T-Cells From Patients with CLL Exhibit Phenotypic and Transcription Factor Profiles of Exhaustion Independent of CMV Serostatus

Abstract Abstract 1780 Cancer is associated with immune dysfunction, contributing to the failure to mount an effective anti-tumor immune response. T-cell exhaustion, a state of acquired T-cell dysfunction initially described in the context of chronic viral infections, has recently been described in human solid tumors. We have previously demonstrated alterations in gene expression and defects in function in T-cells from patients with chronic lymphocytic leukemia (CLL) and noted similarities to those described in exhausted T-cells in murine models. Therefore, we used multiparameter flow cytometry to determine if T-cells from patients with untreated CLL (n=23) had surface phenotypic and transcription factor profiles of exhaustion. When compared with healthy controls (n=10), an increased proportion of circulating CD8+ T-cells showed an effector-memory phenotype (p=0.018), with a shift towards a greater proportion of CCR7-CD45RA+ terminally differentiated cells. We found increased expression of markers of exhaustion including CD279 (PD-1) (p=0.0057), CD160 (p=0.0006), CD244 (p=0.0057), and CD57 (p=0.011), and decreased expression of CD28 (p=0.0058) on CLL CD8+ T-cells compared with healthy CD8+ T-cells. Increased expression of PD-1 (p=0.0019), CD160 (p=0.0011), CD57 (p=0.007), and LAG-3 (p=0.038) was also noted on CLL CD4+ T-cells. We next determined the level of the transcription factors T-bet and eomesodermin and the transcriptional repressor Blimp-1, as these proteins have been implicated in CD8+ effector-memory differentiation and development of T-cell exhaustion. Importantly, CD8+ T-cells from CLL patients showed increased expression of T-bet (p=0.038), eomesodermin (p=0.0037), and Blimp-1 (p=0.0002), compared with CD8+ T-cells from healthy donors. Furthermore, PD-1 expression identified a subset of exhausted CD8+ T-cells with high intranuclear staining of Blimp-1 that was markedly expanded in patients with CLL (p=0.0002). Previous studies have identified expanded populations of CMV specific CD8+ T-cells in CMV seropositive CLL patients. As chronic viral infection is a known cause of T-cell exhaustion, we determined whether our findings were limited to CMV seropositive patients. We observed that increased expression of T-bet and decreased expression of CD28 was seen only in CD8+ T-cells from CMV seropositive patients. T-bet represses expression of PD-1 and sustains CD8+ T-cell responses during chronic viral infection, and we noted relatively lower expression of PD-1 on CD8+ T-cells in seropositive compared with seronegative patients (p=0.049), although PD-1 expression was still higher than in healthy controls. However, CD8+ T-cells from both CMV seronegative and seropositive patients had significantly higher expression of CD160, CD244, and CD57 compared to CD8+ T-cells from healthy donors (Table 1). Furthermore, CD8+ T-cells from both CMV seronegative and seropositive patients had increased expression of Blimp-1 and eomesodermin. Table 1. Surface phenotype/transcription factor profile of CLL according to CMV serostatus Healthy CLL: CMV IgG negative (n=8) CLL: CMV IgG positive (n=8) Phenotype PD-1 LOW INCREASED** INCREASED* CD160 LOW INCREASED** INCREASED** CD57 LOW INCREASED* INCREASED** CD244 LOW INCREASED* INCREASED*** CD28 HIGH NO CHANGE DECREASED** Transcription factor T-bet LOW NO CHANGE INCREASED** Eomes LOW INCREASED* INCREASED*** Blimp-1 LOW INCREASED*** INCREASED*** * p<0.05, ** p<0.01, *** p<0.001 In conclusion, T-cells from patients with CLL show phenotypic and transcription factor profiles of T-cell exhaustion that is not limited to the CMV-seropositive group. These findings may explain the acquired immune deficiency in patients with CLL, and provide potential therapeutic targets to reverse immune dysfunction in this disease. Disclosures: Gribben: Roche: Honoraria; Celgene: Honoraria; GSK: Honoraria; Mundipharma: Honoraria; Gilead: Honoraria; Pharmacyclics: Honoraria.

