Rapid in vitro generation of bona fide exhausted CD8+ T cells is accompanied by Tcf7 promotor methylation


Autoři: Manzhi Zhao aff001;  Caoimhe H. Kiernan aff001;  Christopher J. Stairiker aff001;  Jennifer L. Hope aff002;  Leticia G. Leon aff001;  Marjan van Meurs aff001;  Inge Brouwers-Haspels aff001;  Ruben Boers aff003;  Joachim Boers aff003;  Joost Gribnau aff003;  Wilfred F. J. van IJcken aff005;  Eric M. Bindels aff006;  Remco M. Hoogenboezem aff006;  Stefan J. Erkeland aff001;  Yvonne M. Mueller aff001;  Peter D. Katsikis aff001
Působiště autorů: Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands aff001;  Cancer Immunology and Tumor Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States of America aff002;  Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, the Netherlands aff003;  Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands aff004;  Center for Biomics, Erasmus University Medical Center, Rotterdam, the Netherlands aff005;  Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands aff006
Vyšlo v časopise: Rapid in vitro generation of bona fide exhausted CD8+ T cells is accompanied by Tcf7 promotor methylation. PLoS Pathog 16(6): e32767. doi:10.1371/journal.ppat.1008555
Kategorie: Research Article
doi: 10.1371/journal.ppat.1008555

Souhrn

Exhaustion is a dysfunctional state of cytotoxic CD8+ T cells (CTL) observed in chronic infection and cancer. Current in vivo models of CTL exhaustion using chronic viral infections or cancer yield very few exhausted CTL, limiting the analysis that can be done on these cells. Establishing an in vitro system that rapidly induces CTL exhaustion would therefore greatly facilitate the study of this phenotype, identify the truly exhaustion-associated changes and allow the testing of novel approaches to reverse or prevent exhaustion. Here we show that repeat stimulation of purified TCR transgenic OT-I CTL with their specific peptide induces all the functional (reduced cytokine production and polyfunctionality, decreased in vivo expansion capacity) and phenotypic (increased inhibitory receptors expression and transcription factor changes) characteristics of exhaustion. Importantly, in vitro exhausted cells shared the transcriptomic characteristics of the gold standard of exhaustion, CTL from LCMV cl13 infections. Gene expression of both in vitro and in vivo exhausted CTL was distinct from T cell anergy. Using this system, we show that Tcf7 promoter DNA methylation contributes to TCF1 downregulation in exhausted CTL. Thus this novel in vitro system can be used to identify genes and signaling pathways involved in exhaustion and will facilitate the screening of reagents that prevent/reverse CTL exhaustion.

Klíčová slova:

Anergy – Cytokines – Cytotoxic T cells – DNA methylation – Gene expression – T cell receptors – T cells – Transcription factors


Zdroje

1. McLane LM, Abdel-Hakeem MS, Wherry EJ. CD8 T Cell Exhaustion During Chronic Viral Infection and Cancer. Annual review of immunology. 2019;37:457–95. doi: 10.1146/annurev-immunol-041015-055318 30676822

2. Bengsch B, Ohtani T, Khan O, Setty M, Manne S, O'Brien S, et al. Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells. Immunity. 2018;48(5):1029–45 e5. doi: 10.1016/j.immuni.2018.04.026 29768164

3. Boni C, Fisicaro P, Valdatta C, Amadei B, Di Vincenzo P, Giuberti T, et al. Characterization of hepatitis B virus (HBV)-specific T-cell dysfunction in chronic HBV infection. Journal of virology. 2007;81(8):4215–25. doi: 10.1128/JVI.02844-06 17287266

4. Fraietta JA, Mueller YM, Yang G, Boesteanu AC, Gracias DT, Do DH, et al. Type I interferon upregulates Bak and contributes to T cell loss during human immunodeficiency virus (HIV) infection. PLoS pathogens. 2013;9(10):e1003658. doi: 10.1371/journal.ppat.1003658 24130482

5. Kahan SM, Wherry EJ, Zajac AJ. T cell exhaustion during persistent viral infections. Virology. 2015;479–480:180–93. doi: 10.1016/j.virol.2014.12.033 25620767

6. Mueller YM, De Rosa SC, Hutton JA, Witek J, Roederer M, Altman JD, et al. Increased CD95/Fas-induced apoptosis of HIV-specific CD8(+) T cells. Immunity. 2001;15(6):871–82. doi: 10.1016/s1074-7613(01)00246-1 11754810

7. Petrovas C, Mueller YM, Dimitriou ID, Bojczuk PM, Mounzer KC, Witek J, et al. HIV-specific CD8+ T cells exhibit markedly reduced levels of Bcl-2 and Bcl-xL. Journal of immunology. 2004;172(7):4444–53.

