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200 Million Thymocytes and I: A Beginner’s Survival Guide to T Cell Development

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T-Cell Development

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1323))

Abstract

T lymphocytes (T cells) are essential for proper adaptive immune responses. They perform a variety of functions in defenses against pathogens, and notably control, positively or negatively, other cells involved in immune responses. T cells develop in the thymus from bone marrow-derived precursors. These precursors (thymocytes) proliferate, rearrange the genes encoding subunits of the T cell antigen receptor, which endow them with their unique antigen specificity, and undergo various degrees of pre-programming for their functions in immune responses. Thus, analyzing T cell development in the thymus is essential for understanding their functions in immune responses. In addition, the thymus constitutes an attractive experimental model to analyze mechanisms of cell proliferation, differentiation and survival, all of which are involved in thymocyte development. This chapter presents a quick overview of the key events characterizing intrathymic T cell development, as an introduction for readers entering this field of study.

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References

  1. Kisielow P, Von Boehmer H (1995) Development and selection of T cells: facts and puzzles. Adv Immunol 58:87–209

    Article  CAS  PubMed  Google Scholar 

  2. Carpenter AC, Bosselut R (2010) Decision checkpoints in the thymus. Nat Immunol 11:666–673

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  3. Wucherpfennig KW, Gagnon E, Call MJ, Huseby ES, Call ME (2010) Structural biology of the T-cell receptor: insights into receptor assembly, ligand recognition, and initiation of signaling. Cold Spring Harb Perspect Biol 2:a005140

    Article  PubMed Central  PubMed  Google Scholar 

  4. Samelson LE (2002) Signal transduction mediated by the T cell antigen receptor: the role of adapter proteins. Annu Rev Immunol 20:371–394

    Article  CAS  PubMed  Google Scholar 

  5. Reiner S (2008) Peripheral T lymphocyte responses and function. In: Paul WE (ed) Fundamental immunology. Lippincott Williams & Wilkins, Philadelphia, pp 407–425

    Google Scholar 

  6. Smith-Garvin JE, Koretzky GA, Jordan MS (2009) T cell activation. Annu Rev Immunol 27:591–619

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Mazza C, Malissen B (2007) What guides MHC-restricted TCR recognition? Semin Immunol 19:225–235

    Article  CAS  PubMed  Google Scholar 

  8. Singer A, Bosselut R (2004) CD4/CD8 coreceptors in thymocyte development, selection, and lineage commitment: analysis of the CD4/CD8 lineage decision. Adv Immunol 83:91–131

    Article  CAS  PubMed  Google Scholar 

  9. Bendelac A, Savage PB, Teyton L (2007) The biology of NKT cells. Annu Rev Immunol 25:297–336

    Article  CAS  PubMed  Google Scholar 

  10. Le Bourhis L, Guerri L, Dusseaux M, Martin E, Soudais C, Lantz O (2011) Mucosal-associated invariant T cells: unconventional development and function. Trends Immunol 32:212–218

    Article  PubMed  Google Scholar 

  11. Gold MC, Lewinsohn DM (2013) Co-dependents: MR1-restricted MAIT cells and their antimicrobial function. Nat Rev Microbiol 11:14–19

    Article  CAS  PubMed  Google Scholar 

  12. van Wijk F, Cheroutre H (2009) Intestinal T cells: facing the mucosal immune dilemma with synergy and diversity. Semin Immunol 21:130–138

    Article  PubMed Central  PubMed  Google Scholar 

  13. Gordon J, Manley NR (2011) Mechanisms of thymus organogenesis and morphogenesis. Development 138:3865–3878

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. Nitta T, Murata S, Ueno T, Tanaka K, Takahama Y (2008) Thymic microenvironments for T-cell repertoire formation. Adv Immunol 99:59–94

    Article  CAS  PubMed  Google Scholar 

  15. Rossi SW, Jenkinson WE, Anderson G, Jenkinson EJ (2006) Clonal analysis reveals a common progenitor for thymic cortical and medullary epithelium. Nature 441:988–991