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PD-1 up-regulation is correlated with HIV-specific memory CD8+ T-cell exhaustion in typical progressors but not in long-term nonprogressors

Blood ◽

10.1182/blood-2006-09-044826 ◽

2007 ◽

Vol 109 (11) ◽

pp. 4671-4678 ◽

Cited By ~ 207

Author(s):

Ji-Yuan Zhang ◽

Zheng Zhang ◽

Xicheng Wang ◽

Jun-Liang Fu ◽

Jinxia Yao ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Cd8 T Cells ◽

Cd8 T Cell ◽

Effector Memory ◽

T Cell Exhaustion ◽

Cell Exhaustion ◽

Specific Memory ◽

Memory Cd8 T Cell

Abstract The immunoreceptor PD-1 is significantly up-regulated on exhausted CD8+ T cells during chronic viral infections such as HIV-1. However, it remains unknown whether PD-1 expression on CD8+ T cells differs between typical progressors (TPs) and long-term nonprogressors (LTNPs). In this report, we examined PD-1 expression on HIV-specific CD8+ T cells from 63 adults with chronic HIV infection. We found that LTNPs exhibited functional HIV-specific memory CD8+ T cells with markedly lower PD-1 expression. TPs, in contrast, showed significantly up-regulated PD-1 expression that was closely correlated with a reduction in CD4 T-cell number and an elevation in plasma viral load. Importantly, PD-1 up-regulation was also associated with reduced perforin and IFN-γ production, as well as decreased HIV-specific effector memory CD8+ T-cell proliferation in TPs but not LTNPs. Blocking PD-1/PD-L1 interactions efficiently restored HIV-specific CD8+ T-cell effector function and proliferation. Taken together, these findings confirm the hypothesis that high PD-1 up-regulation mediates HIV-specific CD8+ T-cell exhaustion. Blocking the PD-1/PD-L1 pathway may represent a new therapeutic option for this disease and provide more insight into immune pathogenesis in LTNPs.

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Tissue-Specific Differences in PD-1 and PD-L1 Expression during Chronic Viral Infection: Implications for CD8 T-Cell Exhaustion

Journal of Virology ◽

10.1128/jvi.01579-09 ◽

2009 ◽

Vol 84 (4) ◽

pp. 2078-2089 ◽

Cited By ~ 74

Author(s):

Shawn D. Blackburn ◽

Alison Crawford ◽

Haina Shin ◽

Antonio Polley ◽

Gordon J. Freeman ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Viral Infection ◽

Cd8 T Cells ◽

Therapeutic Interventions ◽

Chronic Viral Infection ◽

Anatomical Location ◽

T Cell Exhaustion ◽

Tissue Specific ◽

Cell Exhaustion

ABSTRACT The PD-1/PD-L pathway plays a major role in regulating T-cell exhaustion during chronic viral infections in animal models, as well as in humans, and blockade of this pathway can revive exhausted CD8+ T cells. We examined the expression of PD-1 and its ligands, PD-L1 and PD-L2, in multiple tissues during the course of chronic viral infection and determined how the amount of PD-1 expressed, as well as the anatomical location, influenced the function of exhausted CD8 T cells. The amount of PD-1 on exhausted CD8 T cells from different anatomical locations did not always correlate with infectious virus but did reflect viral antigen in some tissues. Moreover, lower expression of PD-L1 in some locations, such as the bone marrow, favored the survival of PD-1Hi exhausted CD8 T cells, suggesting that some anatomical sites might provide a survival niche for subpopulations of exhausted CD8 T cells. Tissue-specific differences in the function of exhausted CD8 T cells were also observed. However, while cytokine production did not strictly correlate with the amount of PD-1 expressed by exhausted CD8 T cells from different tissues, the ability to degranulate and kill were tightly linked to PD-1 expression regardless of the anatomical location. These observations have implications for human chronic infections and for therapeutic interventions based on blockade of the PD-1 pathway.

