Molecular Dissection of CD8+ T-Cell Dysfunction

doi:10.1016/j.it.2017.05.008

Trends in Immunology

Volume 38, Issue 8, August 2017, Pages 567-576

https://doi.org/10.1016/j.it.2017.05.008 Get rights and content

Trends

Recent advances have identified novel CD8⁺ T-cell functional states in chronic inflammatory conditions associated with distinct transcriptional programs.

Single-cell analysis has revealed extensive transcriptional heterogeneity in the CD8⁺ T-cell response in cancer.

CRISPR/Cas9 genome editing in mature CD8⁺ T cells has enabled testing of candidate regulators in vivo.

Analysis of the chromatin landscape in CD8⁺ T cells has revealed distinct epigenetic changes associated with distinct functional states.

Chronic viral infections and cancer often lead to the emergence of dysfunctional or ‘exhausted’ CD8⁺ T cells, and the restoration of their functions is currently the focus of therapeutic interventions. In this review, we detail recent advances in the annotation of the gene modules and the epigenetic landscape associated with T-cell dysfunction. Together with analysis of single-cell transcriptomes, these findings have enabled a deeper and more precise understanding of the transcriptional mechanisms that induce and maintain the dysfunctional state and highlight the heterogeneity of CD8⁺ T-cell phenotypes present in chronically inflamed tissue. We discuss the relevance of these findings for understanding the transcriptional and spatial regulation of dysfunctional T cells and for the design of therapeutics.

Section snippets

T-Cell Dysfunction

In chronic disease settings, such as in chronic viral infections and cancer, effector CD8⁺ T cells progressively acquire an ‘exhausted’ or dysfunctional T-cell state characterized by variable deficits in their effector functions, including cytotoxicity and the production of proinflammatory cytokines [interleukin-2 (IL-2), tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ)] [1] (Figure 1A). Importantly, dysfunctional CD8⁺ T cells are not completely inert as it has been shown that they can

Molecular Signatures of T-Cell Dysfunction

Several gene signatures based on analyses of populations of dysfunctional CD8⁺ T cells from cancer and chronic viral infections have been published 9, 21, 22, 23, 24, 25. These signatures have shown that there is great similarity between virus- and cancer-associated CD8⁺ T-cell dysfunction and have greatly advanced our understanding of factors that contribute to dysfunctional phenotype. Comparisons of the gene expression profiles of functional versus dysfunctional virus-specific CD8⁺ T cells

Gene Modules for T-Cell Dysfunction and Activation

While the dysfunction signatures discussed earlier have been useful in identifying factors that contribute to T-cell dysfunction, it was noted early on that these signatures highly overlap with signatures of healthy T-cell activation (reviewed in [29]). For example, co-inhibitory receptors (e.g., PD-1, Tim-3, CTLA-4) and effector molecules (e.g., GZMC, IFN-γ) present in the dysfunction signatures have been shown to be associated with healthy T-cell activation. This overlap between the

Heterogeneity of CD8⁺ T-Cell States within Tumor

The discovery of refined gene modules for T-cell dysfunction, activation/dysfunction, and activation raises the question of how these modules are expressed in individual CD8⁺ T cells and how this relates to their functional phenotype (Figure 1B). For example, do the dysfunctional CD8⁺ T cells previously defined based on surface expression of co-inhibitory receptors uniformly express the activation/dysfunction and dysfunction modules or are there subpopulations that express these modules to

Transcription Factors

In addition to Gata3 [24], several other transcription factors have been shown to play a role in promoting CD8⁺ T-cell dysfunction. The leucine zipper-containing transcription factor Maf was reported to be upregulated in dysfunctional CD8⁺ TILs in murine melanoma tumors and in TILs from melanoma patients when compared with naïve and effector CD8⁺ T cells [9]. Loss of Maf resulted in better tumor control while overexpression resulted in dampened TIL accumulation and antitumor activity. Martinez

Implications for Therapy

Immunotherapies, such as co-inhibitory receptor blockade and adoptive T-cell transfer, are transforming the treatment for advanced cancer [50]. Understanding how these therapies work and finding ways to improve them is an active area of research 51, 52, 53, 54, 55. Technological advances such as in-depth genomic analyses will be instrumental in this regard. Indeed, such analyses have shown that CTLA-4 and PD-1 blockade therapies achieve efficacy through distinct mechanisms [56]. Moreover,

Concluding Remarks and Future Perspectives

Single-cell analysis has the potential to identify new and more refined gene modules in CD8⁺ T cells. It will be important to discern transient from more stable states, potentially with epigenetic analysis coupled with perturbations (see Outstanding Questions). Testing whether the different transcriptional populations identified by single-cell transcriptomics are distinct in cytotoxicity, cytokine secretion, proliferative capacity, and T-cell receptor expression will resolve their functional

Acknowledgments

A.C.A. acknowledges support from the National Institutes of Health (R01CA187975 and P01AI073748).

