Abstract 439: High Dimensional Single-Cell Immune Contexture of Human Atherosclerotic Plaques and Blood

2017 ◽  
Vol 37 (suppl_1) ◽  
Author(s):  
Adeeb Rahman ◽  
Aleksey Chudnovskiy ◽  
El-ad David Amir ◽  
Seunghee Kim-Schulze ◽  
Jennifer R Li ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Cd8 T Cells ◽  
Immune Cells ◽  
High Dimensional ◽  
Specific Cell ◽  
Single Cell Level ◽  
Cell Level ◽  
Immune Contexture

Atherosclerosis is a disease characterized by immune infiltration of the arterial wall in response to tissue damage and systemic inflammation. In the era of precision medicine, is essential to gain insights on immune contexture of atherosclerotic tissue taking into account disease-specific cell variation in patients. We applied high-dimensional technologies for the analysis of multiple parameters at the single-cell level in clinical samples of patients undergoing carotid endatherectomy (CEA, n=15). Using time-of-flight mass-cytometry (CyTOF), we simultaneously analyzed 32 parameters at the single-cell level in peripheral blood mononuclear cells (PBMCs) and atherosclerotic-tissue associated immune cells of the same patient. Using viSNE, we mapped single-cell heterogeneity into two dimensions to discriminate PBMCs and tissue-associated CD45+ immune cells. Next, we employed Phenograph to cluster cells into phenotypically related populations, which were annotated based on canonical marker expression patterns. We identified several major immune subsets including two subsets of macrophages (CD163 low and CD163 high ), monocytes, dendritic cells (DCs), B and T cells. The most prevalent CD45+ cells identified in atherosclerotic tissue were CD4 + (25.8%) and CD8 + (25.2%) T cells, macrophages (12.8%), monocytes (7.7%) and B (2.1%) cells. Using a regression analysis similar to that employed by CITRUS, we determined that macrophages and a subset of CD8 T cells characterized by low expression of CD127 were selectively enriched in tissue vs. blood. Multiplexed immunohistochemistry confirmed that T cells comprised a major portion of the CD45+ cells in atherosclerotic tissue, even more abundant than macrophages. This study of deep phenotyping across-atherosclerotic tissue and blood demonstrate a significant T cell tissue infiltration of a specific subset of CD8 T cells. This suggests that adaptive T cell immunity plays a critical role in advanced atherosclerosis. The extension of this systems biology analysis pipeline to larger datasets can improve our understanding of the core mechanisms of chronic inflammation in atherosclerosis.

773 Adoptive Cell Therapy Response in Melanoma is Mediated by Stem-like CD8 T cells

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A822-A822
Author(s):  
Sri Krishna ◽  
Frank Lowery ◽  
Amy Copeland ◽  
Stephanie Goff ◽  
Grégoire Altan-Bonnet ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Cell Therapy ◽  
Single Cell ◽  
Cd8 T Cells ◽  
Tumor Infiltrating Lymphocytes ◽  
High Dimensional ◽  
Tumor Control ◽  
Intrinsic Factors ◽  
Infiltrating Lymphocytes

