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Translation is actively regulated during the differentiation of CD8+ effector T cells

Nature Immunology volume 18, pages 1046–1057 (2017)Cite this article

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Abstract

Translation is a critical process in protein synthesis, but translational regulation in antigen-specific T cells in vivo has not been well defined. Here we have characterized the translatome of virus-specific CD8+ effector T cells (Teff cells) during acute infection of mice with lymphocytic choriomeningitis virus (LCMV). Antigen-specific T cells exerted dynamic translational control of gene expression that correlated with cell proliferation and stimulation via the T cell antigen receptor (TCR). The translation of mRNAs that encode translation machinery, including ribosomal proteins, was upregulated during the T cell clonal-expansion phase, followed by inhibition of the translation of those transcripts when the CD8+ Teff cells stopped dividing just before the contraction phase. That translational suppression was more pronounced in terminal effector cells than in memory precursor cells and was regulated by antigenic stimulation and signals from the kinase mTOR. Our studies show that translation of transcripts encoding ribosomal proteins is regulated during the differentiation of CD8+ Teff cells and might have a role in fate 'decisions' involved in the formation of memory cells.

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Figure 1: Activated CD8+ T cells change their translational activity.
Figure 2: Translation of Ifng in CD8+ Teff cells is distinct from that of Tbx21.
Figure 3: Genome-wide translational activity in CD8+ T cells.
Figure 4: Translatome reveals genes translationally regulated in CD8+ T cells.
Figure 5: Translational regulation links to cellular activity during the differentiation of CD8+ Teff cells.
Figure 6: Translational inhibition of RP mRNAs and 5′ TOP mRNAs occurs in CD8+ Teff cells when the cells stopped dividing just before the contraction phase.
Figure 7: Greater translational inhibition of RP mRNAs in TTE cells than in TMP cells.
Figure 8: Antigen stimulation contributes to translational regulation of RP mRNAs in virus-specific CD8+ T cells.

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References

  1. Kaech, S.M. & Cui, W. Transcriptional control of effector and memory CD8+ T cell differentiation. Nat. Rev. Immunol. 12, 749–761 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Wherry, E.J. et al. Molecular signature of CD8+ T cell exhaustion during chronic viral infection. Immunity 27, 670–684 (2007).

    CAS  PubMed  Google Scholar 

  3. Kaech, S.M., Hemby, S., Kersh, E. & Ahmed, R. Molecular and functional profiling of memory CD8 T cell differentiation. Cell 111, 837–851 (2002).

    Article  CAS  PubMed  Google Scholar 

  4. Russ, B.E. et al. Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8+ T cell differentiation. Immunity 41, 853–865 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Shin, H.M. et al. Epigenetic modifications induced by Blimp-1 regulate CD8+ T cell memory progression during acute virus infection. Immunity 39, 661–675 (2013).

    CAS  PubMed  Google Scholar 

  6. Scharer, C.D., Barwick, B.G., Youngblood, B.A., Ahmed, R. & Boss, J.M. Global DNA methylation remodeling accompanies CD8 T cell effector function. J. Immunol. 191, 3419–3429 (2013).

    CAS  PubMed  Google Scholar 

  7. Youngblood, B. et al. Chronic virus infection enforces demethylation of the locus that encodes PD-1 in antigen-specific CD8+ T cells. Immunity 35, 400–412 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Sonenberg, N. & Hinnebusch, A.G. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136, 731–745 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Bhat, M. et al. Targeting the translation machinery in cancer. Nat. Rev. Drug Discov. 14, 261–278 (2015).

    CAS  PubMed  Google Scholar 

  10. Santini, E. & Klann, E. Reciprocal signaling between translational control pathways and synaptic proteins in autism spectrum disorders. Sci. Signal. 7, re10 (2014).

    PubMed  PubMed Central  Google Scholar 

  11. Silvera, D., Formenti, S.C. & Schneider, R.J. Translational control in cancer. Nat. Rev. Cancer 10, 254–266 (2010).

    CAS  PubMed  Google Scholar 

  12. Piccirillo, C.A., Bjur, E., Topisirovic, I., Sonenberg, N. & Larsson, O. Translational control of immune responses: from transcripts to translatomes. Nat. Immunol. 15, 503–511 (2014).

    CAS  PubMed  Google Scholar 

  13. Chang, C.H. et al. Posttranscriptional control of T cell effector function by aerobic glycolysis. Cell 153, 1239–1251 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Blagih, J. et al. The energy sensor AMPK regulates T cell metabolic adaptation and effector responses in vivo. Immunity 42, 41–54 (2015).

    CAS  PubMed  Google Scholar 

  15. Scheu, S. et al. Activation of the integrated stress response during T helper cell differentiation. Nat. Immunol. 7, 644–651 (2006).

