TCR-clonotyping-based Analysis of a Frenemy —Public T Cells

 
 
International Journal of Biotech Trends and Technology (IJBTT)
 
© 2015 by IJBTT Journal
Volume - 5 Issue - 1                          
Year of Publication : 2015
Authors : Huihui Qi, Yang Li, Liguang Sun

Huihui Qi, Yang Li, Liguang Sun " TCR-clonotyping-based Analysis of a Frenemy —Public T Cells ", International Journal of Biotech Trends and Technology (IJBTT), V5(1):33-37 Jan - Mar 2015, Published by Seventh Sense Research Group.

Abstract

Public T cells are characterized by a T-cell population bearing identical T-cell receptor (TCR) amino acid sequences in a majority of individuals. However, due to their out-of-balance production, they may serve as both "friend" and "enemy", i.e. a frenemy in many physiological and pathological activities. Thanks to the development of advanced TCR-clonotyping methods, such as next generation sequencing (NGS), we can gain a better understanding of public T-cell responses. In this review, we commenced with the underlying mechanisms of public TCR-production, and then discussed some researches that have been successfully utilized as a new method for the study of the CDR3 regions of the public and private TCRs, and we further explored the merits and demerits of the public T cells in different diseases. Finally, we discussed the current challenges and future hot focuses.

