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Zeb1 represses TCR signaling, promotes the proliferation of T cell progenitors and is essential for NK1.1+ T cell development

Cellular & Molecular Immunology volume 18, pages 2140–2152 (2021)Cite this article

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Abstract

T cell development proceeds under the influence of a network of transcription factors (TFs). The precise role of Zeb1, a member of this network, remains unclear. Here, we report that Zeb1 expression is induced early during T cell development in CD4−CD8− double-negative (DN) stage 2 (DN2). Zeb1 expression was further increased in the CD4+CD8+ double-positive (DP) stage before decreasing in more mature T cell subsets. We performed an exhaustive characterization of T cells in Cellophane mice that bear Zeb1 hypomorphic mutations. The Zeb1 mutation profoundly affected all thymic subsets, especially DN2 and DP cells. Zeb1 promoted the survival and proliferation of both cell populations in a cell-intrinsic manner. In the periphery of Cellophane mice, the number of conventional T cells was near normal, but invariant NKT cells, NK1.1+ γδ T cells and Ly49+ CD8 T cells were virtually absent. This suggested that Zeb1 regulates the development of unconventional T cell types from DP progenitors. A transcriptomic analysis of WT and Cellophane DP cells revealed that Zeb1 regulated the expression of multiple genes involved in the cell cycle and TCR signaling, which possibly occurred in cooperation with Tcf1 and Heb. Indeed, Cellophane DP cells displayed stronger signaling than WT DP cells upon TCR engagement in terms of the calcium response, phosphorylation events, and expression of early genes. Thus, Zeb1 is a key regulator of the cell cycle and TCR signaling during thymic T cell development. We propose that thymocyte selection is perturbed in Zeb1-mutated mice in a way that does not allow the survival of unconventional T cell subsets.

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References

  1. Shah, D. K. & Zúñiga-Pflücker, J. C. An overview of the intrathymic intricacies of T cell development. J. Immunol. 192, 4017–4023 (2014).

    Article  CAS  PubMed  Google Scholar 

  2. Rothenberg, E. V., Moore, J. E. & Yui, M. A. Launching the T-cell-lineage developmental programme. Nat. Rev. Immunol. 8, 9–21 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Kurd, N. & Robey, E. A. T-cell selection in the thymus: a spatial and temporal perspective. Immunol. Rev. 271, 114–126 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Hogquist, K. A. & Jameson, S. C. The self-obsession of T cells: how TCR signaling thresholds affect fate “decisions” and effector function. Nat. Immunol. 15, 815–823 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Gascoigne, N. R. J., Rybakin, V., Acuto, O. & Brzostek, J. TCR signal strength and T cell development. Annu. Rev. Cell Dev. Biol. 32, 327–348 (2016).

    Article  CAS  PubMed  Google Scholar 

  6. Moran, A. E. et al. T cell receptor signal strength in Treg and iNKT cell development demonstrated by a novel fluorescent reporter mouse. J. Exp. Med. 208, 1279–1289 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Godfrey, D. I., Uldrich, A. P., McCluskey, J., Rossjohn, J. & Moody, D. B. The burgeoning family of unconventional T cells. Nat. Immunol. 16, 1114–1123 (2015).

    Article  CAS  PubMed  Google Scholar 

  8. Kronenberg, M. & Kinjo, Y. Innate-like recognition of microbes by invariant natural killer T cells. Curr. Opin. Immunol. 21, 6 (2009).

    Article  CAS  Google Scholar 

  9. Tuttle, K. D. et al. TCR signal strength controls thymic differentiation of iNKT cell subsets. Nat. Commun. 9, 2650 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  10. Zhao, M. et al. Altered thymic differentiation and modulation of arthritis by invariant NKT cells expressing mutant ZAP70. Nat. Commun. 9, 2627 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Malhotra, N. et al. SOX4 controls invariant NKT cell differentiation by tuning TCR signaling. J. Exp. Med 215, 2887–2900 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Ziętara, N. et al. Critical role for miR-181a/b-1 in agonist selection of invariant natural killer T cells. Proc. Natl Acad. Sci. USA 110, 7407–7412 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Henao-Mejia, J. et al. The microRNA miR-181 is a critical cellular metabolic rheostat essential for NKT cell ontogenesis and lymphocyte development and homeostasis. Immunity 38, 984–997 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Wencker, M. et al. Innate-like T cells straddle innate and adaptive immunity by altering antigen-receptor responsiveness. Nat. Immunol. 15, 80–87 (2014).