    Article  CAS  PubMed  Google Scholar 

  16. Bleul CC, Corbeaux T, Reuter A, Fisch P, Monting JS, Boehm T (2006) Formation of a functional thymus initiated by a postnatal epithelial progenitor cell. Nature 441:992–996

    Article  CAS  PubMed  Google Scholar 

  17. Yang Q, Jeremiah Bell J, Bhandoola A (2010) T-cell lineage determination. Immunol Rev 238:12–22

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Bhandoola A, von Boehmer H, Petrie HT, Zuniga-Pflucker JC (2007) Commitment and developmental potential of extrathymic and intrathymic T cell precursors: plenty to choose from. Immunity 26:678–689

    Article  CAS  PubMed  Google Scholar 

  19. Rothenberg EV (2011) T cell lineage commitment: identity and renunciation. J Immunol 186:6649–6655

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Zhang SL, Bhandoola A (2014) Trafficking to the thymus. Curr Top Microbiol Immunol 373:87–111

    CAS  PubMed  Google Scholar 

  21. Hozumi K, Mailhos C, Negishi N, Hirano K, Yahata T, Ando K, Zuklys S, Hollander GA, Shima DT, Habu S (2008) Delta-like 4 is indispensable in thymic environment specific for T cell development. J Exp Med 205:2507–2513

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Koch U, Fiorini E, Benedito R, Besseyrias V, Schuster-Gossler K, Pierres M, Manley NR, Duarte A, Macdonald HR, Radtke F (2008) Delta-like 4 is the essential, nonredundant ligand for Notch1 during thymic T cell lineage commitment. J Exp Med 205:2515–2523

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Pui JC, Allman D, Xu L, DeRocco S, Karnell FG, Bakkour S, Lee JY, Kadesch T, Hardy RR, Aster JC, Pear WS (1999) Notch1 expression in early lymphopoiesis influences B versus T lineage determination. Immunity 11:299–308

    Article  CAS  PubMed  Google Scholar 

  24. Radtke F, Wilson A, Stark G, Bauer M, van Meerwijk J, MacDonald HR, Aguet M (1999) Deficient T cell fate specification in mice with an induced inactivation of Notch1. Immunity 10:547–558

    Article  CAS  PubMed  Google Scholar 

  25. Rothenberg EV (2012) Transcriptional drivers of the T-cell lineage program. Curr Opin Immunol 24:132–138

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Rothenberg EV, Moore JE, Yui MA (2008) Launching the T-cell-lineage developmental programme. Nat Rev Immunol 8:9–21

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Ho IC, Tai TS, Pai SY (2009) GATA3 and the T-cell lineage: essential functions before and after T-helper-2-cell differentiation. Nat Rev Immunol 9:125–135

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Avram D, Califano D (2014) The multifaceted roles of Bcl11b in thymic and peripheral T cells: impact on immune diseases. J Immunol 193(5):2059–2065

    Article  CAS  PubMed  Google Scholar 

  29. Gonzalez-Garcia S, Garcia-Peydro M, Alcain J, Toribio ML (2012) Notch1 and IL-7 receptor signalling in early T-cell development and leukaemia. Curr Top Microbiol Immunol 360:47–73

    CAS  PubMed  Google Scholar 

  30. Jung D, Alt FW (2004) Unraveling V(D)J recombination; insights into gene regulation. Cell 116:299–311

    Article  CAS  PubMed  Google Scholar 

  31. von Boehmer H, Aifantis I, Azogui O, Feinberg J, Saint-Ruf C, Zober C, Garcia C, Buer J (1998) Crucial function of the pre-T-cell receptor (TCR) in TCR beta selection, TCR beta allelic exclusion and alpha beta versus gamma delta lineage commitment. Immunol Rev 165:111–119

    Article  Google Scholar 

  32. von Boehmer H, Aifantis I, Feinberg J, Lechner O, Saint-Ruf C, Walter U, Buer J, Azogui O (1999) Pleiotropic changes controlled by the pre-T-cell receptor. Curr Opin Immunol 11:135–142

