Abstract
T cell exhaustion is an induced state of dysfunction that arises in response to chronic infection and cancer. Exhausted CD8+ T cells acquire a distinct epigenetic state, but it is not known whether that chromatin landscape is fixed or plastic following the resolution of a chronic infection. Here we show that the epigenetic state of exhaustion is largely irreversible, even after curative therapy. Analysis of chromatin accessibility in HCV- and HIV-specific responses identifies a core epigenetic program of exhaustion in CD8+ T cells, which undergoes only limited remodeling before and after resolution of infection. Moreover, canonical features of exhaustion, including super-enhancers near the genes TOX and HIF1A, remain ‘epigenetically scarred.’ T cell exhaustion is therefore a conserved epigenetic state that becomes fixed and persists independent of chronic antigen stimulation and inflammation. Therapeutic efforts to reverse T cell exhaustion may require new approaches that increase the epigenetic plasticity of exhausted T cells.
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Data availability
All sequencing data from this study will be made publicly available through the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) and/or NCBI database of Genotypes and Phenotypes (dbGaP; https://www.ncbi.nlm.nih.gov/gap/). All other relevant data are available from the corresponding authors on request.
References
Hashimoto, M. et al. CD8 T cell exhaustion in chronic infection and cancer: opportunities for interventions. Annu. Rev. Med. 69, 301–318 (2018).
Wherry, E. J. et al. Molecular signature of CD8+ T cell exhaustion during chronic viral infection. Immunity 27, 670–684 (2007).
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).
Sen, D. R. et al. The epigenetic landscape of T cell exhaustion. Science 354, 1165–1169 (2016).
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).
Zajac, A. J. et al. Viral immune evasion due to persistence of activated T cells without effector function. J. Exp. Med. 188, 2205–2213 (1998).
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).
Blackburn, S. D. et al. Coregulation of CD8+ T cell exhaustion by multiple inhibitory receptors during chronic viral infection. Nat. Immunol. 10, 29–37 (2009).
Day, C. L. et al. PD-1 expression on HIV-specific T cells is associated with T-cell exhaustion and disease progression. Nature 443, 350–354 (2006).
Gruener, N. H. et al. Sustained dysfunction of antiviral CD8+ T lymphocytes after infection with hepatitis C virus. J. Virol. 75, 5550–5558 (2001).
Wedemeyer, H. et al. Impaired effector function of hepatitis C virus-specific CD8+ T cells in chronic hepatitis C virus infection. J. Immunol. 169, 3447–3458 (2002).
Radziewicz, H. 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. J. Virol. 81, 2545–2553 (2007).
Wolski, D. et al. Early transcriptional divergence marks virus-specific primary human CD8+ T cells in chronic versus acute infection. Immunity 47, 648–663 (2017).
Micallef, J. M., Kaldor, J. M. & Dore, G. J. Spontaneous viral clearance following acute hepatitis C infection: a systematic review of longitudinal studies. J. Viral Hepat. 13, 34–41 (2006).
Cox, A. L. et al. Cellular immune selection with hepatitis C virus persistence in humans. J. Exp. Med. 201, 1741–1752 (2005).
Kuntzen, T. et al. Viral sequence evolution in acute hepatitis C virus infection. J. Virol. 81, 11658–11668 (2007).
Rutebemberwa, A. et al. High-programmed death-1 levels on hepatitis C virus-specific T cells during acute infection are associated with viral persistence and require preservation of cognate antigen during chronic infection. J. Immunol. 181, 8215–8225 (2008).
Feld, J. J. et al. Treatment of HCV with ABT-450/r-ombitasvir and dasabuvir with ribavirin. N. Engl. J. Med. 370, 1594–1603 (2014).
Ferenci, P. et al. ABT-450/r-ombitasvir and dasabuvir with or without ribavirin for HCV. N. Engl. J. Med. 370, 1983–1992 (2014).
Baumert, T. F., Berg, T., Lim, J. K. & Nelson, D. R. Status of direct-acting antiviral therapy for hepatitis C virus infection and remaining challenges. Gastroenterology 156, 431–445 (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).
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).
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).
Martinez, G. J. et al. The transcription factor NFAT promotes exhaustion of activated CD8+ T cells. Immunity 42, 265–278 (2015).
Gate, R. E. et al. Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Nat. Genet. 50, 1140–1150 (2018).
Rasool, S. T. et al. Increased level of IL-32 during human immunodeficiency virus infection suppresses HIV replication. Immunol. Lett. 117, 161–167 (2008).
El-Far, M. et al. Proinflammatory isoforms of IL-32 as novel and robust biomarkers for control failure in HIV-infected slow progressors. Sci. Rep. 6, 22902 (2016).
Nguyen, S. et al. Elite control of HIV is associated with distinct functional and transcriptional signatures in lymphoid tissue CD8+ T cells. Sci. Transl. Med. https://doi.org/10.1126/scitranslmed.aax4077 (2019).