    CAS  PubMed  Google Scholar 

  16. Bjur, E. et al. Distinct translational control in CD4+ T cell subsets. PLoS Genet. 9, e1003494 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Zoncu, R., Efeyan, A. & Sabatini, D.M. mTOR: from growth signal integration to cancer, diabetes and ageing. Nat. Rev. Mol. Cell Biol. 12, 21–35 (2011).

    CAS  PubMed  Google Scholar 

  18. Araki, K. et al. mTOR regulates memory CD8 T-cell differentiation. Nature 460, 108–112 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Pearce, E.L. et al. Enhancing CD8 T-cell memory by modulating fatty acid metabolism. Nature 460, 103–107 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Wherry, E.J. et al. Lineage relationship and protective immunity of memory CD8+ T cell subsets. Nat. Immunol. 4, 225–234 (2003).

    CAS  PubMed  Google Scholar 

  21. Signer, R.A., Magee, J.A., Salic, A. & Morrison, S.J. Haematopoietic stem cells require a highly regulated protein synthesis rate. Nature 509, 49–54 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Narita, M. et al. Spatial coupling of mTOR and autophagy augments secretory phenotypes. Science 332, 966–970 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Pien, G.C., Nguyen, K.B., Malmgaard, L., Satoskar, A.R. & Biron, C.A. A unique mechanism for innate cytokine promotion of T cell responses to viral infections. J. Immunol. 169, 5827–5837 (2002).

    CAS  PubMed  Google Scholar 

  24. Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Godec, J. et al. Compendium of immune signatures identifies conserved and species-specific biology in response to inflammation. Immunity 44, 194–206 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Meyuhas, O. & Kahan, T. The race to decipher the top secrets of TOP mRNAs. Biochim. Biophys. Acta 1849, 801–811 (2015).

    CAS  PubMed  Google Scholar 

  27. Miloslavski, R. et al. Oxygen sufficiency controls TOP mRNA translation via the TSC-Rheb-mTOR pathway in a 4E-BP-independent manner. J. Mol. Cell Biol. 6, 255–266 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Thoreen, C.C. et al. A unifying model for mTORC1-mediated regulation of mRNA translation. Nature 485, 109–113 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Hsieh, A.C. et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature 485, 55–61 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Kaech, S.M. et al. Selective expression of the interleukin 7 receptor identifies effector CD8 T cells that give rise to long-lived memory cells. Nat. Immunol. 4, 1191–1198 (2003).

    CAS  PubMed  Google Scholar 

  31. Joshi, N.S. et al. Inflammation directs memory precursor and short-lived effector CD8+ T cell fates via the graded expression of T-bet transcription factor. Immunity 27, 281–295 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Sarkar, S. et al. Functional and genomic profiling of effector CD8 T cell subsets with distinct memory fates. J. Exp. Med. 205, 625–640 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Heyer, E.E. & Moore, M.J. Redefining the translational status of 80S monosomes. Cell 164, 757–769 (2016).

    CAS  PubMed  Google Scholar 

  34. Wherry, E.J., Blattman, J.N., 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. J. Virol. 77, 4911–4927 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Morita, M. et al. mTORC1 controls mitochondrial activity and biogenesis through 4E-BP-dependent translational regulation. Cell Metab. 18, 698–711 (2013).

    CAS  PubMed  Google Scholar 

  36. Larsson, O. et al. Distinct perturbation of the translatome by the antidiabetic drug metformin. Proc. Natl. Acad. Sci. USA 109, 8977–8982 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Albert, V. & Hall, M.N. mTOR signaling in cellular and organismal energetics. Curr. Opin. Cell Biol. 33, 55–66 (2015).

    CAS  PubMed  Google Scholar 

  38. Chauvin, C. et al. Ribosomal protein S6 kinase activity controls the ribosome biogenesis transcriptional program. Oncogene 33, 474–483 (2014).

    CAS  PubMed  Google Scholar 

  39. Pollizzi, K.N. et al. mTORC1 and mTORC2 selectively regulate CD8+ T cell differentiation. J. Clin. Invest. 125, 2090–2108 (2015).

    PubMed  PubMed Central  Google Scholar 

  40. Zhang, L. et al. Mammalian target of rapamycin complex 2 controls CD8 T cell memory differentiation in a Foxo1-dependent manner. Cell Rep. 14, 1206–1217 (2016).

