Science translational medicine 5, 171ra119, doi:10.1126/scitranslmed.3004794 (2013).
16. Sherwood, A. M. et al. Deep sequencing of the human TCRgamma and TCRbeta repertoires suggests that TCRbeta rearranges after alphabeta and gammadelta T cell commitment. Science translational medicine 3, 90ra61, doi:10.1126/scitranslmed.3002536 (2011).
17. Robins, H. Immunosequencing: applications of immune repertoire deep sequencing. Current opinion in immunology 25, 646-652 (2013).
18. Boyd, S. D. et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Science translational medicine 1, 12ra23 (2009).
19. Logan, A. C. et al. High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment. Proceedings of the National Academy of Sciences of the United States of America 108, 21194-21199, doi:10.1073/pnas.1118357109 (2011).
20. Wu, D. et al. High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia. Science translational medicine 4, 134ra163, doi:10.1126/scitranslmed.3003656 (2012).
21. Turtle, C. J. & Riddell, S. R. Genetically retargeting CD8+ lymphocyte subsets for cancer immunotherapy. Curr. Opin. Immunol. 23, 299-305, doi:10.1016/j.coi.2010.12.012 (2011).
22. Grupp, S. A. et al. Adoptive transfer of autologous T cells improves T-cell repertoire diversity and long-term B-cell function in pediatric patients with neuroblastoma. Clinical cancer research : an official journal of the American Association for Cancer Research 18, 6732-6741, doi:10.1158/1078-0432.CCR-12-1432 (2012).
23. Brentjens, R. J. et al. CD19-targeted T cells rapidly induce molecular remissions in adults with chemotherapy-refractory acute lymphoblastic leukemia. Science translational medicine 5, 177ra138, doi:10.1126/scitranslmed.3005930 (2013).
24. van Heijst, J. W. et al. Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation. Nature medicine 19, 372-377, doi:10.1038/nm.3100 (2013).
25. Maecker, H. T. et al. New tools for classification and monitoring of autoimmune diseases. Nature reviews. Rheumatology 8, 317-328, doi:10.1038/nrrheum.2012.66 (2012).
26. Emerson, R. O. et al. High-throughput sequencing of T cell receptors reveals a homogeneous repertoire of tumor-infiltrating lymphocytes in ovarian cancer. The Journal of pathology, doi:10.1002/path.4260 (2013).
27. Parameswaran, P. et al. Convergent antibody signatures in human dengue. Cell host & microbe 13, 691-700, doi:10.1016/j. chom.2013.05.008 (2013).
28. Klarenbeek, P. L. et al. Inflamed target tissue provides a specific niche for highly expanded T-cell clones in early human autoimmune disease. Annals of the rheumatic diseases 71, 1088-1093, doi:10.1136/annrheumdis-2011-200612 (2012).
29. Reddy, S. T. et al. Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nature biotechnology 28, 965-969, doi:10.1038/nbt.1673 (2010).
30. DeKosky, B. J. et al. High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nature biotechnology 31, 166-169, doi:10.1038/nbt.2492 (2013).
31. Genolet, R., Stevenson, B. J., Farinelli, L., Osteras, M. & Luescher, I. F. Highly diverse TCRalpha chain repertoire of pre-immune CD8(+) T cells reveals new insights in gene recombination. The EMBO journal 31, 4247-4248, doi:10.1038/emboj.2012.277 (2012).
32. Price, D. A. et al. T cell receptor recognition motifs govern immune escape patterns in acute SIV infection. Immunity 21, 793-803, doi:10.1016/j.immuni.2004.10.010 (2004).
33. Gardner, M. B. & Luciw, P. A. Macaque models of human infectious disease. ILAR journal / National Research Council, Institute of Laboratory Animal Resources 49, 220-255 (2008).
34. Murayama, Y., Mukai, R., Inoue-Murayama, M. & Yoshikawa, Y. An African green monkey lacking peripheral CD4 lymphocytes that retains helper T cell activity and coexists with SIVagm. Clinical and experimental immunology 117, 504-512 (1999).
35. Marcondes, M. C. et al. Simian immunodeficiency virus-induced CD4+ T cell deficits in cytokine secretion profile are dependent on monkey origin. Viral immunology 19, 679-689, doi:10.1089/vim.2006.19.679 (2006).
36. Sircar, P., Furr, K. L., Dorosh, L. A. & Letvin, N. L. Clonal repertoires of virus-specific CD8+ T lymphocytes are shared in mucosal and systemic compartments during chronic simian immunodeficiency virus infection in rhesus monkeys. Journal of immunology 185, 2191-2199, doi:10.4049/jimmunol.1001340 (2010).