    Article  CAS  PubMed  Google Scholar 

  15. Seo, W. & Taniuchi, I. Transcriptional regulation of early T-cell development in the thymus. Eur. J. Immunol. 46, 531–538 (2016).

    Article  CAS  PubMed  Google Scholar 

  16. Maillard, I., Fang, T. & Pear, W. S. Regulation of lymphoid development, differentiation, and function by the Notch pathway. Annu Rev. Immunol. 23, 945–974 (2005).

    Article  CAS  PubMed  Google Scholar 

  17. Murre, C. Helix-loop-helix proteins and lymphocyte development. Nat. Immunol. 6, 1079–1086 (2005).

    Article  CAS  PubMed  Google Scholar 

  18. Hosokawa, H. & Rothenberg, E. V. Cytokines, transcription factors, and the initiation of T-cell development. Cold Spring Harb. Perspect. Biol. 10, a028621 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Gheldof, A., Hulpiau, P., van Roy, F., De Craene, B. & Berx, G. Evolutionary functional analysis and molecular regulation of the ZEB transcription factors. Cell Mol. Life Sci. CMLS 69, 2527–2541 (2012).

    Article  CAS  PubMed  Google Scholar 

  20. Takagi, T., Moribe, H. & Kondoh, H. Higashi Y. DeltaEF1, a zinc finger and homeodomain transcription factor, is required for skeleton patterning in multiple lineages. Dev. Camb. Engl. 125, 21–31 (1998).

    CAS  Google Scholar 

  21. Caramel, J., Ligier, M. & Puisieux, A. Pleiotropic roles for ZEB1 in cancer. Cancer Res. 78, 30–35 (2018).

    Article  CAS  PubMed  Google Scholar 

  22. Conidi, A. et al. Few Smad proteins and many Smad-interacting proteins yield multiple functions and action modes in TGFβ/BMP signaling in vivo. Cytokine Growth Factor Rev. 22, 287–300 (2011).

    Article  CAS  PubMed  Google Scholar 

  23. Scott, C. L. & Omilusik, K. D. ZEBs: novel players in immune cell development and function. Trends Immunol. 40, 431–446 (2019).

    Article  CAS  PubMed  Google Scholar 

  24. van Helden, M. J. et al. Terminal NK cell maturation is controlled by concerted actions of T-bet and Zeb2 and is essential for melanoma rejection. J. Exp. Med. 212, 2015–2025 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  25. Dominguez, C. X. et al. The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation in response to LCMV viral infection. J. Exp. Med. 212, 2041–2056 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Omilusik, K. D. et al. Transcriptional repressor ZEB2 promotes terminal differentiation of CD8+ effector and memory T cell populations during infection. J. Exp. Med. 212, 2027–2039 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  27. Higashi, Y. et al. Impairment of T cell development in deltaEF1 mutant mice. J. Exp. Med. 185, 1467–1479 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Arnold, C. N. et al. A forward genetic screen reveals roles for Nfkbid, Zeb1, and Ruvbl2 in humoral immunity. Proc. Natl Acad. Sci. 109, 12286–12293 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Heng, T. S. P. & Painter, M. W., Immunological Genome Project Consortium. The Immunological Genome Project: networks of gene expression in immune cells. Nat. Immunol. 9, 1091–1094 (2008).

    Article  CAS  PubMed  Google Scholar 

  30. Guan, T. et al. ZEB1, ZEB2, and the miR-200 family form a counterregulatory network to regulate CD8+ T cell fates. J. Exp. Med. 215, 1153–1168 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Jones, M. E. & Zhuang, Y. Stage-specific functions of E-proteins at the β-selection and T-cell receptor checkpoints during thymocyte development. Immunol. Res. 49, 202–215 (2011).