BackgroundAdoptive T cell therapy (ACT) utilizing ex vivo-expanded autologous tumor infiltrating lymphocytes (TILs) can result in complete regression of human cancers.1 Successful immunotherapy is influenced by several tumor-intrinsic factors.2 3 Recently, T cell-intrinsic factors have been associated with immunotherapy response in murine and human studies.4 5 Analyses of tumor-reactive TILs have concluded that anti-tumor neoantigen-specific TILs are enriched in subsets defined by the expression of PD-1 or CD39.6 7 Thus, there is a lack of consensus regarding the tumor-reactive TIL subset that is directly responsible for successful immunotherapies such as ICB and ACT. In this study, we attempted to define the fitness landscape of TIL-enriched infusion products to specifically understand its phenotypic impact on human immunotherapy responses.MethodsWe compared the phenotypic differences that could distinguish bulk ACT infusion products (I.P.) administered to patients who had complete response to therapy (complete responders, CRs, N = 24) from those whose disease progressed following ACT (non-responders, NRs, N = 30) by high dimensional single cell protein and RNA analysis of the I.P. We further analyzed the phenotypic states of anti-tumor neoantigen specific TILs from patient I.P (N = 26) by flow cytometry and single cell transcriptomics.ResultsWe identified two CD8+ TIL populations associated with clinical outcomes: a memory-progenitor CD39-negative stem-like TIL (CD39-CD69-) in the I.P. associated with complete cancer regression (overall survival, P < 0.0001, HR = 0.217, 95% CI 0.101 to 0.463) and TIL persistence, and a terminally differentiated CD39-positive TIL (CD39+CD69+) population associated with poor TIL persistence post-treatment. Although the majority (>65%) of neoantigen-reactive TILs in both responders and non-responders to ACT were found in the differentiated CD39+ state, CR infusion products also contained a pool of CD39- stem-like neoantigen-specific TILs (median = 8.8%) that was lacking in NR infusion products (median = 23.6%, P = 1.86 x 10-5). Tumor-reactive stem-like T cells were capable of self-renewal, expansion, and persistence, and mediated superior anti-tumor response in vivo.ConclusionsOur results support the hypothesis that responders to ACT received infusion products containing a pool of stem-like neoantigen-specific TILs that are able to undergo prolific expansion, give rise to differentiated subsets, and mediate long-term tumor control and T cell persistence, in line with recent murine ICB studies mediated by TCF+ progenitor T cells.4 5 Our data also suggest that TIL subsets mediating ACT-response (stem-like CD39-) might be distinct from TIL subsets enriched for anti-tumor-reactivity (terminally differentiated CD39+) in human TIL.6 7AcknowledgementsWe thank Don White for curating the melanoma patient cohort, and J. Panopoulos (Flowjo) for helpful discussions on high-dimensional analysis, and NCI Surgery Branch members for helpful insights and suggestions. S. Krishna acknowledges funding support from NCI Director’s Innovation Award from the National Cancer Institute.Trial RegistrationNAEthics ApprovalThe study was approved by NCI’s IRB ethics board.ReferencesGoff SL, et al. Randomized, prospective evaluation comparing intensity of lymphodepletion before adoptive transfer of tumor-infiltrating lymphocytes for patients with metastatic melanoma. J Clin Oncol 2016;34:2389–2397.Snyder A, et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med 2014;371:2189–2199.McGranahan N, et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science 2016;351:1463–1469.Sade-Feldman M, et al. Defining T cell states associated with response to checkpoint immunotherapy in melanoma. Cell 2019;176:404.Miller BC, et al. Subsets of exhausted CD8 T cells differentially mediate tumor control and respond to checkpoint blockade. Nat. Immunol 2019;20:326–336.Simoni Y, et al. Bystander CD8 T cells are abundant and phenotypically distinct in human tumour infiltrates. Nature 2018;557:575–579.Gros A, et al. PD-1 identifies the patient-specific CD8+ tumor-reactive repertoire infiltrating human tumors. J Clin Invest 2014;124:2246–2259.

Enhanced IFN-γ Production in Vitro by CD8+ T Cells in Hemophiliacs with AIDS as Demonstrated on the Single-Cell Level

1999 ◽  
Vol 92 (1) ◽  
pp. 111-117 ◽  
Author(s):  
Y. Pae ◽  
H. Minagawa ◽  
J. Hayashi ◽  
S. Kashiwagi ◽  
Y. Yanagi
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Cd8 T Cells ◽  
Single Cell Level ◽  
Cell Level ◽  
Ifn Γ

scholarly journals Single-cell RNA-Seq reveals the link between CD45 isoforms and tumor-infiltrating T cells heterogeneity in liver cancer

2020 ◽  
Author(s):  
Biaofeng Zhou ◽  
Shang Liu ◽  
Liang Wu ◽  
Yan Sun ◽  
Jie Chen ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
T Lymphocytes ◽  
Single Cell ◽  
Cell Function ◽  
Effector Memory ◽  
Single Cell Level ◽  
Cell Level ◽  
Cd45 Isoforms ◽  
And Function

AbstractCD45 isoforms play a major role in characterizing T cell function, phenotype, and development. However, there is lacking comprehensive interrogation about the relationship between CD45 isoforms and T lymphocytes from cancer patients at the single-cell level yet. Here, we investigated the CD45 isoforms component of published 5,063 T cells of hepatocellular carcinoma (HCC), which has been assigned functional states. We found that the distribution of CD45 isoforms in T lymphocytes cells depended on tissue resource, cell type, and functional state. Further, we demonstrated that CD45RO and CD45RA dominate in characterizing the phenotype and function of T cell though multiple CD45 isoforms coexist in T cells, through a novel alternative splicing pattern analysis. We identified a novel development trajectory of tumor-infiltrating T cells from Tcm to Temra (effector memory T cells re-expresses CD45RA) after detecting two subpopulations in state of transition, Tcm (central memory T) and Tem (effector memory T). Temra, capable of high cytotoxic characteristics, was discovered to be associated with the stage of HCC and may be a target of immunotherapy. Our study presents a comprehension of the connection between CD45 isoforms and the function, states, sources of T lymphocytes cells in HCC patients at the single-cell level, providing novel insight for the effect of CD45 isoforms on T cell heterogeneity.