Glossary

Gene module: a set of genes that have similar expression profiles across conditions tested. Gene modules may include hundreds or even thousands of genes. Unlike a gene signature, a module does not necessarily define a specific cell state. For example, a dysfunction/activation module for CD8⁺ T cells consists of genes that are upregulated in both the dysfunction and activation states.
Gene signature: a set of genes that defines a specific cell state. Typically, gene signatures include tens to

References (62)

R. Tinoco
Cell-intrinsic transforming growth factor-beta signaling mediates virus-specific CD8⁺ T cell deletion and viral persistence in vivo
Immunity
(2009)
A. Crawford
Molecular and transcriptional basis of CD4⁺ T cell dysfunction during chronic infection
Immunity
(2014)
A. Oxenius
Comparison of activation versus induction of unresponsiveness of virus-specific CD4⁺ and CD8⁺ T cells upon acute versus persistent viral infection
Immunity
(1998)
E.J. Wherry
Molecular signature of CD8⁺ T cell exhaustion during chronic viral infection
Immunity
(2007)
T.A. Doering
Network analysis reveals centrally connected genes and pathways involved in CD8⁺ T cell exhaustion versus memory
Immunity
(2012)
G.J. Martinez
The transcription factor NFAT promotes exhaustion of activated CD8⁺ T cells
Immunity
(2015)
D.T. Utzschneider
T cell factor 1-expressing memory-like CD8⁺ T cells sustain the immune response to chronic viral infections
Immunity
(2016)
H. Shin
A role for the transcriptional repressor Blimp-1 in CD8⁺ T cell exhaustion during chronic viral infection
Immunity
(2009)
B. Youngblood
Chronic virus infection enforces demethylation of the locus that encodes PD-1 in antigen-specific CD8⁺ T cells
Immunity
(2011)
M.C. Dieu-Nosjean
Tertiary lymphoid structures in cancer and beyond
Trends Immunol.
(2014)

E. Razis

Improved outcome of high-risk early HER2 positive breast cancer with high CXCL13-CXCR5 messenger RNA expression

Clin. Breast Cancer

(2012)

W.A. Lim et al.

The principles of engineering immune cells to treat cancer

Cell

(2017)

P. Sharma et al.

Immune checkpoint targeting in cancer therapy: toward combination strategies with curative potential

Cell

(2015)

W. Hugo

Genomic and transcriptomic features of response to anti-PD-1 therapy in metastatic melanoma

Cell

(2016)

B. Mlecnik

Integrative analyses of colorectal cancer show immunoscore is a stronger predictor of patient survival than microsatellite instability

Immunity

(2016)

E.J. Wherry et al.

Molecular and cellular insights into T cell exhaustion

Nat. Rev. Immunol.

(2015)

A.J. Zajac

Viral immune evasion due to persistence of activated T cells without effector function

J. Exp. Med.

(1998)

D. Moskophidis

Virus persistence in acutely infected immunocompetent mice by exhaustion of antiviral cytotoxic effector T cells

Nature

(1993)

H. Elsaesser

IL-21 is required to control chronic viral infection

Science

(2009)

A. Frohlich

IL-21R on T cells is critical for sustained functionality and control of chronic viral infection

Science

(2009)

J.S. Yi

A vital role for interleukin-21 in the control of a chronic viral infection

Science

(2009)

E.B. Wilson et al.

The role of IL-10 in regulating immunity to persistent viral infections

Curr. Top. Microbiol. Immunol.

(2011)

M. Giordano

Molecular profiling of CD8 T cells in autochthonous melanoma identifies Maf as driver of exhaustion

EMBO J.