    Article  CAS  PubMed  Google Scholar 

  32. Emmanuel, A. O. et al. TCF-1 and HEB cooperate to establish the epigenetic and transcription profiles of CD4+CD8+ thymocytes. Nat. Immunol. 19, 1366–1378 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Rahim, M. M. A. et al. Ly49 receptors: innate and adaptive immune paradigms. Front. Immunol. 5, 145 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Grigoriadou, K., Boucontet, L. & Pereira, P. Most IL-4-producing gamma delta thymocytes of adult mice originate from fetal precursors. J. Immunol. 171, 2413–2420 (2003).

    Article  CAS  PubMed  Google Scholar 

  35. Gapin, L. iNKT cell autoreactivity: what is “self” and how is it recognized? Nat. Rev. Immunol. 10, 272–277 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Tuttle, K. D. & Gapin, L. Characterization of thymic development of natural killer T cell subsets by multiparameter flow cytometry. Methods Mol. Biol. Clifton NJ 1799, 121–133 (2018).

    Article  CAS  Google Scholar 

  37. Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  38. Szklarczyk, D. et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43, D447–D452 (2015).

    Article  CAS  PubMed  Google Scholar 

  39. Liston, A. et al. Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling. Genome Biol. 8, R12 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  40. Kastner, P. et al. Bcl11b represses a mature T-cell gene expression program in immature CD4(+)CD8(+) thymocytes. Eur. J. Immunol. 40, 2143–2154 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Yoshida, H. et al. The cis-regulatory atlas of the mouse immune system. Cell 176, 897–912.e20 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Bedel, R. et al. Effective functional maturation of invariant natural killer T cells is constrained by negative selection and T-cell antigen receptor affinity. Proc. Natl Acad. Sci. 111, E119–E128 (2014).

    Article  CAS  PubMed  Google Scholar 

  43. Hayes, S. M. & Love, P. E. Strength of signal: a fundamental mechanism for cell fate specification. Immunol. Rev. 209, 170–175 (2006).

    Article  PubMed  Google Scholar 

  44. Haks, M. C. et al. Attenuation of gammadeltaTCR signaling efficiently diverts thymocytes to the alphabeta lineage. Immunity 22, 595–606 (2005).

    Article  CAS  PubMed  Google Scholar 

  45. Alonzo, E. S. et al. Development of promyelocytic zinc finger and ThPOK-expressing innate gamma delta T cells is controlled by strength of TCR signaling and Id3. J. Immunol. 184, 1268–1279 (2010).

    Article  CAS  PubMed  Google Scholar 

  46. Ilangumaran, S. et al. Loss of GIMAP5 (GTPase of immunity-associated nucleotide binding protein 5) impairs calcium signaling in rat T lymphocytes. Mol. Immunol. 46, 1256–1259 (2009).

    Article  CAS  PubMed  Google Scholar 

  47. Howie, D. et al. MS4A4B is a GITR-associated membrane adapter, expressed by regulatory T cells, which modulates T cell activation. J. Immunol. 183, 4197–4204 (2009).

    Article  CAS  PubMed  Google Scholar 

  48. Carlson, C. M. et al. Kruppel-like factor 2 regulates thymocyte and T-cell migration. Nature 442, 299–302 (2006).

    Article  CAS  PubMed  Google Scholar 

  49. Gubbels Bupp, M. R. et al. T cells require Foxo1 to populate the peripheral lymphoid organs. Eur. J. Immunol. 39, 2991–2999 (2009).

    Article  CAS  PubMed  Google Scholar 

  50. Li, L. & Bhatia, R. Molecular pathways: stem cell quiescence. Clin. Cancer Res J. Am. Assoc. Cancer Res. 17, 4936–4941 (2011).

    Article  CAS  Google Scholar 

  51. Hedrick, S. M., Michelini, R. H., Doedens, A. L., Goldrath, A. W. & Stone, E. L. FOXO transcription factors throughout T cell biology. Nat. Publ. Group 12, 649–662. (2012).