8. Radziewicz H, Ibegbu CC, Fernandez ML, Workowski KA, Obideen K, Wehbi M, et al. Liver-infiltrating lymphocytes in chronic human hepatitis C virus infection display an exhausted phenotype with high levels of PD-1 and low levels of CD127 expression. Journal of virology. 2007;81(6):2545–53. doi: 10.1128/JVI.02021-06 17182670

9. Shankar P, Russo M, Harnisch B, Patterson M, Skolnik P, Lieberman J. Impaired function of circulating HIV-specific CD8(+) T cells in chronic human immunodeficiency virus infection. Blood. 2000;96(9):3094–101. 11049989

10. Wherry EJ, Blattman JN, Murali-Krishna K, van der Most R, Ahmed R. Viral persistence alters CD8 T-cell immunodominance and tissue distribution and results in distinct stages of functional impairment. Journal of virology. 2003;77(8):4911–27. doi: 10.1128/jvi.77.8.4911-4927.2003 12663797

11. Wherry EJ, Ha SJ, Kaech SM, Haining WN, Sarkar S, Kalia V, et al. Molecular signature of CD8+ T cell exhaustion during chronic viral infection. Immunity. 2007;27(4):670–84. doi: 10.1016/j.immuni.2007.09.006 17950003

12. Doering TA, Crawford A, Angelosanto JM, Paley MA, Ziegler CG, Wherry EJ. Network analysis reveals centrally connected genes and pathways involved in CD8+ T cell exhaustion versus memory. Immunity. 2012;37(6):1130–44. doi: 10.1016/j.immuni.2012.08.021 23159438

13. Barber DL, Wherry EJ, Masopust D, Zhu B, Allison JP, Sharpe AH, et al. Restoring function in exhausted CD8 T cells during chronic viral infection. Nature. 2006;439(7077):682–7. doi: 10.1038/nature04444 16382236

14. Attanasio J, Wherry EJ. Costimulatory and Coinhibitory Receptor Pathways in Infectious Disease. Immunity. 2016;44(5):1052–68. doi: 10.1016/j.immuni.2016.04.022 27192569

15. Jin HT, Anderson AC, Tan WG, West EE, Ha SJ, Araki K, et al. Cooperation of Tim-3 and PD-1 in CD8 T-cell exhaustion during chronic viral infection. Proceedings of the National Academy of Sciences of the United States of America. 2010;107(33):14733–8. doi: 10.1073/pnas.1009731107 20679213

16. Johnston RJ, Comps-Agrar L, Hackney J, Yu X, Huseni M, Yang Y, et al. The immunoreceptor TIGIT regulates antitumor and antiviral CD8(+) T cell effector function. Cancer cell. 2014;26(6):923–37. doi: 10.1016/j.ccell.2014.10.018 25465800

17. Blackburn SD, Shin H, Haining WN, Zou T, Workman CJ, Polley A, et al. Coregulation of CD8+ T cell exhaustion by multiple inhibitory receptors during chronic viral infection. Nature immunology. 2009;10(1):29–37. doi: 10.1038/ni.1679 19043418

18. Youngblood B, Noto A, Porichis F, Akondy RS, Ndhlovu ZM, Austin JW, et al. Cutting edge: Prolonged exposure to HIV reinforces a poised epigenetic program for PD-1 expression in virus-specific CD8 T cells. Journal of immunology. 2013;191(2):540–4.