    Article  Google Scholar 

  33. Hayes SM, Love PE (2006) Strength of signal: a fundamental mechanism for cell fate specification. Immunol Rev 209:170–175

    Article  PubMed  Google Scholar 

  34. Lauritsen JP, Haks MC, Lefebvre JM, Kappes DJ, Wiest DL (2006) Recent insights into the signals that control alphabeta/gammadelta-lineage fate. Immunol Rev 209:176–190

    Article  PubMed  Google Scholar 

  35. Kreslavsky T, Gleimer M, von Boehmer H (2010) Alphabeta versus gammadelta lineage choice at the first TCR-controlled checkpoint. Curr Opin Immunol 22(2):185–192

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  36. Mingueneau M, Kreslavsky T, Gray D, Heng T, Cruse R, Ericson J, Bendall S, Spitzer MH, Nolan GP, Kobayashi K, von Boehmer H, Mathis D, Benoist C, Best AJ, Knell J, Goldrath A, Jojic V, Koller D, Shay T, Regev A, Cohen N, Brennan P, Brenner M, Kim F, Rao TN, Wagers A, Heng T, Ericson J, Rothamel K, Ortiz-Lopez A, Mathis D, Benoist C, Bezman NA, Sun JC, Min-Oo G, Kim CC, Lanier LL, Miller J, Brown B, Merad M, Gautier EL, Jakubzick C, Randolph GJ, Monach P, Blair DA, Dustin ML, Shinton SA, Hardy RR, Laidlaw D, Collins J, Gazit R, Rossi DJ, Malhotra N, Sylvia K, Kang J, Kreslavsky T, Fletcher A, Elpek K, Bellemare-Pelletier A, Malhotra D, Turley S (2013) The transcriptional landscape of alphabeta T cell differentiation. Nat Immunol 14:619–632

    Article  CAS  PubMed  Google Scholar 

  37. Williams JA, Hathcock KS, Klug D, Harada Y, Choudhury B, Allison JP, Abe R, Hodes RJ (2005) Regulated costimulation in the thymus is critical for T cell development: dysregulated CD28 costimulation can bypass the pre-TCR checkpoint. J Immunol 175:4199–4207

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  38. Taghon T, Yui MA, Pant R, Diamond RA, Rothenberg EV (2006) Developmental and molecular characterization of emerging beta- and gammadelta-selected pre-T cells in the adult mouse thymus. Immunity 24:53–64

    Article  CAS  PubMed  Google Scholar 

  39. Starr TK, Jameson SC, Hogquist KA (2003) Positive and negative selection of T cells. Annu Rev Immunol 21:139–176

    Article  CAS  PubMed  Google Scholar 

  40. Klein L, Kyewski B, Allen PM, Hogquist KA (2014) Positive and negative selection of the T cell repertoire: what thymocytes see (and don’t see). Nat Rev Immunol 14:377–391

    Article  CAS  PubMed  Google Scholar 

  41. Nitta T, Ohigashi I, Nakagawa Y, Takahama Y (2011) Cytokine crosstalk for thymic medulla formation. Curr Opin Immunol 23:190–197

    Article  CAS  PubMed  Google Scholar 

  42. Boyman O, Krieg C, Homann D, Sprent J (2012) Homeostatic maintenance of T cells and natural killer cells. Cell Mol Life Sci 69:1597–1608

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  43. McCaughtry TM, Etzensperger R, Alag A, Tai X, Kurtulus S, Park JH, Grinberg A, Love P, Feigenbaum L, Erman B, Singer A (2012) Conditional deletion of cytokine receptor chains reveals that IL-7 and IL-15 specify CD8 cytotoxic lineage fate in the thymus. J Exp Med 209:2263–2276

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  44. Tani-ichi S, Shimba A, Wagatsuma K, Miyachi H, Kitano S, Imai K, Hara T, Ikuta K (2013) Interleukin-7 receptor controls development and maturation of late stages of thymocyte subpopulations. Proc Natl Acad Sci U S A 110:612–617

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  45. Gascoigne NR, Palmer E (2011) Signaling in thymic selection. Curr Opin Immunol 23:207–212

