scholarly journals Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Kyungsoo Kim ◽  
Seyeon Park ◽  
Seong Yong Park ◽  
Gamin Kim ◽  
Su Myeong Park ◽  
...  
Keyword(s):  
T Cell ◽  
Single Cell ◽  
Transcriptome Analysis ◽  
Human Cancer ◽  
T Cell Exhaustion ◽  
Cell Exhaustion ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

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

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.

scholarly journals Single-cell transcriptome analysis of CAR T-cell products reveals subpopulations, stimulation, and exhaustion signatures

2021 ◽  
Vol 10 (1) ◽  
pp. 1866287
Author(s):  
Xiaonan Wang ◽  
Carlotta Peticone ◽  
Ekaterini Kotsopoulou ◽  
Berthold Göttgens ◽  
Fernando J Calero-Nieto
Keyword(s):  
T Cell ◽  
Single Cell ◽  
Transcriptome Analysis ◽  
Car T Cell ◽  
Car T ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

scholarly journals High-Dimensional and Single-Cell Transcriptome Analysis of AITL Tumor Microenvironment Reveals Gross Expansion of Novel Dysfunctional CD8+ T Cell Populations, Global Shift in B Cell Phenotypes

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 42-43
Author(s):  
Joshua C. Pritchett ◽  
Zhi-Zhang Yang ◽  
Hyojin Kim ◽  
Jose C Villasboas ◽  
Andrew L. Feldman ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Single Cell ◽  
Transcriptome Analysis ◽  
Research Funding ◽  
High Dimensional ◽  
Cell Populations ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome ◽  
Cell Phenotypes

BACKGROUND: Angioimmunoblastic T cell lymphoma (AITL) has a unique histological profile comprised of a relatively small number of malignant CD4+ T-cells of TFH phenotype inter-mixed with an extensive infiltrate of multi-lineage immune cells. In our study, we have utilized mass cytometry, high-dimensional analysis, and single-cell transcriptome analysis to provide novel insights into the unique phenotypes that comprise this intra-tumoral microenvironment. We then extended this work to explore clinical associations including peripheral serum analysis of AITL patients and normal controls. To our knowledge, this represents the first such analysis of its kind in AITL. METHODS: We designed two novel CyTOF antibody (Ab) panels to identify and characterize cells of T, B, NK, monocyte and fDC lineages. Samples analyzed included a cohort of 25 biopsy specimens from 8 histologically confirmed AITL patients (5 lymph node (LN), 3 spleen (SP)) and 17 normal controls across key comparator immune tissue types (7 LN, 6 SP, 4 tonsil (TL)). Extensive high-dimensional analysis of CyTOF data was then performed to provide novel insights into key phenotypes and trends of malignant and non-malignant populations in AITL. We then performed CITE-Seq on control and AITL samples to gain further insight into the RNA transcriptome of key T cell populations at the cellular level. Finally, peripheral serum analysis of cytokines, soluble immune receptors, and ligands were then measured by multiplex ELISA from a separate cohort of 22 samples (5 AITL, 17 control) distinct from the individuals analyzed in the original high-dimensional study cohort. RESULTS: While the presence of "reactive" CD8+ populations is a known histologic hallmark of AITL, we describe the gross expansion of novel CD8+ populations with distinctive immunophenotypic features which have not previously been detailed in this malignancy. Using single-cell protein expression data from CyTOF, these expanded CD8+ populations can be broadly categorized as "effector memory" (CCR7-, CD45RO+, CD45RA-) and further characterized phenotypically by markers of progressive exhaustion, checkpoint inhibition, and terminal differentiation (PD1++, TIGIT++, ICOS+, TIM3+). Further analysis of the single-cell transcriptome from these expanded CD8+ populations via CITE-Seq revealed an expression signature consistent with dysfunction and limited cytotoxic activity (including significant down-regulation of granzyme, perforin, and IFN-g) when compared to benign and malignant controls. Interestingly, when compared to CD8+ populations of identical phenotype found in control tissues, these cells also featured marked upregulation of XCL2 and XCL1 in AITL. Additionally, global shifts in infiltrating CD19+ B cell phenotypes were seen in AITL, marked specifically by diminished expression of both CXCR5 and CD73. Finally, soluble PD-1 and other key immune molecules implicated in the expanded tumor microenvironment were found to be significantly increased in the peripheral serum of AITL patients compared to controls (1567.9 pg/mL (1109.3 S.E.) in AITL vs 29.79 (8.84 S.E.) in controls; P<0.0001). CONCLUSIONS: High-dimensional and single-cell transcriptome analysis of the AITL microenvironment yielded several novel insights which have not been previously described in this malignancy. Highlights include the gross expansion of distinct CD8+ populations - the majority of which are of an exhausted, dysfunctional phenotype featuring marked upregulation of XCL2 and XCL1 - and the global loss of CXCR5 and CD73 expression among AITL CD19+ B cell populations. Taken together, this suggests the presence of aberrant non-malignant immune subsets within the AITL microenvironment which may contribute to novel mechanisms of immune escape. Disclosures Cerhan: NanoString: Research Funding; BMS/Celgene: Research Funding. Ansell:Bristol Myers Squibb: Research Funding; ADC Therapeutics: Research Funding; Seattle Genetics: Research Funding; Regeneron: Research Funding; Affimed: Research Funding; AI Therapeutics: Research Funding; Trillium: Research Funding; Takeda: Research Funding.

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