37. Kwofie, T. & Miura, T. Increased Virus Replication and Cytotoxicity of Non-pathogenic Simian Human Immuno Deficiency Viruses-NM-3rN After Serial Passage in a Monkey-Derived Cell Line. Annals of medical and health sciences research 3, 55-61, doi:10.4103/2141-9248.109490 (2013).
38. Ribi, E. et al. Efficacy of mycobacterial cell walls as a vaccine against airborne tuberculosis in the Rheusus monkey. The Journal of infectious diseases 123, 527-538 (1971).
39. Schmidt-Ullrich, R., Wallach, D. F. & Lightholder, J. Two Plasmodium knowlesi-specific antigens on the surface of schizontinfected Rhesus monkey erythrocytes induce antibody production in immune hosts. The Journal of experimental medicine 150, 86-99 (1979).
40. Mahowald, G. K., Mahowald, M. A., Moon, C., Khor, B. & Sleckman, B. P. Out-of-frame T cell receptor beta transcripts are eliminated by multiple pathways in vivo. PloS one 6, e21627, doi:10.1371/journal.pone.0021627 (2011).
41. Brogna, S. & Wen, J. Nonsense-mediated mRNA decay (NMD) mechanisms. Nature structural & molecular biology 16, 107-113, doi:10.1038/nsmb.1550 (2009).
42. Gillet, N. A. et al. The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones. Blood 117, 3113-3122, doi:10.1182/blood-2010-10-312926 (2011).
43. Giudicelli, V., Chaume, D. & Lefranc, M. P. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic acids research 33, D256-261, doi:10.1093/nar/gki010 (2005).
44. Brochet, X., Lefranc, M. P. & Giudicelli, V. IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic acids research 36, W503-508, doi:10.1093/nar/gkn316 (2008).
45. Giudicelli, V., Brochet, X. & Lefranc, M. P. IMGT/V-QUEST: IMGT standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences. Cold Spring Harbor protocols 2011, 695-715, doi:10.1101/pdb.prot5633 (2011).
46. Kondilis-Mangum, H. D., Shih, H. Y., Mahowald, G., Sleckman, B. P. & Krangel, M. S. Regulation of TCRbeta allelic exclusion by gene segment proximity and accessibility. Journal of immunology 187, 6374-6381, doi:10.4049/jimmunol.1102611 (2011).
47. Naramura, M., Kole, H. K., Hu, R. J. & Gu, H. Altered thymic positive selection and intracellular signals in Cbl-deficient mice. Proceedings of the National Academy of Sciences of the United States of America 95, 15547-15552 (1998).
48. Hsieh, C. S., Lee, H. M. & Lio, C. W. Selection of regulatory T cells in the thymus. Nature reviews. Immunology 12, 157-167, doi:10.1038/nri3155 (2012).
49. Clute, S. C. et al. Broad cross-reactive TCR repertoires recognizing dissimilar Epstein-Barr and influenza A virus epitopes. Journal of immunology 185, 6753-6764, doi:10.4049/jimmunol.1000812 (2010).
50. Degauque, N. et al. The blood of healthy individuals exhibits CD8 T cells with a highly altered TCR Vb repertoire but with an unmodified phenotype. PloS one 6, e21240, doi:10.1371/journal.pone.0021240 (2011).
51. Efron B. T. R. Estimating the number of un- seen species: How many words did Shakespeare know? Biometrika 63, 435-447 (1976).
52. Cabaniols, J. P., Fazilleau, N., Casrouge, A., Kourilsky, P. & Kanellopoulos, J. M. Most alpha/beta T cell receptor diversity is due to terminal deoxynucleotidyl transferase. The Journal of experimental medicine 194, 1385-1390 (2001).
53. Bolotin, D. A. et al. Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms. European journal of immunology 42, 3073-3083, doi:10.1002/eji.201242517 (2012).
54. de Bourcy, C. F. et al. A quantitative comparison of single-cell whole genome amplification methods. PloS one 9, e105585, doi:10.1371/journal.pone.0105585 (2014).
55. Shugay, M. et al. Towards error-free profiling of immune repertoires. Nature methods 11, 653-655, doi:10.1038/nmeth.2960 (2014).
56. Qu, W. et al. MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity. Nucleic acids research 40, W205-208, doi:10.1093/nar/gks552 (2012).
57. Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963, doi:10.1093/bioinformatics/btr507 (2011).