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The Exhausted Intratumoral T Cell Population in B-Cell Non-Hodgkin Lymphoma Is Defined By LAG-3, PD-1 andtim-3 Expression

Blood ◽

10.1182/blood.v126.23.2661.2661 ◽

2015 ◽

Vol 126 (23) ◽

pp. 2661-2661 ◽

Cited By ~ 2

Author(s):

Zhi-Zhang Yang ◽

Tammy Price-troska ◽

Anne J Novak ◽

Stephen M Ansell

Keyword(s):

T Cells ◽

T Cell ◽

B Cell ◽

Cd8 T Cells ◽

Conflicts Of Interest ◽

Early Time ◽

Effector Memory ◽

T Cell Exhaustion ◽

Cell Exhaustion ◽

Ifn Γ

Abstract T-cell exhaustion plays an important role in attenuating the function of immune cells in B-cell non-Hodgkin's lymphoma (NHL) and PD-1 expression is typically used to identify exhausted T-cells. We have however previously shown that not all PD-1+ cells are exhausted and that PD-1 is differentially expressed on two distinct T-cell subpopulations, with high expression on T follicular helper cells and dim expression on exhausted T cells. Other markers are therefore needed to more clearly identify exhausted intratumoral T cells. To further define exhaustion of intratumoral T cells, we determined the co-expression, regulation and function of PD-1, TIM-3 and LAG-3 on CD4+ or CD8+ T cells by flow cytometry. Using biopsy specimens from follicular B-cell NHL, we found that the percentages of PD-1+ and TIM-3+ T cells were 53.1% (range: 17.2-81.2%, n=32) and 34.5% (range: 14.9-62.6%, n=34) in CD4+ T cells and 46.8% (range: 12.8-81.7%, n=32) and 40.4% (range: 15.0-78.4%, n=34) in CD8+ T cells, respectively. We observed that TIM-3 was predominantly expressed on PD-1dim T cells and TIM-3+ cells accounted for 40% of CD4+ PD-1dim or 45% of CD8+ PD-1dim T cells. Similarly, LAG-3 was variably expressed on intratumoral T cells from B-cell NHL. A median of 9.54% (range: 3.01-15.46, n=6) of CD4+ or 20.48% (7.93-33.9, n=8) of CD8+ T cells express LAG-3. We found that LAG-3+ T cells almost exclusively came from PD-1+ TIM-3+ cells, forming a defined population of intratumoral PD-1+ TIM-3+ LAG-3+ CD4+ or CD8+ T cells. While the majority of LAG-3+ T cells were effector memory T cells (CD45RA- CCR7-), some LAG-3-expressing T cells displayed a phenotype of terminally-differentiated T cells (CD45RA+ CCR7-). Functionally, the intratumoral TIM-3+ LAG-3+ T cells exhibited reduced capacity to produce cytokines (IL-2, IFN-γ) and granules (perforin, granzyme B). Similar to TIM-3, LAG-3 expression was strongly up-regulated on CD4+ or CD8+ T cells by IL-12, a cytokine that has been shown to induce T-cell exhaustion. Interestingly, we observed that while expression of TIM-3 on CD8+ T cells was upregulated by IL-12 at an early time point (day 1), LAG-3 was only induced after TIM-3 up-regulation (day 3) and almost exclusively on TIM-3+ T cells. Furthermore, we found that blockade of both TIM-3 and LAG-3 signaling was able to reverse the exhausted phenotype of CD8+ T cells resulting in increased IFN-γ and IL-2 production. This effect was further enhanced when CD8+ T cells were treated with both anti-TIM-3 and anti-LAG-3 Abs. Taken together, these results suggest that PD-1, TIM-3 and LAG-3 were involved in the induction of exhaustion of T cells in B-cell NHL. We find that PD-1, TIM-3 and LAG-3 are expressed on the same T cells and that blocking TIM-3 and LAG-3 can reverse T-cell exhaustion signaling. These results suggest that PD-1, TIM-3 and LAG-3 play a synergistic role in the development of T cell exhaustion in NHL. Disclosures No relevant conflicts of interest to declare.

