scholarly journals A comprehensive single-cell map of T cell exhaustion-associated immune environments in human breast cancer

2022 ◽  
Author(s):  
Sandra Tietscher ◽  
Johanna Wagner ◽  
Tobias Anzeneder ◽  
Claus Langwieder ◽  
Martin Rees ◽  
...  
Keyword(s):  
Breast Cancer ◽  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Immune Checkpoint ◽  
Breast Tumors ◽  
Cell Phenotype ◽  
T Cell Exhaustion ◽  
Human Breast ◽  
Cell Exhaustion

Abstract Immune checkpoint therapy in breast cancer remains restricted to triple negative patients, and long-term clinical benefit is rare. The primary aim of immune checkpoint blockade is to prevent or reverse exhausted T cell states, but the causes and implications of T cell exhaustion in breast tumors are not well understood. Here, we used single-cell transcriptomics combined with imaging mass cytometry to comprehensively study exhausted and non-exhausted immune environments in human breast tumors, with a focus on Luminal subtypes. We found that the presence of a PD-1high exhaustion-like T cell phenotype was indicative of an inflammatory immune environment with a characteristic cytotoxic profile and spatial features. Accumulation of natural killer T cells and increased myeloid cell activation in exhausted immune environments provide further support for tissue inflammation in these environments. Consistent with this, our comprehensive map of cellular interactions within the breast tumor microenvironment revealed elevated immunomodulatory, chemotactic, and cytokine signaling in exhausted environments. These data reveal fundamental differences between exhausted and non-exhausted immune environments within Luminal breast cancer, and show that expression of PD-1 and CXCL13 on T cells, and MHC-I – but not PD-L1 – on tumor cells are strong distinguishing features between these environments; these factors are potential new biomarkers for patient stratification.

scholarly journals CD4+ T cells inhibit the neu-specific CD8+ T-cell exhaustion during the priming phase of immune responses against breast cancer

2010 ◽  
Vol 126 (2) ◽  
pp. 385-394 ◽  
Author(s):  
Maciej Kmieciak ◽  
Andrea Worschech ◽  
Hooman Nikizad ◽  
Madhu Gowda ◽  
Mehran Habibi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
T Cells ◽  
T Cell ◽  
Immune Responses ◽  
Cd4 T Cells ◽  
Cd8 T Cell ◽  
T Cell Exhaustion ◽  
Cell Exhaustion ◽  
Priming Phase

scholarly journals Single cell multiomic analysis of T cell exhaustion in vitro

2019 ◽  
Author(s):  
Mirko Corselli ◽  
Suraj Saksena ◽  
Margaret Nakamoto ◽  
Woodrow E. Lomas ◽  
Ian Taylor ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
T Cell Activation ◽  
T Cell Exhaustion ◽  
Chronic Stimulation ◽  
Cell Exhaustion ◽  
Car T ◽  
The Impact

AbstractA key step in the clinical production of CAR-T cells is the expansion of engineered T cells. To generate enough cells for a therapeutic product, cells must be chronically stimulated, which raises the risk of inducing T-cell exhaustion and reducing therapeutic efficacy. As protocols for T-cell expansion are being developed to optimize CAR T cell yield, function and persistence, fundamental questions about the impact of in vitro manipulation on T-cell identity are important to answer. Namely: 1) what types of cells are generated during chronic stimulation? 2) how many unique cell states can be defined during chronic stimulation? We sought to answer these fundamental questions by performing single-cell multiomic analysis to simultaneously measure expression of 39 proteins and 399 genes in human T cells expanded in vitro. This approach allowed us to study – with unprecedented depth - how T cells change over the course of chronic stimulation. Comprehensive immunophenotypic and transcriptomic analysis at day 0 enabled a refined characterization of T-cell maturational states (from naïve to TEMRA cells) and the identification of a donor-specific subset of terminally differentiated T-cells that would have been otherwise overlooked using canonical cell classification schema. As expected, T-cell activation induced downregulation of naïve-associated markers and upregulation of effector molecules, proliferation regulators, co-inhibitory and co-stimulatory receptors. Our deep kinetic analysis further revealed clusters of proteins and genes identifying unique states of activation defined by markers temporarily expressed upon 3 days of stimulation (PD-1, CD69, LTA), markers constitutively expressed throughout chronic activation (CD25, GITR, LGALS1), and markers uniquely up-regulated upon 14 days of stimulation (CD39, ENTPD1, TNFDF10). Notably, different ratios of cells expressing activation or exhaustion markers were measured at each time point. These data indicate high heterogeneity and plasticity of chronically stimulated T cells in response to different kinetics of activation. In this study, we demonstrate the power of a single-cell multiomic approach to comprehensively characterize T cells and to precisely monitor changes in differentiation, activation and exhaustion signatures in response to different activation protocols.

