Differentiation of exhausted CD8+ T cells after termination of chronic antigen stimulation stops short of achieving functional T cell memory
Pierre Tonnerre, David Wolski, Sonu Subudhi, Jihad Aljabban, Ruben C Hoogeveen, Marcos Damasio, Hannah K Drescher, Lea M Bartsch, Damien C Tully, Debattama R Sen, David J Bean, Joelle Brown, Almudena Torres-Cornejo, Maxwell Robidoux, Daniel Kvistad, Nadia Alatrakchi, Ang Cui, David Lieb, James A Cheney, Jenna Gustafson, Lia L Lewis-Ximenez, Lucile Massenet-Regad, Thomas Eisenhaure, Jasneet Aneja, W Nicholas Haining, Raymond T Chung, Nir Hacohen, Todd M Allen, Arthur Y Kim, Georg M Lauer, Pierre Tonnerre, David Wolski, Sonu Subudhi, Jihad Aljabban, Ruben C Hoogeveen, Marcos Damasio, Hannah K Drescher, Lea M Bartsch, Damien C Tully, Debattama R Sen, David J Bean, Joelle Brown, Almudena Torres-Cornejo, Maxwell Robidoux, Daniel Kvistad, Nadia Alatrakchi, Ang Cui, David Lieb, James A Cheney, Jenna Gustafson, Lia L Lewis-Ximenez, Lucile Massenet-Regad, Thomas Eisenhaure, Jasneet Aneja, W Nicholas Haining, Raymond T Chung, Nir Hacohen, Todd M Allen, Arthur Y Kim, Georg M Lauer
Abstract
T cell exhaustion is associated with failure to clear chronic infections and malignant cells. Defining the molecular mechanisms of T cell exhaustion and reinvigoration is essential to improving immunotherapeutic modalities. Here we confirmed pervasive phenotypic, functional and transcriptional differences between memory and exhausted antigen-specific CD8+ T cells in human hepatitis C virus (HCV) infection before and after treatment. After viral cure, phenotypic changes in clonally stable exhausted T cell populations suggested differentiation toward a memory-like profile. However, functionally, the cells showed little improvement, and critical transcriptional regulators remained in the exhaustion state. Notably, T cells from chronic HCV infection that were exposed to antigen for less time because of viral escape mutations were functionally and transcriptionally more similar to memory T cells from spontaneously resolved HCV infection. Thus, the duration of T cell stimulation impacts exhaustion recovery, with antigen removal after long-term exhaustion being insufficient for the development of functional T cell memory.
Trial registration: ClinicalTrials.gov NCT02476617.
Conflict of interest statement
COMPETING INTERESTS
AbbVie sponsored the clinical trial (NCT02476617) and provided input to the trial design and clinical and biological sample collection schedule. W.N.H. is an employee of Merck and Company and holds equity in Tango Therapeutics and Arsenal Biosciences. All other authors declare no competing interests.
© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.
Figures
References
- McLane LM, Abdel-Hakeem MS & Wherry EJ CD8 T Cell Exhaustion During Chronic Viral Infection and Cancer. Annu Rev Immunol 37, 457–495 (2019).
- Wherry EJ & Kurachi M Molecular and cellular insights into T cell exhaustion. Nat Rev Immunol 15, 486–499 (2015).
- 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. J Virol 77, 4911–4927 (2003).
- Kasprowicz V et al. High level of PD-1 expression on hepatitis C virus (HCV)-specific CD8+ and CD4+ T cells during acute HCV infection, irrespective of clinical outcome. J Virol 82, 3154–3160 (2008).
- Bengsch B et al. Coexpression of PD-1, 2B4, CD160 and KLRG1 on exhausted HCV-specific CD8+ T cells is linked to antigen recognition and T cell differentiation. PLoS pathogens 6, e1000947 (2010).
- Blackburn SD et al. Coregulation of CD8+ T cell exhaustion by multiple inhibitory receptors during chronic viral infection. Nat Immunol 10, 29–37 (2009).
- Wherry EJ et al. Molecular signature of CD8+ T cell exhaustion during chronic viral infection. Immunity 27, 670–684 (2007).
- Angelosanto JM, Blackburn SD, Crawford A & Wherry EJ Progressive loss of memory T cell potential and commitment to exhaustion during chronic viral infection. Journal of virology 86, 8161–8170 (2012).
- Shin H, Blackburn SD, Blattman JN & Wherry EJ Viral antigen and extensive division maintain virus-specific CD8 T cells during chronic infection. J Exp Med 204, 941–949 (2007).
- Wherry EJ, Barber DL, Kaech SM, Blattman JN & Ahmed R Antigen-independent memory CD8 T cells do not develop during chronic viral infection. Proc Natl Acad Sci U S A 101, 16004–16009 (2004).
- Gallimore A et al. Induction and exhaustion of lymphocytic choriomeningitis virus-specific cytotoxic T lymphocytes visualized using soluble tetrameric major histocompatibility complex class I-peptide complexes. J Exp Med 187, 1383–1393 (1998).