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Chromatin State and Immunotherapy

Blood ◽

10.1182/blood-2018-99-109432 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. SCI-16-SCI-16

Author(s):

W. Nicholas Haining

Keyword(s):

T Cells ◽

T Cell ◽

Tumor Microenvironment ◽

Viral Infection ◽

Cd8 T Cells ◽

Research Funding ◽

Checkpoint Blockade ◽

Chronic Viral Infection ◽

T Cell Exhaustion ◽

Cell Exhaustion

Abstract The functional impairment of T cell-mediated immunity within the tumor microenvironment (TME) is a defining feature of many cancers. Checkpoint blockade therapy seeks to reinvigorate T cell responses by targeting inhibitory receptors such as PD-1, which are upregulated by dysfunctional TILs. However, the fundamental mechanisms underlying T cell dysfunction in the TME remain poorly understood, as are the mechanisms by which checkpoint blockade overcomes this dysfunction. Initial studies of dysfunctional CD8+ T cells in both human and mouse tumors suggested that they share features of T cell exhaustion, including co-inhibitory receptor upregulation and defects in cytokine production. However, more recent studies have suggested that TIL dysfunction is a unique state that is distinct from T cell exhaustion. Here we show that anti-PD-1 therapy acts on a specific subpopulation of CD8+ tumor-infiltrating lymphocytes (TILs) in melanoma mouse models as well as patients with melanoma. We find that dysfunctional CD8+ TILs possess canonical epigenetic and transcriptional features of T cell exhaustion, mirroring those seen in chronic viral infection. Similar to chronic viral infection, exhausted CD8+ TILs contain a subpopulation of "stem-like exhausted" T cells that have a distinct regulatory state. Stem-like exhausted TILs also have critical functional attributes that are not shared by the majority "terminally exhausted" TILs: they retain more polyfunctionality, persist following transfer into tumor-bearing mice, and differentiate to repopulate terminally exhausted TILs in the TME. As a result, stem-like exhausted CD8+ TILs are better able to control tumor growth than terminally exhausted cells. Stem-like exhausted, but not terminally exhausted, CD8+ TILs can respond to anti-PD-1 therapy without reversion of their exhausted epigenetic state. CD8+ T cells with a stem-like exhausted phenotype can be found in human melanoma samples and patients with a higher fraction of this subpopulation in their tumors have a significantly longer duration of response to combination checkpoint blockade therapy. Responsiveness to checkpoint blockade is therefore restricted to a subpopulation of exhausted TILs that retain specific functional properties which enable them to control tumors. Approaches to expand stem-like exhausted CD8+ T cells in the tumor microenvironment may be an important component of improving checkpoint blockade response. Disclosures Haining: Rheos Medicines: Consultancy; Iomx Therapeutics: Consultancy; Third Rock Ventures: Consultancy; Roche: Research Funding; Calico: Research Funding; Novartis: Research Funding; Tango Therapeutics: Consultancy, Equity Ownership.

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CLL Is Associated with Development of Subclinical Cytomegalovirus Viraemia and Accumulation of Large Populations of “exhausted” CMV-Specific CD4+ T Cells

Blood ◽

10.1182/blood.v124.21.3290.3290 ◽

2014 ◽

Vol 124 (21) ◽

pp. 3290-3290

Author(s):

Helen M Parry ◽

Natasha Cutmore ◽

Nikhil Mirajkar ◽

Annette Pachnio ◽

Tina McSkeane ◽

...