scholarly journals 251 The use of small molecule inhibitors to target novel pathways in exhausted T cells for immuno-oncology therapeutic intervention

2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A271-A271
Author(s):  
Francis Acklam ◽  
Joanne Hay ◽  
Darryl Turner ◽  
Mark Barbour ◽  
Preeti Singh ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Small Molecule ◽  
Therapeutic Intervention ◽  
Checkpoint Inhibitor ◽  
Great Promise ◽  
Cell Phenotype ◽  
T Cell Exhaustion ◽  
Cell Exhaustion

BackgroundThe ability to reverse exhaustion in CD8+ T cells holds great promise for therapeutic intervention in oncology. Indeed, treatment with therapeutics targeted at checkpoint inhibitors, such as Nivolumab (anti-PD-1), have shown great promise in the treatment of a subset of individuals and tumour types. However, pre-clinical success does not always translate to success in clinical trials and resistance to these approaches is prevalent. As such, there is a pressing need to develop novel approaches that target alternative pathways for use alone or potentially in combination with checkpoint inhibitor modulation. A secondary need is the requirement for advanced assays that accurately recapitulate the pathways and cell phenotypes prevalent in the tumour environment.MethodsHere we describe the characteristics of an in vitro human T cell exhaustion assay whereby in vitro stimulated T cells phenotypically and functionally recapitulate the exhausted T cells found within the tumour microenvironment. We also demonstrate the effect of checkpoint blockade as well as small molecule inhibition of a novel target on the exhausted T cell phenotype.ResultsIn this assay, exhaustion can be partially but not fully reversed by treatment with anti-PD-1 alone. In addition, we demonstrate the effect of a small molecule inhibitor targeting IKZF3, a transcription factor shown to be upregulated in T cell exhaustion, on reversing T cell exhaustion alone and in combination with checkpoint inhibitor blockade.ConclusionsThese assays and approaches enable investigation into the ability of compounds to influence reversal of T cell exhaustion where anti-PD-1 treatment does not fully reverse the exhausted phenotype and offers the ability to test combination therapy approaches.AcknowledgementsThis work was aided by the valuable input and insight of Professor Stephen Anderton.Ethics ApprovalThe study obtained ethics approval from West Midlands – Black Country Research Ethics Committee under IRAS project ID 270936. All donors gave informed consent before taking part.

scholarly journals PLAC8 Correlates with Prognosis, Immune Infiltration, and T Cell Exhaustion in Breast Cancer

2021 ◽  
Author(s):  
Pan Liao ◽  
Ying Wang ◽  
Lixia Sun ◽  
Hongpeng Yue
Keyword(s):  
Breast Cancer ◽  
T Cells ◽  
T Cell ◽  
T Cell Activation ◽  
Prognostic Significance ◽  
Her2 Status ◽  
Gene Marker ◽  
T Cell Exhaustion ◽  
Cell Exhaustion ◽  
Immune Infiltration

