Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Ectopic Tcf1 expression instills a stem-like program in exhausted CD8+ T cells to enhance viral and tumor immunity

Cellular & Molecular Immunology volume 18, pages 1262–1277 (2021)Cite this article

Subjects

Abstract

Exhausted CD8+ T (Tex) cells are dysfunctional due to persistent antigen exposure in chronic viral infection and tumor contexts. A stem cell-like Tex (Tex-stem) subset can self-renew and differentiate into terminally exhausted (Tex-term) cells. Here, we show that ectopic Tcf1 expression potently promoted the generation of Tex-stem cells in both a chronic viral infection and preclinical tumor models. Tcf1 overexpression diminished coinhibitory receptor expression and enhanced polycytokine-producing capacity while retaining a heightened responses to checkpoint blockade, leading to enhanced viral and tumor control. Mechanistically, ectopically expressed Tcf1 exploited existing and novel chromatin accessible sites as transcriptional enhancers or repressors and modulated the transcriptome by enforcing pre-existing expression patterns in Tex-stem cells, such as enhanced suppression of Blimp1 and Bim and acquisition of new downstream genes, including Mx1, Tox2, and Runx3. These findings reveal a pronounced impact of ectopic Tcf1 expression on Tex functional restoration and highlight the therapeutic potential of harnessing Tcf1-enforced transcriptional programs.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  1. Omilusik, K. D. & Goldrath, A. W. Remembering to remember: T cell memory maintenance and plasticity. Curr. Opin. Immunol. 58, 89–97 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Youngblood, B., Hale, J. S. & Ahmed, R. Memory CD8 T cell transcriptional plasticity. F1000Prime Rep. 7, 38 (2015).

    PubMed  PubMed Central  Google Scholar 

  3. Martin, M. D. & Badovinac, V. P. Defining memory CD8 T cell. Front. Immunol. 9, 2692 (2018).

    PubMed  PubMed Central  Google Scholar 

  4. McLane, L. M., Abdel-Hakeem, M. S. & Wherry, E. J. CD8 T Cell exhaustion during chronic viral infection and cancer. Annu. Rev. Immunol. 37, 457 (2019).

    CAS  PubMed  Google Scholar 

  5. Blank, C. U. et al. Defining ‘T cell exhaustion’. Nat. Rev. Immunol. 19, 665 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Patel, S. A. & Minn, A. J. Combination cancer therapy with immune checkpoint blockade: mechanisms and strategies. Immunity 48, 417–433 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Ribas, A. & Wolchok, J. D. Cancer immunotherapy using checkpoint blockade. Science 359, 1350–1355 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Pauken, K. E. et al. Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade. Science 354, 1160–1165 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Sen, D. R. et al. The epigenetic landscape of T cell exhaustion. Science 354, 1165–1169 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Doering, T. A. et al. Network analysis reveals centrally connected genes and pathways involved in CD8+ T cell exhaustion versus memory. Immunity 37, 1130–1144 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Philip, M. et al. Chromatin states define tumour-specific T cell dysfunction and reprogramming. Nature 545, 452–456 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Im, S. J. et al. Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy. Nature 537, 417–421 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. He, R. et al. Follicular CXCR5- expressing CD8(+) T cells curtail chronic viral infection. Nature 537, 412–428 (2016).

    CAS  PubMed  Google Scholar 

  14. Leong, Y. A. et al. CXCR5(+) follicular cytotoxic T cells control viral infection in B cell follicles. Nat. Immunol. 17, 1187–1196 (2016).

    CAS  PubMed  Google Scholar 

  15. Siddiqui, I. et al. Intratumoral Tcf1(+)PD-1(+)CD8(+) T cells with stem-like properties promote tumor control in response to vaccination and checkpoint blockade immunotherapy. Immunity 50, 195–211 e110 (2019).