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. Wang L, Xiong Y, Bosselut R (2010) Tenuous paths in unexplored territory: from T cell receptor signaling to effector gene expression during thymocyte selection. Semin Immunol 22:294–302

    Article  PubMed Central  PubMed  Google Scholar 

  47. Mathis D, Benoist C (2009) Aire. Annu Rev Immunol 27:287–312

    Article  CAS  PubMed  Google Scholar 

  48. Sakaguchi S, Yamaguchi T, Nomura T, Ono M (2008) Regulatory T cells and immune tolerance. Cell 133:775–787

    Article  CAS  PubMed  Google Scholar 

  49. Josefowicz SZ, Lu LF, Rudensky AY (2012) Regulatory T cells: mechanisms of differentiation and function. Annu Rev Immunol 30:531–564

    Article  CAS  PubMed  Google Scholar 

  50. Guerau-de-Arellano M, Martinic M, Benoist C, Mathis D (2009) Neonatal tolerance revisited: a perinatal window for Aire control of autoimmunity. J Exp Med 206:1245–1252

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  51. Bouneaud C, Kourilsky P, Bousso P (2000) Impact of negative selection on the T cell repertoire reactive to a self-peptide: a large fraction of T cell clones escapes clonal deletion. Immunity 13:829–840

    Article  CAS  PubMed  Google Scholar 

  52. Verbsky JW, Chatila TA (2013) Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) and IPEX-related disorders: an evolving web of heritable autoimmune diseases. Curr Opin Pediatr 25:708–714

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  53. Daniels MA, Teixeiro E, Gill J, Hausmann B, Roubaty D, Holmberg K, Werlen G, Hollander GA, Gascoigne NR, Palmer E (2006) Thymic selection threshold defined by compartmentalization of Ras/MAPK signalling. Nature 444:724–729

    Article  CAS  PubMed  Google Scholar 

  54. Stritesky GL, Jameson SC, Hogquist KA (2012) Selection of self-reactive T cells in the thymus. Annu Rev Immunol 30:95–114

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  55. Fu G, Rybakin V, Brzostek J, Paster W, Acuto O, Gascoigne NR (2014) Fine-tuning T cell receptor signaling to control T cell development. Trends Immunol 35:311–318

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  56. McGargill MA, Ch’en IL, Katayama CD, Pages G, Pouyssegur J, Hedrick SM (2009) Cutting edge: extracellular signal-related kinase is not required for negative selection of developing T cells. J Immunol 183:4838–4842

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  57. Fassett MS, Jiang W, D’Alise AM, Mathis D, Benoist C (2012) Nuclear receptor Nr4a1 modulates both regulatory T-cell (Treg) differentiation and clonal deletion. Proc Natl Acad Sci U S A 109:3891–3896

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  58. Sekiya T, Kashiwagi I, Yoshida R, Fukaya T, Morita R, Kimura A, Ichinose H, Metzger D, Chambon P, Yoshimura A (2013) Nr4a receptors are essential for thymic regulatory T cell development and immune homeostasis. Nat Immunol 14:230–237

    Article  CAS  PubMed  Google Scholar 

  59. Staton TL, Lazarevic V, Jones DC, Lanser AJ, Takagi T, Ishii S, Glimcher LH (2011) Dampening of death pathways by schnurri-2 is essential for T-cell development. Nature 472:105–109

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  60. Gray DH, Kupresanin F, Berzins SP, Herold MJ, O’Reilly LA, Bouillet P, Strasser A (2012) The BH3-only proteins Bim and Puma cooperate to impose deletional tolerance of organ-specific antigens. Immunity 37:451–462

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  61. Stritesky GL, Xing Y, Erickson JR, Kalekar LA, Wang X, Mueller DL, Jameson SC, Hogquist KA (2013) Murine thymic selection quantified using a unique method to capture deleted T cells. Proc Natl Acad Sci U S A 110:4679–4684

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  62. Wang L, Bosselut R (2009) CD4-CD8 lineage differentiation: Thpok-ing into the nucleus. J Immunol 183:2903–2910