Keyword(s):

T Cells ◽

Viral Load ◽

T Cell ◽

Cd8 T Cells ◽

Cd4 T Cells ◽

Class Ii ◽

Cd4 T Cell ◽

Effector Memory ◽

T Cell Exhaustion ◽

Cell Exhaustion

Abstract Chronic Lymphocytic Leukaemia (CLL) is associated with T cell dysfunction and increased expression of markers of T cell exhaustion. Cytomegalovirus is a common herpesvirus infection and is associated with development of accelerated immune senescence in older adults. Within patients with CLL, CMV leads to marked expansion of virus-specific CD4 and CD8 T cells and development of oligoclonal T cell populations. However these features are not known to be associated with clinical symptoms and CMV viral load remains essentially undetectable by conventional qPCR. In this study we used digital PCR to determine CMV viral load in patients with CLL and correlated this with the magnitude and phenotype of the CMV-specific T cell immune response. In particular, we utilised HLA class II tetramers for the first time, in order to assess the contribution of CMV-specific T cell populations to the profile of T cell exhaustion seen in this disease. 68 CMV-seropositive CLL patients and 19 age-matched healthy donors (HD) were recruited for study. All patients were either untreated or had not received chemotherapy for at least 6 months. CMV viral load was determined within purified monocyte populations using a digital droplet PCR method. Viral load per monocyte was increased in CLL patients compared to HD (p=0.04), with the highest viral loads detected in stage C patients. In order to investigate the CMV-specific immune response, nine HLA class I tetramers were generated, containing viral epitopes from pp65, pp50 and IE-1, and two class II tetramers were also available, with epitopes from glycoprotein B and pp65. CMV-specific CD4 T cell responses were increased in CLL patients (n=14) compared to HD (n=11) (4.1 % vs. 0.9 %; p=0.049). Remarkably, in one patient more than half (50.9%) of all CD4 T cells were directed against a single CMV epitope. CD4 CMV-specific T cells were nearly always effector memory in phenotype (78%), somewhat in contrast to CD8 populations where the memory phenotype is split between effector memory (CCR7-, CD45RA-) and terminally differentiated memory cells (CCR7-, CD45RA+). PD1 is an important marker of T cell exhaustion and expression was increased on both CD8 T cells (16.9% Vs 9.6%; p=0.003); and CD4 T cells (16.2 % Vs 8.7 %; p=0.0007) in CLL patients compared to HD. Interestingly, PD1 expression was much higher on CMV-specific CD4 T cells compared to the total CD4 T cell repertoire (50.6% Vs 21%; p=0.01), whereas the opposite profile was observed in relation to CD8 populations. CMV-specific CD4 T cells demonstrated a Th1 cytotoxic phenotype with production of TNF-alpha, IFN-y and Granzyme B. Production of IFN-y and TNF-alpha was reduced in PD1+ populations, consistent with an exhausted phenotype. No CD25+FoxP3 + regulatory T cells were observed within the CMV-specific CD4 T cell population which is of interest given the well documented expansion of this population in patients with CLL. In order to investigate the replicative history of CMV-specific T cells we investigated the telomere length of antigen-specific cells using single cell telomere length analysis. CMV-specific cells had markedly shortened telomere lengths compared to background CD4 and CD8 T cells, with the mean difference of 0.911 kb (maximum 1.836 kb) indicating that they have undergone extensive proliferation in vivo. This work is the first to use digital PCR to measure the subclinical CMV load within peripheral blood and also to examine CMV-specific CD4 T cells using HLA class II tetramers. Our results indicate that immune control of CMV viral load is impaired during the clinical progression of CLL and that a proportion of virus-specific CD4 T cells show signs of exhaustion. These data may reflect ‘cross presentation’ of viral protein by B-CLL tumour cells, which are known to have poor capacity for antigen presentation. The potential clinical importance of these observations is now being addressed. Disclosures No relevant conflicts of interest to declare.