    CAS  PubMed  Google Scholar 

  16. Kurtulus, S. et al. Checkpoint blockade immunotherapy induces dynamic changes in PD-1(−)CD8(+) tumor-infiltrating T cells. Immunity 50, 181–194 e186 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Miller, B. C. et al. Subsets of exhausted CD8(+) T cells differentially mediate tumor control and respond to checkpoint blockade. Nat. Immunol. 20, 326–336 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Kallies, A., Zehn, D. & Utzschneider, D. T. Precursor exhausted T cells: key to successful immunotherapy? Nat. Rev. Immunol. 20, 128 (2019).

    PubMed  Google Scholar 

  19. Martinez, G. J. et al. The transcription factor NFAT promotes exhaustion of activated CD8(+) T cells. Immunity 42, 265–278 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Man, K. et al. Transcription factor IRF4 promotes CD8(+) T cell exhaustion and limits the development of memory-like t cells during chronic infection. Immunity 47, 1129–1141 e1125 (2017).

    CAS  PubMed  Google Scholar 

  21. Alfei, F. et al. TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection. Nature 571, 265–269 (2019).

    CAS  PubMed  Google Scholar 

  22. Scott, A. C. et al. TOX is a critical regulator of tumour-specific T cell differentiation. Nature 571, 270–274 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Khan, O. et al. TOX transcriptionally and epigenetically programs CD8(+) T cell exhaustion. Nature 571, 211–218 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Yao, C. et al. Single-cell RNA-seq reveals TOX as a key regulator of CD8(+) T cell persistence in chronic infection. Nat. Immunol. 20, 890–901 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Seo, H. et al. TOX and TOX2 transcription factors cooperate with NR4A transcription factors to impose CD8(+) T cell exhaustion. Proc. Natl Acad. Sci. USA 116, 12410–12415 (2019).

    CAS  PubMed  Google Scholar 

  26. Wu, T. et al. The TCF1-Bcl6 axis counteracts type I interferon to repress exhaustion and maintain T cell stemness. Sci. Immunol. 1, eaai8593 (2016).

    PubMed  PubMed Central  Google Scholar 

  27. Shan, Q. et al. The transcription factor Runx3 guards cytotoxic CD8(+) effector T cells against deviation towards follicular helper T cell lineage. Nat. Immunol. 18, 931–939 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Steinke, F. C. & Xue, H. H. From inception to output, Tcf1 and Lef1 safeguard development of T cells and innate immune cells. Immunol. Res. 59, 45–55 (2014).

    CAS  PubMed  Google Scholar 

  29. Xue, H. H. & Zhao, D. M. Regulation of mature T cell responses by the Wnt signaling pathway. Ann. N.Y. Acad. Sci. 1247, 16–33 (2012).

    CAS  PubMed  Google Scholar 

  30. Raghu, D., Xue, H. H. & Mielke, L. A. Control of lymphocyte fate, infection, and tumor immunity by TCF-1. Trends Immunol. 40, 1149–1162 (2019).

    CAS  PubMed  Google Scholar 

  31. Xing, S. et al. Tcf1 and Lef1 transcription factors establish CD8(+) T cell identity through intrinsic HDAC activity. Nat. Immunol. 17, 695–703 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Zhou, X. et al. Differentiation and persistence of memory CD8(+) T cells depend on T cell factor 1. Immunity 33, 229–240 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Jeannet, G. et al. Essential role of the Wnt pathway effector Tcf-1 for the establishment of functional CD8 T cell memory. Proc. Natl Acad. Sci. USA 107, 9777–9782 (2010).

    CAS  PubMed  Google Scholar 

  34. Utzschneider, D. T. et al. T cell factor 1-expressing memory-like CD8(+) T cells sustain the immune response to chronic viral infections. Immunity 45, 415–427 (2016).