Zaidan, S. M. et al. Upregulation of IL-32 isoforms in virologically suppressed HIV-infected individuals: potential role in persistent inflammation and transcription from stable HIV-1 reservoirs. J. Acquir. Immune Defic. Syndr. 82, 503–513 (2019).
Chinnaswamy, S. Genetic variants at the IFNL3 locus and their association with hepatitis C virus infections reveal novel insights into host-virus interactions. J. Interferon Cytokine Res. 34, 479–497 (2014).
Monteleone, K. et al. Interleukin-32 isoforms: expression, interaction with interferon-regulated genes and clinical significance in chronically HIV-1-infected patients. Med. Microbiol. Immunol. 203, 207–216 (2014).
Wherry, E. J. & Kurachi, M. Molecular and cellular insights into T cell exhaustion. Nat. Rev. Immunol. 15, 486–499 (2015).
Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).
Chipumuro, E. et al. CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer. Cell 159, 1126–1139 (2014).
Adam, R. C. et al. Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice. Nature 521, 366–370 (2015).
Vahedi, G. et al. Super-enhancers delineate disease-associated regulatory nodes in T cells. Nature 520, 558–562 (2015).
Ma, S. et al. Chromatin potential identified by shared single-cell profiling of RNA and chromatin. Cell 183, 1103–1116 (2020).
Khan, O. et al. TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion. Nature 571, 211–218 (2019).
Scott, A. C. et al. TOX is a critical regulator of tumour-specific T cell differentiation. Nature 571, 270–274 (2019).
Alfei, F. et al. TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection. Nature 571, 265–269 (2019).
Urbani, S. et al. PD-1 expression in acute hepatitis C virus (HCV) infection is associated with HCV-specific CD8 exhaustion. J. Virol. 80, 11398–11403 (2006).
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 Pathog. 6, e1000947 (2010).
Pauken, K. E. et al. Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade. Science 354, 1160–1165 (2016).
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).
Alatrakchi, N. et al. Hepatitis C virus (HCV)-specific CD8+ cells produce transforming growth factor β that can suppress HCV-specific T-cell responses. J. Virol. 81, 5882–5892 (2007).
Brooks, D. G. et al. Interleukin-10 determines viral clearance or persistence in vivo. Nat. Med. 12, 1301–1309 (2006).
Ejrnaes, M. et al. Resolution of a chronic viral infection after interleukin-10 receptor blockade. J. Exp. Med. 203, 2461–2472 (2006).
Tinoco, R., Alcalde, V., Yang, Y., Sauer, K. & Zuniga, E. I. Cell-intrinsic transforming growth factor-β signaling mediates virus-specific CD8+ T cell deletion and viral persistence in vivo. Immunity 31, 145–157 (2009).
Kroy, D. C. et al. Liver environment and HCV replication affect human T-cell phenotype and expression of inhibitory receptors. Gastroenterology 146, 550–561 (2014).
Lynn, R. C. et al. c-Jun overexpression in CAR T cells induces exhaustion resistance. Nature 576, 293–300 (2019).
Rutishauser, R. L. et al. Early and delayed antiretroviral therapy results in comparable reductions in CD8+ T cell exhaustion marker expression. AIDS Res. Hum. Retroviruses 33, 658–667 (2017).
Youngblood, B. et al. Cutting edge: prolonged exposure to HIV reinforces a poised epigenetic program for PD-1 expression in virus-specific CD8 T cells. J. Immunol. 191, 540–544 (2013).
The SPARTAC Trial Investigators. Short-course antiretroviral therapy in primary HIV infection. N. Engl. J. Med. 368, 207–217 (2013).
Hoffmann, M. et al. Exhaustion of activated CD8 T cells predicts disease progression in primary HIV-1 infection. PLoS Pathog. 12, e1005661 (2016).
Amemiya, H. M., Kundaje, A. & Boyle, A. P. The ENCODE blacklist: identification of problematic regions of the genome. Sci. Rep. 9, 9354 (2019).
Acknowledgements
We thank the members of the Haining laboratory for their input and the research participants for their participation. This work was supported by NIH grant no. U19 AI086230 and funding from the Parker Institute for Cancer Immunotherapy. S.A.W. was supported by NIH grant nos. T32 GM007753 and T32 CA207021; R.T.C. was supported by AI136715 and the MGH Research Scholars Program. We also thank the Center for Virology and Vaccine Research Flow Cytometry Core at Beth Israel Deaconess Medical Center for their assistance.