scholarly journals O3 High-dimensional analysis of tumor architecture predicts cancer immunotherapy response

2020 ◽  
Vol 8 (Suppl 2) ◽  
pp. A4.2-A5
Author(s):  
CM Schürch ◽  
DJ Phillips ◽  
M Matusiak ◽  
B Rivero Gutierrez ◽  
SS Bhate ◽  
...  
Keyword(s):  
Single Cell ◽  
Tumor Cells ◽  
Immune Cells ◽  
Cell Types ◽  
Advisory Board ◽  
High Dimensional ◽  
Single Cell Level ◽  
Cell Type ◽  
Cell Level ◽  
Research Grant

BackgroundImmunotherapies have induced long-lasting remissions in countless advanced-stage cancer patients, but many more patients have not benefitted. Therefore, novel predictive markers are needed to stratify patients before treatment and select those who will most likely benefit from immunotherapy, while avoiding potentially devastating adverse effects and high treatment costs for those who will not. We reasoned that thoroughly characterizing the architecture of the tumor microenvironment (TME) at the single-cell level by highly multiplexed tissue imaging should reveal novel spatial biomarkers of immunotherapy response.Materials and MethodsWe used CODEX (CO-Detection by indEXing) highly multiplexed fluorescence microscopy to investigate the TME of cutaneous T cell lymphoma (CTCL) in samples from patients treated with pembrolizumab. 55 protein markers were visualized simultaneously using a tissue microarray of matched pre- and post-treatment skin biopsies from 7 pembrolizumab responders and 7 non-responders. After computational image processing and extraction of single-cell information, cell types were identified by unsupervised clustering followed by supervised curation, and cell-cell distances and ‘cellular neighborhoods’ were computed. We also performed RNA sequencing on laser-capture microdissected tissue microarray cores to extract cell-type specific gene expression profiles by CIBERSORTx analysis.ResultsCODEX enabled the identification and characterization of malignant CD4+ tumor cells and reactive immune cells in the CTCL TME at the single-cell level, resulting in 21 different cell type clusters with spatial information. Cluster frequencies were not significantly different between responders and non-responders pre- and post-treatment. However, advanced computational analysis of the tumor architecture revealed cellular neighborhoods (CNs) that dynamically changed during pembrolizumab therapy and were correlated with response. Effector-type CNs enriched in tumor-infiltrating CD4+ T cells and dendritic cells were significantly increased after treatment in responders. In contrast, a regulatory T cell-enriched CN was significantly increased in non-responders before and after therapy. Furthermore, a spatial signature of cell-cell distances between tumor cells and effector/regulatory immune cells predicted therapy outcome. In addition, CIBERSORTx analysis revealed that tumor cells in responders, but not in non-responders, increased their expression of immune-activating genes.ConclusionsHigh-dimensional spatial analysis of CTCL tumors revealed a pre-existing immunosuppressive state in pembrolizumab non-responders. Thorough analysis of the TME therefore enables the discovery of novel spatial biomarkers in a concept that accounts for both cell type information and higher-order tumor architecture. Combining highly multiplexed microscopy with CIBERSORTx allows for the discovery of novel, predictive spatial biomarkers of immunotherapy response and will pave the way for future studies that functionally address these cell types and their interactions.Disclosure InformationC.M. Schürch: F. Consultant/Advisory Board; Modest; Enable Medicine, LLC. D.J. Phillips: None. M. Matusiak: None. B. Rivero Gutierrez: None. S.S. Bhate: None. G.L. Barlow: None. M.S. Khodadoust: B. Research Grant (principal investigator, collaborator or consultant and pending grants as well as grants already received); Significant; Corvus Pharmaceuticals. R. West: None. Y.H. Kim: B. Research Grant (principal investigator, collaborator or consultant and pending grants as well as grants already received); Significant; Merck, Horizon, Soligenix, miRagen, Forty Seven Inc., Neumedicine, Trillium, Galderma, Elorac. D. Speakers Bureau/Honoraria (speakers bureau, symposia, and expert witness); Significant; Innate Pharma, Eisai, Kyowa Hakko Kirin, Takeda, Seattle Genetics, Medivir, Portola Pharmaceuticals, Corvus Pharmaceuticals. G.P. Nolan: E. Ownership Interest (stock, stock options, patent or other intellectual property); Significant; Akoya Biosciences. F. Consultant/Advisory Board; Significant; Akoya Biosciences.