    CAS  PubMed  Google Scholar 

  41. Zinzalla, V., Stracka, D., Oppliger, W. & Hall, M.N. Activation of mTORC2 by association with the ribosome. Cell 144, 757–768 (2011).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  43. 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 

  44. 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 

  45. 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 

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

    Google Scholar 

  47. Wirth, T.C. et al. Repetitive antigen stimulation induces stepwise transcriptome diversification but preserves a core signature of memory CD8+ T cell differentiation. Immunity 33, 128–140 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Chang, J.T., Wherry, E.J. & Goldrath, A.W. Molecular regulation of effector and memory T cell differentiation. Nat. Immunol. 15, 1104–1115 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Colina, R. et al. Translational control of the innate immune response through IRF-7. Nature 452, 323–328 (2008).

    CAS  PubMed  Google Scholar 

  50. Merico, D., Isserlin, R., Stueker, O., Emili, A. & Bader, G.D. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One 5, e13984 (2010).

    PubMed  PubMed Central  Google Scholar 

  51. Tripathi, S. et al. Meta- and orthogonal integration of influenza “OMICs” data defines a role for ubr4 in virus budding. Cell Host Microbe 18, 723–735 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

Supported by the US National Institutes of Health (R01 AI030048 to R.A.) and the Mérieux Foundation (R.A.).

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Author notes

  1. Masahiro Morita

    Present address: Department of Molecular Medicine and Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA

Authors and Affiliations

  1. Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA

    Koichi Araki, Annelise G Bederman, Bogumila T Konieczny, Haydn T Kissick & Rafi Ahmed

  2. Department of Biochemistry, McGill University, Montreal, Canada

    Masahiro Morita & Nahum Sonenberg

  3. Goodman Cancer Research Centre, McGill University, Montreal, Canada

    Masahiro Morita & Nahum Sonenberg

  4. Department of Urology, Emory University School of Medicine, Atlanta, Georgia, USA

    Haydn T Kissick

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Contributions

K.A. and R.A. designed the experiments and wrote the paper; M.M. and N.S. provided critical guidance for performing the experiments; K.A., A.G.B. and B.T.K. performed the experiments; and K.A., H.T.K. and R.A. analyzed the data.

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Correspondence to Koichi Araki or Rafi Ahmed.

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Integrated supplementary information

Supplementary Figure 1 Translation of mRNAs encoding products involved in the differentiation of effector and memory CD8+ T cells.

qRT-PCR analysis of several transcripts among total mRNA isolated from splenic P14 Tn, D5 Teff, D8 Teff, and Tm cells; results are presented relative to those of total RNA from Tn cells (left). qRT-PCR quantification of several mRNAs in fractions obtained by sucrose-gradient ultracentrifugation of lysates of indicated cells (key), and the proportion of individual mRNAs in the polysome fractions of those cells (right). (a) Cd8a, (b) Il7r and Sell, (c) Gzmb. LCMV specific P14 transgenic CD8+ T cells were adoptively transferred into B6 mice, followed by LCMV Armstrong infection. Tn, D5 Teff, D8 Teff, and Tm indicate naive, day 5 effector, day 8 effector, and memory CD8+ T cells, respectively. The mRNA level in total mRNA and polysome fractions was calculated from the 3-5 independent experiments. Naive P14 cells were obtained from uninfected P14 transgenic mice. Memory P14 cells were analyzed 40~60 days after LCMV infection. Each symbol represents an individual experiment.

Supplementary Figure 2 The majority of transcriptionally upregulated mRNAs encoding products related to cell proliferation in D5 Teff cells are loaded on polysomes.

Microarray analysis was performed as described in Fig. 4a. Correlation of the expression change in total mRNAs with that polysome-associated mRNAs responsible for enrichment data of proliferation related gene sets identified in Fig. 5a Tn vs D5 Teff analysis. Pearson correlation r2 and p-value are shown.

Supplementary Figure 3 Schematic design for identification of translationally regulated genes in D8 Teff cells compared with D5 Teff cells by GSEA using the ImmuneSigDB gene set.

Schematic design showing flow chart for identification of translationally regulated genes in D8 Teff cells compared to D5 Teff cells using ImmuneSigDB gene set.

Supplementary Figure 4 Expression of RP mRNAs per cell in virus-specific CD8+ T cells in total mRNA.

qRT-PCR analysis of ribosomal-protein-encoding mRNA among total mRNA isolated from splenic P14 Tn, D5 Teff, and D8 Teff cells; amount of each mRNA per cell is presented relative to that of total RNA from Tn cells. LCMV specific P14 transgenic CD8+ T cells were adoptively transferred into B6 mice, followed by LCMV Armstrong infection. P14 cells were purified day 5 and day 8 after infection. Naive P14 cells were purified from uninfected P14 transgenic mice. Data were calculated from 3 independent experiments with samples pooled from 3-10 mice per each group. **p<0.01, ***p<0.001, ****p<0.0001 (one-way ANOVA). Each symbol represents an individual experiment.