- Pardoll DM The blockade of immune checkpoints in cancer immunotherapy. Nat Rev Cancer 12, 252–264 (2012).
- Wei SC, Duffy CR & Allison JP Fundamental Mechanisms of Immune Checkpoint Blockade Therapy. Cancer Discov 8, 1069–1086 (2018).
- Hegde PS & Chen DS Top 10 Challenges in Cancer Immunotherapy. Immunity 52, 17–35 (2020).
- Hamid O et al. Five-year survival outcomes for patients with advanced melanoma treated with pembrolizumab in KEYNOTE-001. Ann Oncol 30, 582–588 (2019).
- Seder RA, Darrah PA & Roederer M T-cell quality in memory and protection: implications for vaccine design. Nat Rev Immunol 8, 247–258 (2008).
- Hoogeveen RC & Boonstra A Checkpoint Inhibitors and Therapeutic Vaccines for the Treatment of Chronic HBV Infection. Front Immunol 11, 401 (2020).
- Fisicaro P et al. Pathogenetic Mechanisms of T Cell Dysfunction in Chronic HBV Infection and Related Therapeutic Approaches. Front Immunol 11, 849 (2020).
- Wherry EJ T cell exhaustion. Nature immunology 12, 492–499 (2011).
- Day CL et al. PD-1 expression on HIV-specific T cells is associated with T-cell exhaustion and disease progression. Nature 443, 350–354 (2006).
- Schuch A et al. Phenotypic and functional differences of HBV core-specific versus HBV polymerase-specific CD8+ T cells in chronically HBV-infected patients with low viral load. Gut (2019).
- Hoogeveen RC et al. Phenotype and function of HBV-specific T cells is determined by the targeted epitope in addition to the stage of infection. Gut (2018).
- Kasprowicz V et al. Hepatitis C virus (HCV) sequence variation induces an HCV-specific T-cell phenotype analogous to spontaneous resolution. J Virol 84, 1656–1663 (2010).
- Lauer GM & Walker BD Hepatitis C virus infection. N Engl J Med 345, 41–52. (2001).
- Wolski D et al. Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8(+) T Cells in Chronic versus Acute Infection. Immunity 47, 648–663 e648 (2017).
- Holmes JA, Rutledge SM & Chung RT Direct-acting antiviral treatment for hepatitis C. Lancet 393, 1392–1394 (2019).
- Wieland D et al. TCF1+ hepatitis C virus-specific CD8+ T cells are maintained after cessation of chronic antigen stimulation. Nat Commun 8, 15050 (2017).
- Martin B et al. Restoration of HCV-specific CD8+ T cell function by interferon-free therapy. J Hepatol 61, 538–543 (2014).
- Alfei F et al. TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection. Nature 571, 265–269 (2019).
- Hensel N et al. Memory-like HCV-specific CD8(+) T cells retain a molecular scar after cure of chronic HCV infection. Nat Immunol 22, 229–239 (2021).
- Holmes JA et al. Dynamic changes in innate immune responses during direct-acting antiviral therapy for HCV infection. J Viral Hepat 26, 362–372 (2019).
- Kuntzen T et al. Viral sequence evolution in acute hepatitis C virus infection. J Virol 81, 11658–11668 (2007).
- Cox AL et al. Cellular immune selection with hepatitis C virus persistence in humans. J Exp Med 201, 1741–1752 (2005).
- Timm J et al. CD8 epitope escape and reversion in acute HCV infection. J Exp Med 200, 1593–1604 (2004).
- Gruener NH et al. Sustained dysfunction of antiviral CD8(+) T lymphocytes after infection with hepatitis c virus. J Virol 75, 5550–5558. (2001).
- Araki K et al. Translation is actively regulated during the differentiation of CD8(+) effector T cells. Nat Immunol 18, 1046–1057 (2017).
- Khan O et al. TOX transcriptionally and epigenetically programs CD8(+) T cell exhaustion. Nature 571, 211–218 (2019).
- 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).
- Utzschneider DT 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).
- Henn MR et al. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 8, e1002529 (2012).
- Tully DC et al. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus. PLoS Pathog 12, e1005619 (2016).
- Kotecha N, Krutzik PO & Irish JM Web-based analysis and publication of flow cytometry experiments. Curr Protoc Cytom Chapter 10, Unit10 17 (2010).
- Metsalu T & Vilo J ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. Nucleic Acids Res 43, W566–570 (2015).
- Picelli S et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014).
- Robinson MD, McCarthy DJ & Smyth GK edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
- Law CW, Chen Y, Shi W & Smyth GK voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 15, R29 (2014).
- Ritchie ME et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43, e47 (2015).
- Benjamini Y & Hochberg Y Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society: Series B (Methodological) 57, 289–300 (1995).
- Johnson WE, Li C & Rabinovic A Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118–127 (2007).
- Subramanian A et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102, 15545–15550 (2005).
- Mootha VK et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34, 267–273 (2003).
- Khan A et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res 46, D1284 (2018).
- Consortium, E.P. A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9, e1001046 (2011).
Source: PubMed