References

[1] D. Koning, A. I. Costa, I. Hoof, J. J. Miles, N. M. Nanlohy, K. Ladell, et al., "CD8+ TCR repertoire formation is guided primarily by the peptide component of the antigenic complex," J Immunol, vol. 190, pp. 931-9, Feb 1 2013.
[2] E. W. Newell and M. M. Davis, "Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells," Nat Biotechnol, vol. 32, pp. 149-57, Feb 2014.
[3] M. Chapman, E. H. Warren, 3rd, and C. J. Wu, "Applications of next-generation sequencing to blood and marrow transplantation," Biol Blood Marrow Transplant, vol. 18, pp. S151-60, Jan 2012.
[4] J. D. Freeman, R. L. Warren, J. R. Webb, B. H. Nelson, and R. A. Holt, "Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing," Genome Res, vol. 19, pp. 1817-24, Oct 2009.
[5] K. J. Jackson, M. J. Kidd, Y. Wang, and A. M. Collins, "The shape of the lymphocyte receptor repertoire: lessons from the B cell receptor," Front Immunol, vol. 4, p. 263, 2013.
[6] S. Li, M. P. Lefranc, J. J. Miles, E. Alamyar, V. Giudicelli, P. Duroux, et al., "IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling," Nat Commun, vol. 4, p. 2333, 2013.
[7] A. Mori, S. Deola, L. Xumerle, V. Mijatovic, G. Malerba, and V. Monsurro, "Next generation sequencing: new tools in immunology and hematology," Blood Res, vol. 48, pp. 242-9, Dec 2013.
[8] M. Estorninho, V. B. Gibson, D. Kronenberg-Versteeg, Y. F. Liu, C. Ni, K. Cerosaletti, et al., "A novel approach to tracking antigen-experienced CD4 T cells into functional compartments via tandem deep and shallow TCR clonotyping," J Immunol, vol. 191, pp. 5430-40, Dec 1 2013.
[9] N. Niklas, J. Proll, J. Weinberger, A. Zopf, K. Wiesinger, K. Krismer, et al., "Qualifying high-throughput immune repertoire sequencing," Cell Immunol, vol. 288, pp. 31-8, Mar-Apr 2014.
[10] O. V. Britanova, E. V. Putintseva, M. Shugay, E. M. Merzlyak, M. A. Turchaninova, D. B. Staroverov, et al., "Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling," J Immunol, vol. 192, pp. 2689-98, Mar 15 2014.
[11] I. Z. Mamedov, O. V. Britanova, I. V. Zvyagin, M. A. Turchaninova, D. A. Bolotin, E. V. Putintseva, et al., "Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling," Front Immunol, vol. 4, p. 456, 2013.
[12] R. M. Brennan, J. Petersen, M. A. Neller, J. J. Miles, J. M. Burrows, C. Smith, et al., "The impact of a large and frequent deletion in the human TCR beta locus on antiviral immunity," J Immunol, vol. 188, pp. 2742-8, Mar 15 2012.
[13] N. A. Bowerman, M. T. Falta, D. G. Mack, F. Wehrmann, F. Crawford, M. M. Mroz, et al., "Identification of multiple public TCR repertoires in chronic beryllium disease," J Immunol, vol. 192, pp. 4571-80, May 15 2014.
[14] G. Thorborn, G. R. Young, and G. Kassiotis, "Effective T helper cell responses against retroviruses: are all clonotypes equal?," J Leukoc Biol, vol. 96, pp. 27-37, Jul 2014.
[15] M. C. Iglesias, J. R. Almeida, S. Fastenackels, D. J. van Bockel, M. Hashimoto, V. Venturi, et al., "Escape from highly effective public CD8+ T-cell clonotypes by HIV," Blood, vol. 118, pp. 2138-49, Aug 25 2011.
[16] V. Venturi, D. A. Price, D. C. Douek, and M. P. Davenport, "The molecular basis for public T-cell responses?," Nat Rev Immunol, vol. 8, pp. 231-8, Mar 2008.
[17] W. Sun, H. Nie, N. Li, Y. C. Zang, D. Zhang, G. Feng, et al., "Skewed T-cell receptor BV14 and BV16 expression and shared CDR3 sequence and common sequence motifs in synovial T cells of rheumatoid arthritis," Genes Immun, vol. 6, pp. 248-61, May 2005.
[18] Q. Qi, Y. Liu, Y. Cheng, J. Glanville, D. Zhang, J. Y. Lee, et al., "Diversity and clonal selection in the human T-cell repertoire," Proc Natl Acad Sci U S A, vol. 111, pp. 13139-44, Sep 9 2014.
[19] J. J. Miles, D. Thammanichanond, S. Moneer, U. K. Nivarthi, L. Kjer-Nielsen, S. L. Tracy, et al., "Antigen-driven patterns of TCR bias are shared across diverse outcomes of human hepatitis C virus infection," J Immunol, vol. 186, pp. 901-12, Jan 15 2011.
[20] H. Li, C. Ye, G. Ji, X. Wu, Z. Xiang, Y. Li, et al., "Recombinatorial biases and convergent recombination determine interindividual TCRbeta sharing in murine thymocytes," J Immunol, vol. 189, pp. 2404-13, Sep 1 2012.
[21] H. S. Robins, P. V. Campregher, S. K. Srivastava, A. Wacher, C. J. Turtle, O. Kahsai, et al., "Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells," Blood, vol. 114, pp. 4099-107, Nov 5 2009.
[22] M. Yassai, D. Bosenko, M. Unruh, G. Zacharias, E. Reed, W. Demos, et al., "Naive T cell repertoire skewing in HLA-A2 individuals by a specialized rearrangement mechanism results in public memory clonotypes," J Immunol, vol. 186, pp. 2970-7, Mar 1 2011.
[23] A. M. Sherwood, R. O. Emerson, D. Scherer, N. Habermann, K. Buck, J. Staffa, et al., "Tumor-infiltrating lymphocytes in colorectal tumors display a diversity of T cell receptor sequences that differ from the T cells in adjacent mucosal tissue," Cancer Immunol Immunother, vol. 62, pp. 1453-61, Sep 2013.
[24] A. Madi, E. Shifrut, S. Reich-Zeliger, H. Gal, K. Best, W. Ndifon, et al., "T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity," Genome Res, vol. 24, pp. 1603-12, Oct 2014.
[25] R. L. Warren, J. D. Freeman, T. Zeng, G. Choe, S. Munro, R. Moore, et al., "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, vol. 21, pp. 790-7, May 2011.
