IMMU-43. IMMUNE CONTEXTURE OF ISOCITRATE DEHYDROGENASE STRATIFIED HUMAN GLIOMAS REVEALED BY SINGLE-CELL TRANSCRIPTOMICS AND ACCESSIBLE CHROMATIN

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi102-vi102
Author(s):  
Pravesh Gupta ◽  
Minghao Dang ◽  
Dapeng Hao Hao ◽  
Krishna Bojja ◽  
Tuan M Tran ◽  
...  
Keyword(s):  
T Cells ◽  
Antigen Presentation ◽  
Single Cell ◽  
Immune Cells ◽  
Isocitrate Dehydrogenase ◽  
Zinc Finger Protein ◽  
Immune Cell ◽  
Human Gliomas ◽  
Immune Contexture ◽  
Accessible Chromatin

Abstract The immune cell composition of isocitrate dehydrogenase wild type (IDH-wt) glioma patients significantly differs compared to IDH-mutant (IDH-mut) yet a detailed and unbiased understanding of their transcriptomic and epigenetic landscapes remains elusive. To this end, we performed single-cell RNA-sequencing (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin using sequencing (sc-ATAC-seq) on ~100,000 tumor-associated immune cells from seventeen IDH mutation classified primary and recurrent human gliomas and non-glioma brains (NGBs). Our analyses revealed sixty-two transcriptionally distinct myeloid and lymphoid cell states within and across glioma subtypes and we noted microglial attrition with increasing disease severity concomitant with invading monocyte-derived cells (MDCs) and lymphocytes. Specifically, certain microglial and monocyte-derived subpopulations were associated with antigen presentation gene modules, akin to cross-presenting dendritic cells. As tissue macrophages exhibit multifaceted polarization in response to microenvironmental cues, we clarify the existence of microglia/macrophage functional states beyond M1/M2 paradigms exemplified by the presence of palmitic-, oleic- acid, and glucocorticoid responsive polarized states. We identified cytotoxic T cells with poly-functional cytolytic states mostly in recurrent IDH-wt gliomas. Furthermore, ligand-receptor interactome analyses showed a preponderance of antigen presentation/phagocytosis over the checkpoint axis in IDH-wt compared to IDH-mut gliomas. Additionally, our sc-ATAC-seq analyses revealed differences in regulatory networks in NGBs, IDH-mut, and IDH-wt glioma-associated immune cells. In particular, we noted reduced microglial usage of an iron recycling SPIC transcription factor and Interferon Regulatory Factors (IRFs); IRF1 and IRF2 in IDH-wt relative to IDH-mut and NGBs. Unique features such as amplification of 11-Zinc Finger Protein accessibility were restricted to MDCs. Finally, sc-ATAC-seq profiles of CD8+ exhausted T cells from IDH-wt showed strong enhancer accessibility on CTLA-4, Layilin, and TIM-3 but no enrichment on PD1 was seen. In summary, our study provides unprecedented granular detail of transcriptionally and epigenomically defined glioma-specific immune contexture that can be exploited for immunotherapy applications.

scholarly journals OTME-23. Single-cell transcriptomic and epigenomic immune landscape of isocitrate dehydrogenase stratified human gliomas

2021 ◽  
Vol 3 (Supplement_2) ◽  
pp. ii18-ii18
Author(s):  
Pravesh Gupta ◽  
Minghao Dang ◽  
Dapeng Hao ◽  
Krishna Bojja ◽  
Tuan M Tran ◽  
...  
Keyword(s):  
T Cells ◽  
Antigen Presentation ◽  
Single Cell ◽  
Immune Cells ◽  
Isocitrate Dehydrogenase ◽  
Zinc Finger Protein ◽  
Immune Cell ◽  
Hepatitis A Virus ◽  
Cancer Center ◽  
Human Gliomas