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Immunogenomic, single-cell and spatial dissection of CD8+T cell exhaustion reveals critical determinants of cancer immunotherapy

10.1101/2021.11.22.468617 ◽

2021 ◽

Author(s):

Stefan Naulaerts ◽

Daniel M Borras ◽

Asier Antoranz Martinez ◽

Julie Messiaen ◽

Yannick Van Herck ◽

...

Keyword(s):

Wound Healing ◽

T Cells ◽

T Cell ◽

Single Cell ◽

Cd8 T Cells ◽

Cd8 T Cell ◽

Immune Checkpoints ◽

Effector Memory ◽

T Cell Exhaustion ◽

Cell Exhaustion

Tumoural-CD8+T cells exhibit exhausted or dysfunctional states. Contrary to immunotherapy-responsive exhausted-CD8+T cells, the clinical features of dysfunctional-CD8+T cells are disputed. Hence, we conducted large-scale multi-omics and multi-dimensional mapping of CD8+T cell-states across multiple cancer patient-cohorts. This identified tumour-specific continuum of CD8+T cell-states across 6 human cancers, partly imprinted by organ-specific immuno-modulatory niches. Herein, melanoma and glioblastoma enriched prototypical exhausted (CD8+TEXT) and severely-dysfunctional (CD8+TSDF) states, respectively. Contrary to CD8+TEXT, CD8+TSDF displayed transcriptomic and epigenetic effector/cytolytic dysfunctions, and dysregulated effector/memory single-cell trajectories, culminating into maladaptive pro-death stress and cell-cycle defects. Suboptimal antigen-priming underscored CD8+TSDF, which was distinct from immune-checkpoints 'rich' CD8+TEXT, reflecting chronic antigen-stimulation. Continuum variation also existed on tumour spatial-level, with convergent (CD8+TEXT-supportive vascular regions) and divergent features (dysfunctional CD4+T::CD8+TSDF cell-to-cell interactions) between melanoma and glioblastoma. Globally, IFNG-IL2 disparities, paucity of intra-tumoural CD4+/CD8+T cells, and myeloid TGFB/wound healing responses, distinguished CD8+TSDF-landscape. Within immuno-oncology clinical-trials, anti-PD1 immunotherapy failed to 'reinvigorate' CD8+TSDF-landscape, and instead facilitated effector-dysfunction and TGFB/wound healing. However, cellular immunotherapies (dendritic cell-vaccines, adoptive T-cell therapy) ameliorated assorted CD8+TSDF-landscape disparities, highlighting a roadmap for anti-glioblastoma multimodal-immunotherapy. Collectively, our study comprehensively expands clinical-knowledge on CD8+T cell-exhaustion and suggests that tumour-specific, pre-existing CD8+TEXT/TSDF-states, determine immunotherapy-responses.

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Partial restoration of immune response in Hepatitis C patients after viral clearance by direct-acting antiviral therapy

PLoS ONE ◽

10.1371/journal.pone.0254243 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0254243

Author(s):

Meritxell Llorens-Revull ◽

Maria Isabel Costafreda ◽

Angie Rico ◽

Mercedes Guerrero-Murillo ◽

Maria Eugenia Soria ◽

...

Keyword(s):