    CAS  Google Scholar 

  52. Shi, L. Z. et al. Gfi1-Foxo1 axis controls the fidelity of effector gene expression and developmental maturation of thymocytes. Proc. Natl Acad. Sci. USA 114, E67–E74. (2017).

    Article  CAS  PubMed  Google Scholar 

  53. D’Cruz, L. M., Knell, J., Fujimoto, J. K. & Goldrath, A. W. An essential role for the transcription factor HEB in thymocyte survival, Tcra rearrangement and the development of natural killer T cells. Nat. Immunol. 11, 240–249 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  54. Brabletz, T. et al. Negative regulation of CD4 expression in T cells by the transcriptional repressor ZEB. Int. Immunol. 11, 1701–1708 (1999).

    Article  CAS  PubMed  Google Scholar 

  55. Postigo, A. A., Ward, E., Skeath, J. B. & Dean, D. C. zfh-1, the Drosophila homologue of ZEB, is a transcriptional repressor that regulates somatic myogenesis. Mol. Cell Biol. 19, 7255–7263 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Grégoire, J. M. & Roméo, P. H. T-cell expression of the human GATA-3 gene is regulated by a non-lineage-specific silencer. J. Biol. Chem. 274, 6567–6578 (1999).

    Article  PubMed  Google Scholar 

  57. Wang, L. et al. Genomic profiling of Sézary syndrome identifies alterations of key T cell signaling and differentiation genes. Nat. Genet. 47, 1426–1434 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Mishra, A. et al. Mechanism, consequences, and therapeutic targeting of abnormal IL15 signaling in cutaneous T-cell lymphoma. Cancer Discov. 6, 986–1005 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Doisne, J.-M. et al. iNKT cell development is orchestrated by different branches of TGF- signaling. J. Exp. Med. 206, 1365–1378 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171–181 (2014).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors acknowledge the contribution of the SFR Biosciences facilities (UMS3444/CNRS, ENSL, UCBL, and US8/INSERM), particularly the Plateau de Biologie Expérimentale de la Souris and the flow cytometry facility. We thank Bruce Beutler for sharing the Cellophane mutant mice. We also thank Andrew Griffiths and Kiyoto Kurima for discussions regarding Twirler mutant mice and Fotini Gounari and Christophe Benoist for providing RNA-seq/ChIP-seq data on T cell development. The TW lab is supported by the Agence Nationale de la Recherche (ANR GAMBLER to TW and ANR JC BaNK to AM) and the Institut National du Cancer and receives institutional grants from the Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon and ENS de Lyon, and the Joint Research Institute for Science and Society (JORISS). JZ is the recipient of a fellowship from the China Scholarship Council (CSC). RS and YGH were funded by an FRM grant (AJE20161236686) to YGH.

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Authors and Affiliations

  1. CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France

    Jiang Zhang, Mélanie Wencker, Quentin Marliac, Aurore Berton, Uzma Hasan, Daphné Laubreton, Dylan E. Cherrier, Anne-Laure Mathieu, Amaury Rey, Antoine Marçais, Jacqueline Marvel & Thierry Walzer

  2. Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China

    Jiang Zhang & Wenzheng Jiang

  3. Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, F-69364, Lyon, France

    Raphaël Schneider & Yad Ghavi-Helm

  4. CRCL, Centre de Recherche sur le Cancer de Lyon, INSERM U1052—CNRS UMR5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Lyon, France

    Julie Caramel & Laurent Genestier

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Contributions

JZ, AB, MW, DL, DEC, ALM, AR, and AM performed the experiments. RS and QM performed the in silico analyses. JC, LG, and YGH provided reagents and conceptual insight and helped write the paper. TW wrote the paper and supervised the work.

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Correspondence to Thierry Walzer.

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Zhang, J., Wencker, M., Marliac, Q. et al. Zeb1 represses TCR signaling, promotes the proliferation of T cell progenitors and is essential for NK1.1+ T cell development. Cell Mol Immunol 18, 2140–2152 (2021). https://doi.org/10.1038/s41423-020-0459-y

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Keywords

  • T cell selection
  • TCR signaling
  • Zeb1
  • transcription
  • development

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