(2015)

Y. Yang

IL-6 plays a unique role in initiating c-Maf expression during early stage of CD4 T cell activation

J. Immunol.

(2005)

J.S. Yi

T-cell exhaustion: characteristics, causes and conversion

Immunology

(2010)

S. Hwang

Blimp-1-mediated CD4 T cell exhaustion causes CD8 T cell dysfunction during chronic toxoplasmosis

J. Exp. Med.

(2016)

D.G. Brooks

Intrinsic functional dysregulation of CD4 T cells occurs rapidly following persistent viral infection

J. Virol.

(2005)

J. Schulze Zur Wiesch

Broadly directed virus-specific CD4⁺ T cell responses are primed during acute hepatitis C infection, but rapidly disappear from human blood with viral persistence

J. Exp. Med.

(2012)

L.M. Fahey

Viral persistence redirects CD4 T cell differentiation toward T follicular helper cells

J. Exp. Med.

(2011)

R. He

Follicular CXCR5-expressing CD8⁺ T cells curtail chronic viral infection

Nature

(2016)

Y.A. Leong

CXCR5⁺ follicular cytotoxic T cells control viral infection in B cell follicles

Nat. Immunol.

(2016)

Cited by (44)

Influence of different conjugation methods for activating antibodies on polymeric nanoparticles: Effects for polyclonal expansion of human CD8+ T cells
2024, International Immunopharmacology
Particle-based systems have become a state-of-the-art method for in vitro expanding cytotoxic T cells by tailoring their surface with activating molecules. However, commonly used methods utilize facile carbodiimide chemistry leading to uncontrolled orientation of the immobilized antibodies on the particle surface that can lead to poor binding to target cells. To address this, selective coupling strategies utilizing regioselective chemical groups such as disulfide bridges offer a simple approach. In this work we present a set of methods to investigate the effect of polymeric nanoparticles, conjugated with either regioselective- or randomly-immobilized antiCD3 and antiCD28 antibodies, on the activation potential, expansion and expression of activation markers in T cells. We show that nanoparticles with well-oriented monovalent antibodies conjugated via maleimide require fewer ligands on the surface to efficiently expand T cells compared to bivalent antibodies randomly-immobilized via carbodiimide conjugation. Analysis of the T cell expression markers reveal that the T cell phenotype can be fine-tuned by adjusting the surface density of well-oriented antibodies, while randomly immobilized antibodies showed no differences despite their ligand density. Both conjugation techniques induced cytotoxic T cells, evidenced by analyzing their Granzyme B secretion. Furthermore, antibody orientation affects the immunological synapse and T cell activation by changing the calcium influx profile upon activation. Nanoparticles with well-oriented antibodies showed lower calcium influx compared to their bivalent randomly-immobilized counterparts. These results highlight the importance of controlling the antibody density and orientation on the nanoparticle surface via controlled coupling chemistries, helping to develop improved particle-based expansion protocols to enhance T cell therapies.
Metronomic chemotherapy, dampening of immunosuppressive cells, antigen presenting cell activation, and T cells. A quartet against refractoriness and resistance to checkpoint inhibitors
2023, Cancer Letters
Chemotherapeutic agents have profound effects on cancer, stroma and immune cells that – in most cases – depend upon the dosage and schedule of administration. Preclinical and clinical studies summarized and discussed in the present review have demonstrated that maximum tolerable dosage (MTD) vs low-dosage, continuous (metronomic) administration of most chemotherapeutics have polarized effects on immune cells. In particular, metronomic schedules might be associated – among others effects – with activation of antigen presenting cells and generation of new T cell clones to enhance the activity of several types of immunotherapies. Ongoing and planned clinical trials in different types of cancer will confirm or dismiss this hypothesis and provide candidate biomarker data for the selection of patients who are likely to benefit from these combinatorial strategies.
BMI1-induced CD127+KLRG1+ memory T cells enhance the efficacy of liver cancer immunotherapy
2023, Cancer Letters
The efficacy of HCC (hepatocellular carcinoma) immunotherapy is hindered by the limited reactivity and short duration of tumor-infiltrating T cells. These deficiencies may be ascribed to the proliferative ability of T cells. The primary objective of this study was to identify the key factor regulating tumor-infiltrating lymphocytes (TIL) proliferation within the HCC microenvironment. Through the utilization of tissue-infiltrated T cell proteomics and fraction proteomics, we analyzed the differential proteins in T cells among HCC, liver fibrosis, and hemangioma (serving as controls) groups. Additionally, we examined the differential regulatory TFs of T cells between the HCC and VH (volunteer healthy, as a control) groups. Using cyTOF and flow cytometry technologies, as well as generating CD8⁺ T-specific BMI1 knockout mice, we confirmed that BMI1 controls CD127⁺KLRG1⁺ memory cell differentiation. Through RNA-seq and MeRIP-seq, we verified that BMI1 regulates TCF1 expression independently of its classical function. Furthermore, by conducting Tyramide signal amplification (TSA) IHC analysis, employing a hydrodynamic mouse HCC model, and utilizing liver-specific nanoparticle targeting therapy, we demonstrated that BMI1 in HCC influences the proliferation of infiltrating CD8+T. BMI1 inhibition promotes effector T cell differentiation while suppressing memory T cell differentiation. Moreover, liver-specific BMI1 knockdown proves beneficial in ameliorating T cell dysfunction and decelerating HCC progression. Our research group has pioneered the exploration of the proteomics of HCC-infiltrated T cells, shedding light on the pivotal role of BMI1 in controlling CD127+KLRG1+ memory CD8⁺ T cell differentiation, which serves as the cornerstone for achieving immunotherapy efficacy in HCC.