Immune Response ◽

T Cells ◽

Hepatitis C ◽

T Cell ◽

Cd8 T Cells ◽

Viral Clearance ◽

Cd4 T Cell ◽

Care Hospital ◽

T Cell Exhaustion ◽

Cell Exhaustion

Background & aims HCV CD4+ and CD8+ specific T cells responses are functionally impaired during chronic hepatitis C infection. DAAs therapies eradicate HCV infection in more than 95% of treated patients. However, the impact of HCV elimination on immune responses remain controversial. Here, we aimed to investigate whether HCV cure by DAAs could reverse the impaired immune response to HCV. Methods We analyzed 27 chronic HCV infected patients undergoing DAA treatment in tertiary care hospital, and we determined the phenotypical and functional changes in both HCV CD8+ and CD4+ specific T-cells before and after viral clearance. PD-1, TIM-3 and LAG-3 cell-surface expression was assessed by flow cytometry to determine CD4+ T cell exhaustion. Functional responses to HCV were analyzed by IFN-Ɣ ELISPOT, intracellular cytokine staining (IL-2 and IFN-Ɣ) and CFSE-based proliferation assays. Results We observed a significant decrease in the expression of PD-1 in CD4+ T-cells after 12 weeks of viral clearance in non-cirrhotic patients (p = 0.033) and in treatment-naive patients (p = 0.010), indicating a partial CD4 phenotype restoration. IFN-Ɣ and IL-2 cytokines production by HCV-specific CD4+ and CD8+ T cells remained impaired upon HCV eradication. Finally, a significant increase of the proliferation capacity of both HCV CD4+ and CD8+ specific T-cells was observed after HCV elimination by DAAs therapies. Conclusions Our results show that in chronically infected patients HCV elimination by DAA treatment lead to partial reversion of CD4+ T cell exhaustion. Moreover, proliferative capacity of HCV-specific CD4+ and CD8+ T cells is recovered after DAA’s therapies.

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644 Tumor-mediated suppressive signaling and hypoxia supports altered chromatin landscapes that limit the transcriptional and functional potential of terminal T cell exhaustion

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2021-sitc2021.644 ◽

2021 ◽

Vol 9 (Suppl 3) ◽

pp. A673-A673

Author(s):

Rhodes Ford ◽

Natalie Rittenhouse ◽

Nicole Scharping ◽

Paolo Vignali ◽

Greg Delgoffe ◽

...

Keyword(s):

Gene Expression ◽

T Cells ◽

T Cell ◽

Tumor Microenvironment ◽

Histone Modifications ◽

Cd8 T Cells ◽

Tumor Hypoxia ◽

T Cell Subsets ◽

T Cell Exhaustion ◽

Cell Exhaustion

BackgroundCD8+ T cells are a fundamental component of the anti-tumor response; however, tumor-infiltrating CD8+ T cells (TIL) are rendered dysfunctional by the tumor microenvironment. CD8+ TIL display an exhausted phenotype with decreased cytokine expression and increased expression of co-inhibitory receptors (IRs), such as PD-1 and Tim-3. The acquisition of IRs mark the progression of dysfunctional TIL from progenitors (PD-1Low) to terminally exhausted (PD-1+Tim-3+). How the chromatin landscape changes during this progression has not been described.MethodsUsing a low-input ChIP-based assay called Cleavage Under Targets and Release Using Nuclease (CUT&RUN), we have profiled the histone modifications at the chromatin of tumor-infiltrating CD8+ T cell subsets to better understand the relationship between the epigenome and the transcriptome as TIL progress towards terminal exhaustion.ResultsWe have identified two epigenetic characteristics unique to terminally exhausted cells. First, we have identified a unique set of genes, characterized by active histone modifications that do not have correlated gene expression. These regions are enriched for AP-1 transcription factor motifs, yet most AP-1 family factors are actively downregulated in terminally exhausted cells, suggesting signals that promote downregulation of AP-1 expression negatively impacts gene expression. We have shown that inducing expression of AP-1 factors with a 41BB agonist correlates with increased expression of these anticorrelated genes. We have also found a substantial increase in the number of genes that exhibit bivalent chromatin marks, defined by the presence of both active (H3K4me3) and repressive (H3K27me3) chromatin modifications that inhibit gene expression. These bivalent genes in terminally exhausted T cells are not associated with plasticity and represent aberrant hypermethylation in response to tumor hypoxia, which is necessary and sufficient to promote downregulation of bivalent genes.ConclusionsOur study defines for the first time the roles of costimulation and the tumor microenvironment in driving epigenetic features of terminally exhausted tumor-infiltrating T cells. These results suggest that terminally exhausted T cells have genes that are primed for expression, given the right signals and are the basis for future work that will elucidate that factors that drive progression towards terminal T cell exhaustion at the epigenetic level and identify novel therapeutic targets to restore effector function of tumor T cells and mediate tumor clearance.