    CAS  PubMed  Google Scholar 

  35. Chen, Z. et al. TCF-1-centered transcriptional network drives an effector versus exhausted CD8 T cell-fate decision. Immunity 51, 840–855 e845 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Sade-Feldman, M. et al. Defining T cell states associated with response to checkpoint immunotherapy in Melanoma. Cell 175, 998–1013 e1020 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Wang, Y. et al. The transcription factor TCF1 preserves the effector function of exhausted CD8 T cells during chronic viral infection. Front. Immunol. 10, 169 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Ellis, J. Silencing and variegation of gammaretrovirus and lentivirus vectors. Hum. Gene Ther. 16, 1241–1246 (2005).

    CAS  PubMed  Google Scholar 

  39. Zhao, D. M. et al. Constitutive activation of Wnt signaling favors generation of memory CD8 T cells. J. Immunol. 184, 1191–1199 (2010).

    CAS  PubMed  Google Scholar 

  40. Xu, Z. et al. Cutting edge: beta-catenin-Interacting Tcf1 isoforms are essential for thymocyte survival but dispensable for thymic maturation transitions. J. Immunol. 198, 3404–3409 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Gullicksrud, J. A. et al. Differential requirements for Tcf1 long isoforms in CD8(+) and CD4(+) T cell responses to acute viral infection. J. Immunol. 199, 911–919 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Ioannidis, V., Beermann, F., Clevers, H. & Held, W. The beta-catenin–TCF-1 pathway ensures CD4(+)CD8(+) thymocyte survival. Nat. Immunol. 2, 691–697 (2001).

    CAS  PubMed  Google Scholar 

  43. Xie, H., Huang, Z., Sadim, M. S. & Sun, Z. Stabilized beta-catenin extends thymocyte survival by up-regulating Bcl-xL. J. Immunol. 175, 7981–7988 (2005).

    CAS  PubMed  Google Scholar 

  44. Yang, Q. et al. TCF-1 upregulation identifies early innate lymphoid progenitors in the bone marrow. Nat. Immunol. 16, 1044–1050 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Paley, M. A. et al. Progenitor and terminal subsets of CD8+ T cells cooperate to contain chronic viral infection. Science 338, 1220–1225 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Wherry, E. J. T cell exhaustion. Nat. Immunol. 12, 492–499 (2011).

    CAS  PubMed  Google Scholar 

  47. Yu, S. et al. Hematopoietic and leukemic stem cells have distinct dependence on Tcf1 and Lef1 transcription factors. J. Biol. Chem. 291, 11148–11160 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    PubMed  PubMed Central  Google Scholar 

  49. Shin, H. et al. A role for the transcriptional repressor Blimp-1 in CD8(+) T cell exhaustion during chronic viral infection. Immunity 31, 309–320 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Zhou, S., Cerny, A. M., Fitzgerald, K. A., Kurt-Jones, E. A. & Finberg, R. W. Role of interferon regulatory factor 7 in T cell responses during acute lymphocytic choriomeningitis virus infection. J. Virol. 86, 11254–11265 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Shin, H. M. et al. Transient expression of ZBTB32 in anti-viral CD8+ T cells limits the magnitude of the effector response and the generation of memory. PLoS Pathog. 13, e1006544 (2017).

    PubMed  PubMed Central  Google Scholar 

  52. Conze, D. et al. Activation of p38 MAP kinase in T cells facilitates the immune response to the influenza virus. Mol. Immunol. 37, 503–513 (2000).

    CAS  PubMed  Google Scholar 

  53. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).

    PubMed  PubMed Central  Google Scholar 

  54. Steinke, F. C. et al. TCF-1 and LEF-1 act upstream of Th-POK to promote the CD4(+) T cell fate and interact with Runx3 to silence Cd4 in CD8(+) T cells. Nat. Immunol. 15, 646–656 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Li, H. et al. Dysfunctional CD8 T cells form a proliferative, dynamically regulated compartment within human melanoma. Cell 176, 775–789 e718 (2019).