Abstract Background: Lysosomal protein placenta-specific 8 (PLAC8) with abundant cysteine, also referred to as onzin, participates in numerous cancers, and its effect is greatly determined by the cellular and tumor microenvironment (TME). Ourstudy focused on investigating the prognostic significance of PLAC8 and examined the association between PLAC8, immune infiltration, and T cells function in multiple malignancies comprehensively, particularly in breast cancer (BRCA).Methods: PLAC8 expression in various malignancies was analyzed using TIMER. PrognoScan, Kaplan-Meier Plotter, and GEPIA2 were utilized to explore the significance of PLAC8 in prognostic prediction. Moreover, PLAC8 functions were systematically analyzed through cancerSEA. Additionally, TISIDB, TIMER, and GEPIA2 were also employed for analyzing the associations among PLAC8, immune infiltration, related gene marker sets, and clinical stages. Finally, PLAC8 and its co-expressed genes biological process and KEGG were analyzed. Results: PLAC8 expression decreased in most malignancies and was related to poor prognosis in BRCA. PLAC8 significantly affected the survival of BRCA with ER status – array, PR status – IHC, HER2 status – array, Intrinsic subtype, Grade, and Pietenpol subtype. Increased PLAC8 expression positively correlated with the increased immune infiltration levels within immune cells and many functional T cells (such as exhausted T cells). In BRCA cells, PLAC8 functional phenotypesshowed a negative correlation with invasion, metastasis, apoptosis, DNA damage, and DNA repair. Besides, PD-1, TIM-3, TIGIT, LAG3, and GZMB, critical genes of exhausted T cells, interacted with PLAC8. Further analysis indicated that PLAC8 was related to T cell activation, proliferation and adhesion of leukocytes,adaptive immune response, cell adhesion molecules (CAMs), cytotoxicity-mediated by natural killer cells, and the NF-kappa B signal transduction pathway.Conclusion:PLAC8 is a prognostic indicator in pan-cancers, especially BRCA. Elevated PLAC8 level could significantly enhance immune infiltration in CD4+ T cells, CD8+ T cells, and functional T cells. Additionally, PLAC8 was tightly associatedwith T cell exhaustion which possibly enhances the latterwithin BRCA. PLAC8 expression determination might help in prognosis, and modulation of PLAC8level within exhausted T cells, a novel approach for optimizing the therapeutic effect of immunotherapy on BRCA cases.

scholarly journals Mechanisms of T-Cell Exhaustion in Pancreatic Cancer

Cancers ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2274
Author(s):  
Didem Saka ◽  
Muazzez Gökalp ◽  
Betül Piyade ◽  
Nedim Can Cevik ◽  
Elif Arik Sever ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Immune Checkpoint ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Critical Role ◽  
Single Agent ◽  
T Cell Exhaustion ◽  
Inhibitory Receptors ◽  
Cell Exhaustion

T-cell exhaustion is a phenomenon that represents the dysfunctional state of T cells in chronic infections and cancer and is closely associated with poor prognosis in many cancers. The endogenous T-cell immunity and genetically edited cell therapies (CAR-T) failed to prevent tumor immune evasion. The effector T-cell activity is perturbed by an imbalance between inhibitory and stimulatory signals causing a reprogramming in metabolism and the high levels of multiple inhibitory receptors like programmed cell death protein-1 (PD-1), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), T cell immunoglobulin and mucin domain-containing protein 3 (TIM-3), and Lymphocyte-activation gene 3 (Lag-3). Despite the efforts to neutralize inhibitory receptors by a single agent or combinatorial immune checkpoint inhibitors to boost effector function, PDAC remains unresponsive to these therapies, suggesting that multiple molecular mechanisms play a role in stimulating the exhaustion state of tumor-infiltrating T cells. Recent studies utilizing transcriptomics, mass cytometry, and epigenomics revealed a critical role of Thymocyte selection-associated high mobility group box protein (TOX) genes and TOX-associated pathways, driving T-cell exhaustion in chronic infection and cancer. Here, we will review recently defined molecular, genetic, and cellular factors that drive T-cell exhaustion in PDAC. We will also discuss the effects of available immune checkpoint inhibitors and the latest clinical trials targeting various molecular factors mediating T-cell exhaustion in PDAC.

scholarly journals Single-cell transcriptome analysis reveals TOX as a promoting factor for T-cell exhaustion and a predictor for anti-PD1 responses in human cancer

2019 ◽  
Author(s):  
Kyungsoo Kim ◽  
Seyeon Park ◽  
Seong Yong Park ◽  
Gamin Kim ◽  
Su Myeong Park ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Human Melanoma ◽  
T Cell Exhaustion ◽  
Cell Exhaustion ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Candidate Regulator