Targeting TCF19 sensitizes MSI endometrial cancer to anti-PD-1 therapy by alleviating CD8<sup>+</sup> T cell exhaustion via TRIM14-IFN-β axis
2023, Cell Reports
Immune checkpoint blockade (ICB) therapies display clinical efficacy in microsatellite instable (MSI) endometrial cancer (EC) treatment, the key mechanism of which is reversing T cell exhaustion and restoration of anti-tumor immunity. Here, we demonstrate that transcription factor 19 (TCF19), one of the most significantly differentially expressed genes between MSI and microsatellite stable (MSS) patients in The Cancer Genome Atlas (TCGA)-EC cohort, is associated with poor prognosis and immune exhaustion signature. Specifically, TCF19 is significantly elevated in MSI EC, which in turn promotes tripartite motif-containing 14 (TRIM14) transcription and correlates with hyperactive signaling of the TANK-binding kinase 1 (TBK1)-interferon regulatory factor 3 (IRF3)-interferon β (IFN-β) pathway. The TCF19-TRIM14 axis promotes tumorigenicity under non-immunological background, and the enhanced downstream secretion of IFN-β facilitates CD8⁺ T cell exhaustion through cell differentiation reprogramming. Finally, using humanized models, we show that a combination of TCF19 inhibition and ICB therapy demonstrates more effective anti-tumor responses. Together, our study indicates that targeting TCF19 is a potent strategy for alleviating CD8⁺ T cell exhaustion and synergizing with ICB in tumor treatment.
Modulation of the tumor microenvironment (TME) by melatonin
2021, European Journal of Pharmacology
Citation Excerpt :
MT1 and MT2 play a key role in the proliferation and activation of CD8+ T lymphocytes (Chen et al., 2016). It has been revealed that the dysfunctional CD8+ T lymphocytes show loss of both MT1 and MT2 (Wang et al., 2017). Downregulation of MT1/MT2 in Jurkat cells is associated with a remarkable reduction in the production of IL-2 (Reppert, 1997).
The tumor microenvironment (TME) includes a number of non-cancerous cells that affect cancer cell survival. Although CD8⁺ T lymphocytes and natural killer (NK) cells suppress tumor growth through induction of cell death in cancer cells, there are various immunosuppressive cells such as regulatory T cells (Tregs), tumor-associated macrophages (TAMs), cancer-associated fibroblasts (CAFs), myeloid-derived suppressor cells (MDSCs), etc., which drive cancer cell proliferation. These cells may also support tumor growth and metastasis by stimulating angiogenesis, epithelial-mesenchymal transition (EMT), and resistance to apoptosis. Interactions between cancer cells and other cells, as well as molecules released into EMT, play a key role in tumor growth and suppression of antitumoral immunity. Melatonin is a natural hormone that may be found in certain foods and is also available as a drug. Melatonin has been demonstrated to modulate cell activity and the release of cytokines and growth factors in TME. The purpose of this review is to explain the cellular and molecular mechanisms of cancer cell resistance as a result of interactions with TME. Next, we explain how melatonin affects cells and interactions within the TME.
Asynchronous blockade of PD-L1 and CD155 by polymeric nanoparticles inhibits triple-negative breast cancer progression and metastasis
2021, Biomaterials
PD-L1/PD-1 blockade therapy shows durable responses to triple-negative breast cancer (TNBC), but the response rate is low. CD155 promotes tumor metastasis intrinsically and modulates the immune response extrinsically as the ligand of DNAM-1 (costimulatory receptor) and TIGIT/CD96 (coinhibitory receptors). Herein, we verified that TNBC cells coexpressed PD-L1 and CD155. By examining the receptors of PD-L1 and CD155 on TNBC tumor-infiltrating lymphocytes (TILs) over time, we observed that PD-1 and DNAM-1 were upregulated early, whereas CD96 and TIGIT were upregulated late in CD8⁺ TILs. Based on these findings, we developed CD155 siRNA (siCD155)-loaded mPEG-PLGA-PLL (PEAL) nanoparticles (NPs) coated with PD-L1 blocking antibodies (P/PEAL_siCD155) to asynchronously block PD-L1 and CD155 in a spatiotemporal manner. P/PEAL_siCD155 maximized early-stage CD8⁺ T cell immune surveillance against 4T1 tumor, whereas reversed inhibition status of the late stage CD8⁺ T cells to prevent 4T1 tumor immune escape. In addition, the combination of P/PEAL_siCD155 and tumor-specific CD8 T cells induced immunogenic cell death (ICD) of 4T1 cells to further boost immune checkpoint therapy. Most importantly, P/PEAL_siCD155 displayed excellent TNBC targeting and induced CD8⁺ TILs-dominant intratumor antitumor immunity to efficiently inhibit TNBC progression and metastasis with excellent safety in a syngeneic 4T1 orthotopic TNBC tumor model.