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  63. Xiong Y, Bosselut R (2012) CD4-CD8 differentiation in the thymus: connecting circuits and building memories. Curr Opin Immunol 24:139–145

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  64. Xiong Y, Bosselut R (2011) The enigma of CD4-lineage specification. Eur J Immunol 41:568–574

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  65. Cyster JG, Schwab SR (2012) Sphingosine-1-phosphate and lymphocyte egress from lymphoid organs. Annu Rev Immunol 30:69–94

    Article  CAS  PubMed  Google Scholar 

  66. Hart GT, Hogquist KA, Jameson SC (2012) Kruppel-like factors in lymphocyte biology. J Immunol 188:521–526

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  67. Hedrick SM, Hess Michelini R, Doedens AL, Goldrath AW, Stone EL (2012) FOXO transcription factors throughout T cell biology. Nat Rev Immunol 12:649–661

    Article  CAS  PubMed  Google Scholar 

  68. Cannons JL, Tangye SG, Schwartzberg PL (2011) SLAM family receptors and SAP adaptors in immunity. Annu Rev Immunol 29:665–705

    Article  CAS  PubMed  Google Scholar 

  69. Nitta T, Nitta S, Lei Y, Lipp M, Takahama Y (2009) CCR7-mediated migration of developing thymocytes to the medulla is essential for negative selection to tissue-restricted antigens. Proc Natl Acad Sci U S A 106:17129–17133

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  70. Nakagawa T, Roth W, Wong P, Nelson A, Farr A, Deussing J, Villadangos JA, Ploegh H, Peters C, Rudensky AY (1998) Cathepsin L: critical role in Ii degradation and CD4 T cell selection in the thymus. Science 280:450–453

    Article  CAS  PubMed  Google Scholar 

  71. Klein L, Hinterberger M, Wirnsberger G, Kyewski B (2009) Antigen presentation in the thymus for positive selection and central tolerance induction. Nat Rev Immunol 9:833–844

    Article  CAS  PubMed  Google Scholar 

  72. Nitta T, Murata S, Sasaki K, Fujii H, Ripen AM, Ishimaru N, Koyasu S, Tanaka K, Takahama Y (2010) Thymoproteasome shapes immunocompetent repertoire of CD8+ T cells. Immunity 32:29–40

    Article  CAS  PubMed  Google Scholar 

  73. Shores EW, Van Ewijk W, Singer A (1991) Disorganization and restoration of thymic medullary epithelial cells in T cell receptor-negative scid mice: evidence that receptor-bearing lymphocytes influence maturation of the thymic microenvironment. Eur J Immunol 21:1657–1661

    Article  CAS  PubMed  Google Scholar 

  74. Philpott KL, Viney JL, Kay G, Rastan S, Gardiner EM, Chae S, Hayday AC, Owen MJ (1992) Lymphoid development in mice congenitally lacking T cell receptor alpha beta-expressing cells. Science 256:1448–1452

    Article  CAS  PubMed  Google Scholar 

  75. Dudakov JA, Hanash AM, Jenq RR, Young LF, Ghosh A, Singer NV, West ML, Smith OM, Holland AM, Tsai JJ, Boyd RL, van den Brink MR (2012) Interleukin-22 drives endogenous thymic regeneration in mice. Science 336:91–95

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  76. Bosselut R, Guinter TI, Sharrow SO, Singer A (2003) Unraveling a revealing paradox: why major histocompatibility complex I-signaled thymocytes “Paradoxically” appear as CD4+8lo transitional cells during positive selection of CD8+ T cells. J Exp Med 197:1709–1719

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Correspondence to Rémy Bosselut .

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Vacchio, M.S., Ciucci, T., Bosselut, R. (2016). 200 Million Thymocytes and I: A Beginner’s Survival Guide to T Cell Development. In: Bosselut, R., S. Vacchio, M. (eds) T-Cell Development. Methods in Molecular Biology, vol 1323. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2809-5_1

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  • DOI: https://doi.org/10.1007/978-1-4939-2809-5_1

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2808-8

  • Online ISBN: 978-1-4939-2809-5

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