19. Pauken KE, Sammons MA, Odorizzi PM, Manne S, Godec J, Khan O, et al. Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade. Science. 2016;354(6316):1160–5. doi: 10.1126/science.aaf2807 27789795

20. Sen DR, Kaminski J, Barnitz RA, Kurachi M, Gerdemann U, Yates KB, et al. The epigenetic landscape of T cell exhaustion. Science. 2016;354(6316):1165–9. doi: 10.1126/science.aae0491 27789799

21. Im SJ, Hashimoto M, Gerner MY, Lee J, Kissick HT, Burger MC, et al. Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy. Nature. 2016;537(7620):417–21. doi: 10.1038/nature19330 27501248

22. Snell LM, MacLeod BL, Law JC, Osokine I, Elsaesser HJ, Hezaveh K, et al. CD8(+) T Cell Priming in Established Chronic Viral Infection Preferentially Directs Differentiation of Memory-like Cells for Sustained Immunity. Immunity. 2018;49(4):678–94 e5. doi: 10.1016/j.immuni.2018.08.002 30314757

23. Alfei F, Kanev K, Hofmann M, Wu M, Ghoneim HE, Roelli P, et al. TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection. Nature. 2019.

24. Khan O, Giles JR, McDonald S, Manne S, Ngiow SF, Patel KP, et al. TOX transcriptionally and epigenetically programs CD8(+) T cell exhaustion. Nature. 2019;571(7764):211–8. doi: 10.1038/s41586-019-1325-x 31207603

25. Scott AC, Dundar F, Zumbo P, Chandran SS, Klebanoff CA, Shakiba M, et al. TOX is a critical regulator of tumour-specific T cell differentiation. Nature. 2019;571(7764):270–4. doi: 10.1038/s41586-019-1324-y 31207604

26. Yao C, Sun HW, Lacey NE, Ji Y, Moseman EA, Shih HY, et al. Single-cell RNA-seq reveals TOX as a key regulator of CD8(+) T cell persistence in chronic infection. Nature immunology. 2019;20(7):890–901. doi: 10.1038/s41590-019-0403-4 31209400

27. Seo H, Chen J, Gonzalez-Avalos E, Samaniego-Castruita D, Das A, Wang YH, et al. TOX and TOX2 transcription factors cooperate with NR4A transcription factors to impose CD8(+) T cell exhaustion. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(25):12410–5. doi: 10.1073/pnas.1905675116 31152140

28. Man K, Gabriel SS, Liao Y, Gloury R, Preston S, Henstridge DC, et al. Transcription Factor IRF4 Promotes CD8(+) T Cell Exhaustion and Limits the Development of Memory-like T Cells during Chronic Infection. Immunity. 2017;47(6):1129–41 e5. doi: 10.1016/j.immuni.2017.11.021 29246443

29. Chen J, Lopez-Moyado IF, Seo H, Lio CJ, Hempleman LJ, Sekiya T, et al. NR4A transcription factors limit CAR T cell function in solid tumours. Nature. 2019;567(7749):530–4. doi: 10.1038/s41586-019-0985-x 30814732

30. Quigley M, Pereyra F, Nilsson B, Porichis F, Fonseca C, Eichbaum Q, et al. Transcriptional analysis of HIV-specific CD8+ T cells shows that PD-1 inhibits T cell function by upregulating BATF. Nat Med. 2010;16(10):1147–51. doi: 10.1038/nm.2232 20890291

31. Kao C, Oestreich KJ, Paley MA, Crawford A, Angelosanto JM, Ali MA, et al. Transcription factor T-bet represses expression of the inhibitory receptor PD-1 and sustains virus-specific CD8+ T cell responses during chronic infection. Nature immunology. 2011;12(7):663–71. doi: 10.1038/ni.2046 21623380

32. Zhou X, Yu S, Zhao DM, Harty JT, Badovinac VP, Xue HH. Differentiation and persistence of memory CD8(+) T cells depend on T cell factor 1. Immunity. 2010;33(2):229–40. doi: 10.1016/j.immuni.2010.08.002 20727791

33. Zhou S, Ou R, Huang L, Price GE, Moskophidis D. Differential tissue-specific regulation of antiviral CD8+ T-cell immune responses during chronic viral infection. Journal of virology. 2004;78(7):3578–600. doi: 10.1128/jvi.78.7.3578-3600.2004 15016881

34. Ahmadzadeh M, Johnson LA, Heemskerk B, Wunderlich JR, Dudley ME, White DE, et al. Tumor antigen-specific CD8 T cells infiltrating the tumor express high levels of PD-1 and are functionally impaired. Blood. 2009;114(8):1537–44. doi: 10.1182/blood-2008-12-195792 19423728