ABSTRACTBackgroundT cells exhibit heterogeneous functional states in the tumor microenvironment. Immune checkpoint inhibitors (ICIs) can reinvigorate only the stem cell-like progenitor exhausted T cells, which suggests that inhibiting the exhaustion progress will improve the efficacy of immunotherapy. Thus, regulatory factors promoting T-cell exhaustion could serve as potential targets for delaying the process and improving ICI efficacy.MethodsWe analyzed the single-cell transcriptome data derived from human melanoma and non-small cell lung cancer (NSCLC) samples and classified the tumor-infiltrating (TI) CD8+ T-cell population based on PDCD1 (PD-1) levels, i.e. PDCD1-high and PDCD1-low cells. Additionally, we identified differentially expressed genes as candidate factors regulating intra-tumoral T-cell exhaustion. The co-expression of candidate genes with immune checkpoint (IC) molecules in the TI CD8+ T cells was confirmed by single-cell trajectory and flow-cytometry analyses. The loss-of-function effect of the candidate regulator was examined by a cell-based knockdown assay. The clinical effect of the candidate regulator was evaluated based on the overall survival and anti-PD-1 responses.ResultsWe retrieved many known factors for regulating T-cell exhaustion among the differentially expressed genes between PDCD1-high and PDCD1-low subsets of the TI CD8+ T cells in human melanoma and NSCLC. TOX was the only transcription factor (TF) predicted in both tumor types. TOX levels tend to increase as CD8+ T cells become more exhausted. Flow-cytometry analysis revealed a correlation between TOX expression and severity of intra-tumoral T-cell exhaustion. TOX knockdown in the human TI CD8+ T cells resulted in downregulation of PD-1, TIM-3, TIGIT, and CTLA-4, which suggests that TOX promotes intra-tumoral T-cell exhaustion by upregulating IC proteins in cancer. Finally, the TOX level in the TI T cells was found to be highly predictive of overall survival and anti-PD-1 efficacy in melanoma and NSCLC.ConclusionsWe predicted the regulatory factors involved in T-cell exhaustion using single-cell transcriptome profiles of human TI lymphocytes. TOX promoted intra-tumoral CD8+ T-cell exhaustion via upregulation of IC molecules. This suggested that TOX inhibition can potentially impede T-cell exhaustion and improve ICI efficacy. Additionally, TOX expression in the TI T cells can be used for patient stratification during anti-tumor treatments, including anti-PD-1 immunotherapy.

scholarly journals Divergent clonal differentiation trajectories of T cell exhaustion

2021 ◽  
Author(s):  
Bence Daniel ◽  
Kathryn E Yost ◽  
Katalin Sandor ◽  
Yu Xia ◽  
Yanyan Qi ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Phenotypic Diversity ◽  
Killer Cell ◽  
T Cell Response ◽  
T Cell Exhaustion ◽  
T Cell Clones ◽  
Cell Exhaustion ◽  
Cell Clones

T cells activated by chronic antigen exposure in the setting of viral infections or cancer can adopt an exhausted T cell (Tex) state, characterized by reduced effector function and proliferative capacity, and the upregulation of inhibitory receptors. However, whether all antigen-specific T cell clones follow the same molecular and cellular Tex differentiation trajectory remains unclear. Here, we generate a single-cell multi-omic atlas of T cell exhaustion that redefines the phenotypic diversity and molecular regulation of Tex phenotypes. Longitudinal analysis during chronic viral infection identifies an early effector phenotype that is epigenetically primed for Tex differentiation and two late-stage Tex cell states with either a terminal exhaustion or a killer cell lectin-like receptor (KLR)-expressing cytotoxic gene signature. We define clonal trajectories of antigen-specific T cells using paired single-cell RNA and T cell receptor sequencing and reveal distinct differentiation trajectories resulting in terminal Tex-biased, KLR Tex-biased, or divergent clones that differentiate into both phenotypes. Comparison of Tex phenotypes among shared T cell clones that traffic to multiple organs reveals that clonal differentiation trajectories are maintained across tissues. Finally, we show that differences in clonal differentiation trajectory are driven by TCR signal strength, whereby high-affinity T cell clones preferentially adopt a terminal Tex fate, while low-affinity clones adopt an effector-like KLR Tex fate that is detectable long-term but depleted in high antigen settings. These findings reveal clonal heterogeneity in the T cell response to chronic antigen and genomic programs that underlie Tex fates and persistence.

Sign in / Sign up

Export Citation Format

Share Document