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Contributions
D.R.S. and W.N.H. conceived the study and designed the experiments. D.R.S., K.B.Y., G.E.M., U.G., R.A.A., D.E.C. and S.A.W. performed experiments and/or data analysis. P.T., D.W., D.C.T., R.T.C., T.M.A., A.Y.K. and G.M.L. contributed to the HCV clinical trial design, patient recruitment, sample processing, viral sequencing studies and/or transcriptional analysis. G.E.M., S.F., J. Frater. and J. Fox contributed to the HIV clinical trial design, patient recruitment and/or sample processing. D.R.S. and W.N.H. wrote the manuscript; all authors reviewed and edited the manuscript.
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Competing interests
AbbVie sponsored the clinical trial (NCT02476617) and gave input to the trial design as well as the 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. The other authors declare no competing interests.
Additional information
Peer review information Nature Immunology thanks Hazem Ghoneim, Barbara Rehermann and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Zoltan Fehervari was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
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Extended data
Extended Data Fig. 1 Isolation and chromatin accessibility profiling of Flu and HCV multimer+ CD8+ T cells in HCV infection.
a, Representative flow cytometry sorting strategy for Flu and HCV multimer+ CD8+ T cells. b, Recovered numbers of Flu (top) and HCV (bottom) multimer+ cells for each donor during chronic HCV infection. c, Recovered numbers of HCV multimer+ cells for each donor during resolved HCV infection. d, Combined ATAC signal across all TSSs for each biological condition from each donor. Green and range bands indicate ranges for ideal and acceptable values, respectively, for TSS enrichment per ENCODE standards. e, Boxplots of pairwise Pearson correlations for data from individual donors within each biological condition. Center, median; box limits, first and third percentiles; whiskers, min and max. N = 6 donors. f, Combined ATAC signal across all H3K27ac peaks (red), H3K27me3 (green) and H3K4me3 (purple). Histone mark peaks were determined from the following samples on ENCODE: ENCFF653OGM - H3K27ac, ENCFF285FID - H3K4me3, ENCFF367HSC - H3K27me3. g, Clustered similarity matrix between the indicated biological conditions in the chronically-infected and spontaneously resolved cohort. h, Density of overlapping GWAS SNPs per 1000 bp in Flu-specific, HCV-specific or non-differential ChARs.
Extended Data Fig. 2 Isolation and chromatin accessibility profiling of HIV multimer+ CD8+ T cells in HIV infection.
a, Representative flow cytometry sorting strategy for HIV multimer+ CD8+ T cells. b, Boxplots of pairwise Pearson correlations for data from individual donors within each biological condition. Center, median; box limits, first and third percentiles; whiskers, min and max. N = 11 donors. c, Combined principal component analysis of naïve, HIV-, HCV- and Flu- specific CD8+ T cells from the HIV and HCV cohorts.
Extended Data Fig. 3 Features of HCV-specific CD8+ T cells before and after DAA therapy.
a, PD-1 and CD39 staining on tetramer populations before (top) and after (bottom) DAA therapy. b, Partitioning of scarred and reversed regions into those overlapping promoters, UTRs, exons, introns and intergenic areas as indicated. c, Classification of SNPs falling within scarred, reversed or gained ChARs. SNPs that were subcategorized into those associated with chronic viral infection are summarized in Supplementary Table 3.
Extended Data Fig. 4 Minimal impact of the inflammatory milieu on chromatin accessibility within bystander populations in chronic HCV.
a, CCR7 and CD45RA staining on all CD8+ T cells (left) and Flu-specific T cells (right). b, Venn diagram of ChAR overlap in Flu tet+ cells (bottom) from HCV-infected donors and healthy donors. c, PD-1 and CD39 staining on tetramer populations before (top) and after (bottom) DAA therapy. d, Combined principal component analysis of naïve, effector memory, HCV-, and Flu- specific CD8+ T cells from the healthy and HCV cohorts. e, Heatmap showing pathway enrichment (rows) within clustered ChARs from Fig. 4g (columns).
Extended Data Fig. 5 Validation of ATAC-seq-based super-enhancer inference across multiple datasets.
a, H3K27ac ChIP-seq signal (top) and ATAC-seq signal (bottom) at the ETS1 gene locus. b, ROC plots of varying cutoff for ATAC-based ranking of super-enhancer to predict bona fide super-enhancers defined using matched tissue-specific H3K27ac ChIP-seq. c, Boxplots of tissue-specific mRNA expression, partitioned by genes with or without an associated super-enhancer. Center, median; box limits, first and third percentiles. d, Tox mRNA expression in HCV tetramer populations before and after DAA therapy. Mean ± s.d., two-sided Student’s t-test with Welch’s correction; *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001. N = 6 donors.
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Yates, K.B., Tonnerre, P., Martin, G.E. et al. Epigenetic scars of CD8+ T cell exhaustion persist after cure of chronic infection in humans. Nat Immunol 22, 1020–1029 (2021). https://doi.org/10.1038/s41590-021-00979-1
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DOI: https://doi.org/10.1038/s41590-021-00979-1
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