35. Schietinger A, Philip M, Krisnawan VE, Chiu EY, Delrow JJ, Basom RS, et al. Tumor-Specific T Cell Dysfunction Is a Dynamic Antigen-Driven Differentiation Program Initiated Early during Tumorigenesis. Immunity. 2016;45(2):389–401. doi: 10.1016/j.immuni.2016.07.011 27521269

36. Mueller SN, Ahmed R. High antigen levels are the cause of T cell exhaustion during chronic viral infection. Proceedings of the National Academy of Sciences of the United States of America. 2009;106(21):8623–8. doi: 10.1073/pnas.0809818106 19433785

37. Bucks CM, Norton JA, Boesteanu AC, Mueller YM, Katsikis PD. Chronic antigen stimulation alone is sufficient to drive CD8+ T cell exhaustion. Journal of immunology. 2009;182(11):6697–708.

38. Utzschneider DT, Alfei F, Roelli P, Barras D, Chennupati V, Darbre S, et al. High antigen levels induce an exhausted phenotype in a chronic infection without impairing T cell expansion and survival. The Journal of experimental medicine. 2016;213(9):1819–34. doi: 10.1084/jem.20150598 27455951

39. Balkhi MY, Wittmann G, Xiong F, Junghans RP. YY1 Upregulates Checkpoint Receptors and Downregulates Type I Cytokines in Exhausted, Chronically Stimulated Human T Cells. iScience. 2018;2:105–22. doi: 10.1016/j.isci.2018.03.009 30428369

40. Miller BC, Sen DR, Al Abosy R, Bi K, Virkud YV, LaFleur MW, et al. Subsets of exhausted CD8(+) T cells differentially mediate tumor control and respond to checkpoint blockade. Nature immunology. 2019;20(3):326–36. doi: 10.1038/s41590-019-0312-6 30778252

41. Utzschneider DT, Charmoy M, Chennupati V, Pousse L, Ferreira DP, Calderon-Copete S, et al. T Cell Factor 1-Expressing Memory-like CD8(+) T Cells Sustain the Immune Response to Chronic Viral Infections. Immunity. 2016;45(2):415–27. doi: 10.1016/j.immuni.2016.07.021 27533016

42. Paley MA, Kroy DC, Odorizzi PM, Johnnidis JB, Dolfi DV, Barnett BE, et al. Progenitor and terminal subsets of CD8+ T cells cooperate to contain chronic viral infection. Science. 2012;338(6111):1220–5. doi: 10.1126/science.1229620 23197535

43. Youngblood B, Oestreich KJ, Ha SJ, Duraiswamy J, Akondy RS, West EE, et al. Chronic virus infection enforces demethylation of the locus that encodes PD-1 in antigen-specific CD8(+) T cells. Immunity. 2011;35(3):400–12. doi: 10.1016/j.immuni.2011.06.015 21943489

44. Boers R, Boers J, de Hoon B, Kockx C, Ozgur Z, Molijn A, et al. Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI. Genome Res. 2018;28(1):88–99. doi: 10.1101/gr.222885.117 29222086

45. Chou FC, Kuo CC, Chen HY, Chen HH, Sytwu HK. DNA demethylation of the TIM-3 promoter is critical for its stable expression on T cells. Genes Immun. 2016;17(3):179–86. doi: 10.1038/gene.2016.6 26890332

46. Zha Y, Marks R, Ho AW, Peterson AC, Janardhan S, Brown I, et al. T cell anergy is reversed by active Ras and is regulated by diacylglycerol kinase-alpha. Nature immunology. 2006;7(11):1166–73. doi: 10.1038/ni1394 17028589

47. Schietinger A, Greenberg PD. Tolerance and exhaustion: defining mechanisms of T cell dysfunction. Trends Immunol. 2014;35(2):51–60. doi: 10.1016/j.it.2013.10.001 24210163

48. Schwartz RH. T cell anergy. Annual review of immunology. 2003;21:305–34. doi: 10.1146/annurev.immunol.21.120601.141110 12471050

49. Mescher MF, Popescu FE, Gerner M, Hammerbeck CD, Curtsinger JM. Activation-induced non-responsiveness (anergy) limits CD8 T cell responses to tumors. Semin Cancer Biol. 2007;17(4):299–308. doi: 10.1016/j.semcancer.2007.06.008 17656106