scholarly journals Gene Expression-Based Identification of Antigen-Responsive CD8+ T Cells on a Single-Cell Level

2019 ◽  
Vol 10 ◽  
Author(s):  
Yannick F. Fuchs ◽  
Virag Sharma ◽  
Anne Eugster ◽  
Gloria Kraus ◽  
Robert Morgenstern ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Single Cell ◽  
Cd8 T Cells ◽  
Single Cell Level ◽  
Cell Level

scholarly journals Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers

Nature ◽  
2021 ◽  
Author(s):  
Justina X. Caushi ◽  
Jiajia Zhang ◽  
Zhicheng Ji ◽  
Ajay Vaghasia ◽  
Boyang Zhang ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
T Cell Activation ◽  
Cd8 T Cells ◽  
T Cell Receptors ◽  
Tumour Microenvironment ◽  
Lung Cancers ◽  
Cell Receptors ◽  
Interleukin 7

AbstractPD-1 blockade unleashes CD8 T cells1, including those specific for mutation-associated neoantigens (MANA), but factors in the tumour microenvironment can inhibit these T cell responses. Single-cell transcriptomics have revealed global T cell dysfunction programs in tumour-infiltrating lymphocytes (TIL). However, the majority of TIL do not recognize tumour antigens2, and little is known about transcriptional programs of MANA-specific TIL. Here, we identify MANA-specific T cell clones using the MANA functional expansion of specific T cells assay3 in neoadjuvant anti-PD-1-treated non-small cell lung cancers (NSCLC). We use their T cell receptors as a ‘barcode’ to track and analyse their transcriptional programs in the tumour microenvironment using coupled single-cell RNA sequencing and T cell receptor sequencing. We find both MANA- and virus-specific clones in TIL, regardless of response, and MANA-, influenza- and Epstein–Barr virus-specific TIL each have unique transcriptional programs. Despite exposure to cognate antigen, MANA-specific TIL express an incompletely activated cytolytic program. MANA-specific CD8 T cells have hallmark transcriptional programs of tissue-resident memory (TRM) cells, but low levels of interleukin-7 receptor (IL-7R) and are functionally less responsive to interleukin-7 (IL-7) compared with influenza-specific TRM cells. Compared with those from responding tumours, MANA-specific clones from non-responding tumours express T cell receptors with markedly lower ligand-dependent signalling, are largely confined to HOBIThigh TRM subsets, and coordinately upregulate checkpoints, killer inhibitory receptors and inhibitors of T cell activation. These findings provide important insights for overcoming resistance to PD-1 blockade.

scholarly journals Direct and Indirect endocrine-mediated suppression of human endometrial CD8+T cell cytotoxicity

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Z. Shen ◽  
M. Rodriguez-Garcia ◽  
M. V. Patel ◽  
C. R. Wira
Keyword(s):  
T Cells ◽  
T Cell ◽  
Immune Responses ◽  
Cytotoxic Activity ◽  
Cd8 T Cells ◽  
Immune Cells ◽  
Cd8 T Cell ◽  
Gynecological Cancers ◽  
Protective Strategies ◽  
T Cell Cytotoxicity

AbstractRegulation of endometrial (EM) CD8+T cells is essential for successful reproduction and protection against pathogens. Suppression of CD8+T cells is necessary for a tolerogenic environment that promotes implantation and pregnancy. However, the mechanisms regulating this process remain unclear. Sex hormones are known to control immune responses directly on immune cells and indirectly through the tissue environment. When the actions of estradiol (E2), progesterone (P) and TGFβ on EM CD8+T cells were evaluated, cytotoxic activity, perforin and granzymes were directly suppressed by E2 and TGFβ but not P. Moreover, incubation of polarized EM epithelial cells with P, but not E2, increased TGFβ secretion. These findings suggest that E2 acts directly on CD8+T cell to suppress cytotoxic activity while P acts indirectly through induction of TGFβ production. Understanding the mechanisms involved in regulating endometrial CD8+T cells is essential for optimizing reproductive success and developing protective strategies against genital infections and gynecological cancers.

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