    CAS  PubMed  Google Scholar 

  56. Brummelman, J. et al. High-dimensional single cell analysis identifies stem-like cytotoxic CD8(+) T cells infiltrating human tumors. J. Exp. Med. 215, 2520–2535 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Danahy, D. B. et al. Sepsis-induced state of immunoparalysis is defined by diminished CD8 T cell-mediated antitumor immunity. J. Immunol. 203, 725–735 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Milner, J. J. et al. Runx3 programs CD8(+) T cell residency in nonlymphoid tissues and tumours. Nature 552, 253–257 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Gattinoni, L. et al. Wnt signaling arrests effector T cell differentiation and generates CD8+ memory stem cells. Nat. Med. 15, 808–813 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Jadhav, R. R. et al. Epigenetic signature of PD-1+ TCF1+ CD8 T cells that act as resource cells during chronic viral infection and respond to PD-1 blockade. Proc. Natl Acad. Sci. USA 116, 14113–14118 (2019).

    CAS  PubMed  Google Scholar 

  61. Weber, B. N. et al. A critical role for TCF-1 in T-lineage specification and differentiation. Nature 476, 63–68 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Johnson, J. L. et al. Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T Cells. Immunity 48, 243–257 e210 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Li, F. et al. Ezh2 programs TFH differentiation by integrating phosphorylation-dependent activation of Bcl6 and polycomb-dependent repression of p19Arf. Nat. Commun. 9, 5452 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Xing, S. et al. Tle corepressors are differentially partitioned to instruct CD8(+) T cell lineage choice and identity. J. Exp. Med 215, 2211–2226 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank Werner Held (University of Lausanne, Switzerland) and Zuoming Sun (City of Hope) for providing p45 Tcf1 transgenic and β-catenin transgenic mice, respectively; Ananda Goldrath (UCSD) for sharing the B16-GP33 melanoma cells; Jian Zhang (U of Iowa) for sharing TCRα–/– mice; the University of Iowa Flow Cytometry Core facility for cell sorting, the Genomics Division of Iowa Institute of Human Genetics and Admera Health for next-generation sequencing. This study was supported by grants from the NIH (AI112579, AI121080 and AI139874 to H.-H.X., GM133712 to C.Z., and GM113961, AI147064 and AI114543 to V.P.B.), and the Veteran Affairs BLR&D Merit Review Program (BX002903) to H.-H.X.

Author information

Author notes

  1. These authors contributed equally: Qiang Shan, Sheng’en Hu

Authors and Affiliations

  1. Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA

    Qiang Shan, Xia Chen & Hai-Hui Xue

  2. Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA

    Qiang Shan, Xia Chen, Vladimir P. Badovinac & Hai-Hui Xue

  3. Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA

    Sheng’en Hu & Chongzhi Zang

  4. Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA

    Derek B. Danahy & Vladimir P. Badovinac

  5. Interdisciplinary Immunology Graduate Program, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA

    Derek B. Danahy & Vladimir P. Badovinac

  6. Iowa City Veterans Affairs Health Care System, Iowa City, IA, 52246, USA

    Hai-Hui Xue

Authors
  1. Qiang Shan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sheng’en Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xia Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Derek B. Danahy
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Vladimir P. Badovinac
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chongzhi Zang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hai-Hui Xue
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Q.S., with assistance from X.C. and D.B.D., performed the experiments and analyzed the data; S.H. analyzed the high-throughput sequencing data under the supervision of C.Z.; V.P.B., C.Z., and H.H.X. designed and supervised the study.

Corresponding authors

Correspondence to Chongzhi Zang or Hai-Hui Xue.

Ethics declarations

Competing interests

The authors declare no competing interests.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shan, Q., Hu, S., Chen, X. et al. Ectopic Tcf1 expression instills a stem-like program in exhausted CD8+ T cells to enhance viral and tumor immunity. Cell Mol Immunol 18, 1262–1277 (2021). https://doi.org/10.1038/s41423-020-0436-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41423-020-0436-5

Keywords

This article is cited by

Search

Advanced search

Quick links