50. Beverly B, Kang SM, Lenardo MJ, Schwartz RH. Reversal of in vitro T cell clonal anergy by IL-2 stimulation. Int Immunol. 1992;4(6):661–71. doi: 10.1093/intimm/4.6.661 1616898

51. Macian F, Garcia-Cozar F, Im SH, Horton HF, Byrne MC, Rao A. Transcriptional mechanisms underlying lymphocyte tolerance. Cell. 2002;109(6):719–31. doi: 10.1016/s0092-8674(02)00767-5 12086671

52. Mueller YM, Do DH, Altork SR, Artlett CM, Gracely EJ, Katsetos CD, et al. IL-15 treatment during acute simian immunodeficiency virus (SIV) infection increases viral set point and accelerates disease progression despite the induction of stronger SIV-specific CD8+ T cell responses. Journal of immunology. 2008;180(1):350–60.

53. Mueller YM, Bojczuk PM, Halstead ES, Kim AH, Witek J, Altman JD, et al. IL-15 enhances survival and function of HIV-specific CD8+ T cells. Blood. 2003;101(3):1024–9. doi: 10.1182/blood-2002-07-1957 12393488

54. Liao W, Lin JX, Leonard WJ. Interleukin-2 at the crossroads of effector responses, tolerance, and immunotherapy. Immunity. 2013;38(1):13–25. doi: 10.1016/j.immuni.2013.01.004 23352221

55. Chihara N, Madi A, Kondo T, Zhang H, Acharya N, Singer M, et al. Induction and transcriptional regulation of the co-inhibitory gene module in T cells. Nature. 2018;558(7710):454–9. doi: 10.1038/s41586-018-0206-z 29899446

56. Harker JA, Wong KA, Dallari S, Bao P, Dolgoter A, Jo Y, et al. Interleukin-27R Signaling Mediates Early Viral Containment and Impacts Innate and Adaptive Immunity after Chronic Lymphocytic Choriomeningitis Virus Infection. Journal of virology. 2018;92(12).

57. Prabhu Das MR, Zamvil SS, Borriello F, Weiner HL, Sharpe AH, Kuchroo VK. Reciprocal expression of co-stimulatory molecules, B7-1 and B7-2, on murine T cells following activation. Eur J Immunol. 1995;25(1):207–11. doi: 10.1002/eji.1830250134 7531145

58. Weintraub JP, Eisenberg RA, Cohen PL. Up-regulation of Fas and the costimulatory molecules B7-1 and B7-2 on peripheral lymphocytes in autoimmune B6/gld mice. Journal of immunology. 1997;159(8):4117–26.

59. He R, Hou S, Liu C, Zhang A, Bai Q, Han M, et al. Follicular CXCR5- expressing CD8(+) T cells curtail chronic viral infection. Nature. 2016;537(7620):412–28. doi: 10.1038/nature19317 27501245

60. Hirano F, Kaneko K, Tamura H, Dong H, Wang S, Ichikawa M, et al. Blockade of B7-H1 and PD-1 by monoclonal antibodies potentiates cancer therapeutic immunity. Cancer Res. 2005;65(3):1089–96. 15705911

61. Stelekati E, Chen Z, Manne S, Kurachi M, Ali MA, Lewy K, et al. Long-Term Persistence of Exhausted CD8 T Cells in Chronic Infection Is Regulated by MicroRNA-155. Cell reports. 2018;23(7):2142–56. doi: 10.1016/j.celrep.2018.04.038 29768211

62. Dolfi DV, Duttagupta PA, Boesteanu AC, Mueller YM, Oliai CH, Borowski AB, et al. Dendritic cells and CD28 costimulation are required to sustain virus-specific CD8+ T cell responses during the effector phase in vivo. Journal of immunology. 2011;186(8):4599–608.

63. Hope JL, Stairiker CJ, Spantidea PI, Gracias DT, Carey AJ, Fike AJ, et al. The Transcription Factor T-Bet Is Regulated by MicroRNA-155 in Murine Anti-Viral CD8(+) T Cells via SHIP-1. Front Immunol. 2017;8:1696. doi: 10.3389/fimmu.2017.01696 29358931

64. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21. doi: 10.1093/bioinformatics/bts635 23104886

65. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923–30. doi: 10.1093/bioinformatics/btt656 24227677

66. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi: 10.1186/s13059-014-0550-8 25516281


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