View all citing articles on Scopus

View full text

Trends in Immunology

ReviewMolecular Dissection of CD8+ T-Cell Dysfunction

Trends

Section snippets

T-Cell Dysfunction

Molecular Signatures of T-Cell Dysfunction

Gene Modules for T-Cell Dysfunction and Activation

Heterogeneity of CD8+ T-Cell States within Tumor

Transcription Factors

Implications for Therapy

Concluding Remarks and Future Perspectives

Acknowledgments

Glossary

Immunity

Immunity

Immunity

Immunity

Immunity

Immunity

Immunity

Immunity

Immunity

Trends Immunol.

Clin. Breast Cancer

Cell

Cell

Cell

Immunity

Molecular and cellular insights into T cell exhaustion

Nat. Rev. Immunol.

Viral immune evasion due to persistence of activated T cells without effector function

J. Exp. Med.

Virus persistence in acutely infected immunocompetent mice by exhaustion of antiviral cytotoxic effector T cells

Nature

IL-21 is required to control chronic viral infection

Science

IL-21R on T cells is critical for sustained functionality and control of chronic viral infection

Science

A vital role for interleukin-21 in the control of a chronic viral infection

Science

The role of IL-10 in regulating immunity to persistent viral infections

Curr. Top. Microbiol. Immunol.

Molecular profiling of CD8 T cells in autochthonous melanoma identifies Maf as driver of exhaustion

EMBO J.

IL-6 plays a unique role in initiating c-Maf expression during early stage of CD4 T cell activation

J. Immunol.

T-cell exhaustion: characteristics, causes and conversion

Immunology

Blimp-1-mediated CD4 T cell exhaustion causes CD8 T cell dysfunction during chronic toxoplasmosis

J. Exp. Med.

Intrinsic functional dysregulation of CD4 T cells occurs rapidly following persistent viral infection

J. Virol.

Broadly directed virus-specific CD4+ T cell responses are primed during acute hepatitis C infection, but rapidly disappear from human blood with viral persistence

J. Exp. Med.

Viral persistence redirects CD4 T cell differentiation toward T follicular helper cells

J. Exp. Med.

Follicular CXCR5-expressing CD8+ T cells curtail chronic viral infection

Nature

CXCR5+ follicular cytotoxic T cells control viral infection in B cell follicles

Nat. Immunol.

Review
Molecular Dissection of CD8⁺ T-Cell Dysfunction

Heterogeneity of CD8⁺ T-Cell States within Tumor

Broadly directed virus-specific CD4⁺ T cell responses are primed during acute hepatitis C infection, but rapidly disappear from human blood with viral persistence

Follicular CXCR5-expressing CD8⁺ T cells curtail chronic viral infection

CXCR5⁺ follicular cytotoxic T cells control viral infection in B cell follicles