Supplementary Figure 5 Cd8a mRNA in fractions obtained sucrose-gradient ultracentrifugation of P14 TTE and TMP cells.

(a) Purification methods of CD127hi memory precursor (TMP) and CD127lo terminal effector (TTE) P14 CD8+ T cells from spleen of day 8 LCMV-infected mice in which P14 transgenic T cells were adoptively transferred before infection. (b) qRT-PCR quantification of Cd8a transcripts in fractions (horizontal axes) obtained by sucrose-gradient ultracentrifugation of lysates of P14 CD127hi TMP cells and CD127lo TTE cells (key), among the total in all fractions. This data is control for ribosomal-protein-encoding mRNAs in Fig. 7. Data are representative of six independent experiments with samples pooled from 3-5 mice per each group.

Supplementary Figure 6 Rapamycin inhibits the translation of RP mRNAs in virus-specific CD8+ T cells.

(a and b) Effect of rapamycin on CD127hi memory precursor effector (TMP) cells. (a) Experimental design. LCMV specific P14 transgenic CD8+ T cells were adoptively transferred into B6 mice, followed by LCMV Armstrong infection. Mice were treated or not with rapamycin at day 8 post infection. Twelve hours later, CD127hi TMP P14 effector cells were isolated from spleen for sucrose gradient ultracentrifugation. (b) Proportion of ribosomal-protein-encoding mRNA in polysome fractions of P14 cells obtained from LCMV-infected mice treated or not with rapamycin (key). (c and d) Effect of rapamycin on translational regulation of ribosomal-protein-encoding mRNAs during the early activation of CD8+ T cells. (c) Experimental design. LCMV TCR P14 transgenic mice were treated or not with rapamycin 12 hours before and 12 hours after LCMV infection. Splenic P14 CD8+ T cells were isolated at 24 hours after infection for sucrose gradient ultracentrifugation. (d) Proportion of ribosomal-protein-encoding mRNA in polysome fractions of P14 cells obtained from LCMV-infected mice treated or not with rapamycin (key). Paired data were connected with a solid line in (d). Horizontal doted lines in (b, d) indicate the average percentage of each mRNA in polysome fractions in naive CD8+ T cells (this was calculated from the data of Fig. 6). Data (b) were obtained from six independent experiments with samples pooled from 3-5 mice per each group. Data from five independent experiments were combined in (d). Each symbol in (b,d) represents an individual experiment (b) or an individual mouse (d). *p<0.05, **p<0.01. Unpaired t-test for (b), paired t-test for (d).

Supplementary Figure 7 Translation in effector CD8+ T cells generated in mice infected with either LCMV Arm or LCMV clone 13.

(a) qRT-PCR quantification of Cd8a transcripts in fractions (horizontal axes) obtained by sucrose-gradient ultracentrifugation of lysates of Teff P14 CD8+ cells obtained from spleen of either LCMV Arm- or LCMV clone 13-infected mice (key) at day 8 post-infection. P14 cells were adoptively transferred before infection. This is a control of ribosomal-protein-encoding mRNAs in Fig. 8. (b) Amount of ribosomal-protein-encoding mRNA per cell in polysome fractions of D8 Teff cells obtained from LCMV-Arm- or LCMV-clone 13-infected mice (key); results are presented relative to those of LCMV Arm. Data (a) are representative of 5-6 independent experiments with samples pooled from 3-5 mice per each group. Data (b) were obtained from 5-6 independent experiments with samples pooled from 3-5 mice per each group. ****p<0.0001 (unpaired t-test). Each symbol in (b) represents an individual experiment.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7. (PDF 595 kb)

Supplementary Table 1

Translation activity in naive CD8 T cells. (XLSX 104 kb)

Supplementary Table 2

Translation activity in day 5 effector CD8 T cells. (XLSX 114 kb)

Supplementary Table 3

Translation activity in day 8 effector CD8 T cells. (XLSX 170 kb)

Supplementary Table 4

Translationally regulated genes in day 5 and day 8 effector CD8 T cells compared to naive CD8 T cells. (XLSX 179 kb)

Supplementary Table 5

Fold changes of total and polysome-associated mRNAs responsible for enrichment of proliferation-related gene sets by GSEA. (XLSX 102 kb)

Supplementary Table 6

Genes responsible for translationally regulated gene sets by GSEA in Figure 5. (XLSX 68 kb)

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Araki, K., Morita, M., Bederman, A. et al. Translation is actively regulated during the differentiation of CD8+ effector T cells. Nat Immunol 18, 1046–1057 (2017). https://doi.org/10.1038/ni.3795

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