[26] K. K. Wynn, Z. Fulton, L. Cooper, S. L. Silins, S. Gras, J. K. Archbold, et al., "Impact of clonal competition for peptide-MHC complexes on the CD8+ T-cell repertoire selection in a persistent viral infection," Blood, vol. 111, pp. 4283-92, Apr 15 2008.
[27] X. Sun, M. Fujiwara, Y. Shi, N. Kuse, H. Gatanaga, V. Appay, et al., "Superimposed epitopes restricted by the same HLA molecule drive distinct HIV-specific CD8+ T cell repertoires," J Immunol, vol. 193, pp. 77-84, Jul 1 2014.
[28] P. Billam, K. L. Bonaparte, J. Liu, T. J. Ruckwardt, M. Chen, A. B. Ryder, et al., "T Cell receptor clonotype influences epitope hierarchy in the CD8+ T cell response to respiratory syncytial virus infection," J Biol Chem, vol. 286, pp. 4829-41, Feb 11 2011.
[29] M. J. Clemente, B. Przychodzen, A. Jerez, B. E. Dienes, M. G. Afable, H. Husseinzadeh, et al., "Deep sequencing of the T-cell receptor repertoire in CD8+ T-large granular lymphocyte leukemia identifies signature landscapes," Blood, vol. 122, pp. 4077-85, Dec 12 2013.
[30] K. Kedzierska, P. G. Thomas, V. Venturi, M. P. Davenport, P. C. Doherty, S. J. Turner, et al., "Terminal deoxynucleotidyltransferase is required for the establishment of private virus-specific CD8+ TCR repertoires and facilitates optimal CTL responses," J Immunol, vol. 181, pp. 2556-62, Aug 15 2008.
[31] H. Li, C. Ye, G. Ji, and J. Han, "Determinants of public T cell responses," Cell Res, vol. 22, pp. 33-42, Jan 2012.
[32] A. Sainz-Perez, A. Lim, B. Lemercier, and C. Leclerc, "The T-cell receptor repertoire of tumor-infiltrating regulatory T lymphocytes is skewed toward public sequences," Cancer Res, vol. 72, pp. 3557-69, Jul 15 2012.
[33] S. Wieckowski, P. Baumgaertner, P. Corthesy, V. Voelter, P. Romero, D. E. Speiser, et al., "Fine structural variations of alphabetaTCRs selected by vaccination with natural versus altered self-antigen in melanoma patients," J Immunol, vol. 183, pp. 5397-406, Oct 15 2009.
[34] C. Linnemann, B. Heemskerk, P. Kvistborg, R. J. Kluin, D. A. Bolotin, X. Chen, et al., "High-throughput identification of antigen-specific TCRs by TCR gene capture," Nat Med, vol. 19, pp. 1534-41, Nov 2013.
[35] L. J. D'Orsogna, D. L. Roelen, Doxiadis, II, and F. H. Claas, "TCR cross-reactivity and allorecognition: new insights into the immunogenetics of allorecognition," Immunogenetics, vol. 64, pp. 77-85, Feb 2012.
[36] R. O. Emerson, J. M. Mathew, I. M. Konieczna, H. S. Robins, and J. R. Leventhal, "Defining the alloreactive T cell repertoire using high-throughput sequencing of mixed lymphocyte reaction culture," PLoS One, vol. 9, p. e111943, 2014.
[37] M. Dziubianau, J. Hecht, L. Kuchenbecker, A. Sattler, U. Stervbo, C. Rodelsperger, et al., "TCR repertoire analysis by next generation sequencing allows complex differential diagnosis of T cell-related pathology," Am J Transplant, vol. 13, pp. 2842-54, Nov 2013.
[38] D. Li, G. Gao, Z. Li, W. Sun, X. Li, N. Chen, et al., "Profiling the T-cell receptor repertoire of patient with pleural tuberculosis by high-throughput sequencing," Immunol Lett, vol. 162, pp. 170-80, Nov 2014.
[39] A. Balamurugan, H. L. Ng, and O. O. Yang, "Rapid T cell receptor delineation reveals clonal expansion limitation of the magnitude of the HIV-1-specific CD8+ T cell response," J Immunol, vol. 185, pp. 5935-42, Nov 15 2010.
[40] E. Shifrut, K. Baruch, H. Gal, W. Ndifon, A. Deczkowska, M. Schwartz, et al., "CD4(+) T Cell-Receptor Repertoire Diversity is Compromised in the Spleen but Not in the Bone Marrow of Aged Mice Due to Private and Sporadic Clonal Expansions," Front Immunol, vol. 4, p. 379, 2013.
[41] T. Cukalac, J. Chadderton, A. Handel, P. C. Doherty, S. J. Turner, P. G. Thomas, et al., "Reproducible selection of high avidity CD8+ T-cell clones following secondary acute virus infection," Proc Natl Acad Sci U S A, vol. 111, pp. 1485-90, Jan 28 2014.
[42] G. A. Rempala, M. Seweryn, and L. Ignatowicz, "Model for comparative analysis of antigen receptor repertoires," J Theor Biol, vol. 269, pp. 1-15, Jan 21 2011.
[43] E. Bar-Haim, N. Erez, A. M. Malloy, B. S. Graham, and T. J. Ruckwardt, "CD8+ TCR transgenic strains expressing public versus private TCR targeting the respiratory syncytial virus K(d)M2(82-90) epitope demonstrate similar functional profiles," PLoS One, vol. 9, p. e99249, 2014.
[44] N. Thomas, K. Best, M. Cinelli, S. Reich-Zeliger, H. Gal, E. Shifrut, et al., "Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence," Bioinformatics, vol. 30, pp. 3181-8, Nov 15 2014.
[45] S. A. Valkenburg, E. B. Day, N. G. Swan, H. A. Croom, F. R. Carbone, P. C. Doherty, et al., "Fixing an irrelevant TCR alpha chain reveals the importance of TCR beta diversity for optimal TCR alpha beta pairing and function of virus-specific CD8+ T cells," Eur J Immunol, vol. 40, pp. 2470-81, Sep 2010.
[46] Udgire M., Vivek S., Sinha P, "Isolation of Thermos table Extracellular Alkaline Protease and Lipase Producing Bacteria from Tannery Effluents," IJBTT, vol. 10, pp. 9-13, June 2015.
[47] Bhagavathi S, Gulshan Wadhwa, Anil Prakash, "In-Silico approach to phylogentic analysis of differentially expressed protein Matrix Metalloproteinase proteinase -12 associated with Lung Cancer," IJBTT, vol. 10, pp. 1-8, June 2015.

Keywords
public T cells, TCR clonotyping, public TCR, private TCR, NGS.