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Single-Cell Transcriptome Analysis Reveals RGS1 as a New Marker and Promoting Factor for T-Cell Exhaustion in Multiple Cancers

Frontiers in Immunology ◽

10.3389/fimmu.2021.767070 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yunmeng Bai ◽

Meiling Hu ◽

Zixi Chen ◽

Jinfen Wei ◽

Hongli Du

Keyword(s):

T Cells ◽

T Cell ◽

Cd8 T Cells ◽

Poor Prognosis ◽

Effector T Cells ◽

T Cell Exhaustion ◽

Cell Exhaustion ◽

Cell Transcriptome ◽

Cancer Tissues ◽

Single Cell Transcriptome

T-cell exhaustion is one of the main reasons of tumor immune escape. Using single-cell transcriptome data of CD8+ T cells in multiple cancers, we identified different cell types, in which Pre_exhaust and exhausted T cells participated in negative regulation of immune system process. By analyzing the coexpression network patterns and differentially expressed genes of Pre_exhaust, exhausted, and effector T cells, we identified 35 genes related to T-cell exhaustion, whose high GSVA scores were associated with significantly poor prognosis in various cancers. In the differentially expressed genes, RGS1 showed the greatest fold change in Pre_exhaust and exhausted cells of three cancers compared with effector T cells, and high expression of RGS1 was also associated with poor prognosis in various cancers. Additionally, RGS1 protein was upregulated significantly in tumor tissues in the immunohistochemistry verification. Furthermore, RGS1 displayed positive correlation with the 35 genes, especially highly correlated with PDCD1, CTLA4, HAVCR2, and TNFRSF9 in CD8+ T cells and cancer tissues, indicating the important roles of RGS1 in CD8+ T-cell exhaustion. Considering the GTP-hydrolysis activity of RGS1 and significantly high mRNA and protein expression in cancer tissues, we speculated that RGS1 potentially mediate the T-cell retention to lead to the persistent antigen stimulation, resulting in T-cell exhaustion. In conclusion, our findings suggest that RGS1 is a new marker and promoting factor for CD8+ T-cell exhaustion and provide theoretical basis for research and immunotherapy of exhausted cells.

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Unraveling the Multifaceted Nature of CD8 T Cell Exhaustion Provides the Molecular Basis for Therapeutic T Cell Reconstitution in Chronic Hepatitis B and C

Cells ◽

10.3390/cells10102563 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2563

Author(s):

Valeria Barili ◽

Andrea Vecchi ◽

Marzia Rossi ◽

Ilaria Montali ◽

Camilla Tiezzi ◽

...

Keyword(s):

T Cells ◽

Chronic Hepatitis ◽

T Cell ◽

Hepatitis B ◽

Chronic Hepatitis B ◽

Cd8 T Cells ◽

Stress Responses ◽

T Cell Exhaustion ◽

Virus Infections ◽

Cell Exhaustion

In chronic hepatitis B and C virus infections persistently elevated antigen levels drive CD8+ T cells toward a peculiar differentiation state known as T cell exhaustion, which poses crucial constraints to antiviral immunity. Available evidence indicates that T cell exhaustion is associated with a series of metabolic and signaling deregulations and with a very peculiar epigenetic status which all together lead to reduced effector functions. A clear mechanistic network explaining how intracellular metabolic derangements, transcriptional and signaling alterations so far described are interconnected in a comprehensive and unified view of the T cell exhaustion differentiation profile is still lacking. Addressing this issue is of key importance for the development of innovative strategies to boost host immunity in order to achieve viral clearance. This review will discuss the current knowledge in HBV and HCV infections, addressing how innate immunity, metabolic derangements, extensive stress responses and altered epigenetic programs may be targeted to restore functionality and responsiveness of virus-specific CD8 T cells in the context of chronic virus infections.

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