Abstract The brain tumor immune microenvironment (TIME) continuously evolves during glioma progression, but a comprehensive characterization of the glioma-centric immune cell repertoire beyond a priori cell states is uncharted. In this study, we performed single-cell RNA-sequencing (scRNA-seq) and single cell- Assay for Transposase-Accessible Chromatin using sequencing (sc-ATAC-seq) on ~100,000 tumor-associated immune cells from seventeen isocitrate dehydrogenase (IDH) mutation classified primary and recurrent human gliomas and non-glioma brains (NGBs). Our analyses revealed sixty-two transcriptionally distinct myeloid and lymphoid cell states within and across glioma subtypes and we noted microglial attrition with increasing disease severity concomitant with invading monocyte-derived cells and lymphocytes. Specifically, certain microglial and monocyte-derived subpopulations were associated with antigen presentation gene modules, akin to cross-presenting dendritic cells (DCs). We identified cytotoxic T cells with poly-functional cytolytic states mostly in recurrent IDH-wt gliomas. Furthermore, ligand-receptor interactome analyses showed a preponderance of antigen presentation and phagocytosis over the checkpoint axis in IDH-wt compared to IDH-mut gliomas. Additionally, our sc-ATAC-seq analyses revealed differences in regulatory networks in NGBs, IDH-mut and IDH-wt glioma associated immune cells. In particular, we noted abundant usage of inflammatory transcription factors (TFs) as exemplified by Nuclear factor kappa B and Activator Protein-1 TF family in IDH-wt microglia when compared with microglia from IDH-mut and NGBs. Unique features such as amplification of 11- Zinc Finger Protein accessibility were restricted to monocyte derived cells and were not observed in microglia. Finally, sc-ATAC-seq profiles of CD8+ exhausted T cells from IDH-wt showed strong enhancer accessibility on Cytotoxic T-lymphocyte-associated protein 4, Layilin and Hepatitis A Virus Cellular Receptor 2 but no enrichment on PDCD1 (gene encoding Programmed cell death protein 1) was seen. In summary, our study provides unprecedented granular detail of transcriptionally defined glioma- specific immune contexture that can be exploited for immunotherapy applications. This study in K.B. laboratory was supported by the generous philanthropic contributions to The University of Texas (UT) MD Anderson Cancer Center (MDACC) Moon Shots Program™, Marnie Rose Foundation, NIH grants: R21 CA222992 and R01CA225963. This study was partly supported by the UT MDACC start-up research fund to L.W. and CPRIT Single Core grant RP180684 to N. E. N.

Single Cell Profiling Reveals Unique CXCL13 Positive T Cell Subsets in the Tumor Microenvironment of Lymphocyte Rich Classic Hodgkin Lymphoma

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 32-33
Author(s):  
Tomohiro Aoki ◽  
Lauren C. Chong ◽  
Katsuyoshi Takata ◽  
Katy Milne ◽  
Elizabeth Chavez ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
B Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Research Funding ◽  
Immune Cell ◽  
Expression Patterns ◽  
The Other ◽  
Tfh Cells

Introduction: Classic Hodgkin lymphoma (CHL) features a unique crosstalk between malignant cells and different types of normal immune cells in the tumor-microenvironment (TME). On the basis of histomorphologic and immunophenotypic features of the malignant Hodgkin and Reed-Sternberg (HRS) cells and infiltrating immune cells, four histological subtypes of CHL are recognized: Nodular sclerosing (NS), Mixed cellularity, Lymphocyte-rich (LR) and Lymphocyte-depleted CHL. Recently, our group described the high abundance of various types of immunosuppressive CD4+ T cells including LAG3+ and/or CTLA4+ cells in the TME of CHL using single cell RNA sequencing (scRNAseq). However, the TME of LR-CHL has not been well characterized due to the rarity of the disease. In this study, we aimed at characterizing the immune cell profile of LR-CHL at single cell resolution. METHODS: We performed scRNAseq on cell suspensions collected from lymph nodes of 28 primary CHL patients, including 11 NS, 9 MC and 8 LR samples, with 5 reactive lymph nodes (RLN) serving as normal controls. We merged the expression data from all cells (CHL and RLN) and performed batch correction and normalization. We also performed single- and multi-color immunohistochemistry (IHC) on tissue microarray (TMA) slides from the same patients. In addition, an independent validation cohort of 31 pre-treatment LR-CHL samples assembled on a TMA, were also evaluated by IHC. Results: A total of 23 phenotypic cell clusters were identified using unsupervised clustering (PhenoGraph). We assigned each cluster to a cell type based on the expression of genes described in published transcriptome data of sorted immune cells and known canonical markers. While most immune cell phenotypes were present in all pathological subtypes, we observed a lower abundance of regulatory T cells (Tregs) in LR-CHL in comparison to the other CHL subtypes. Conversely, we found that B cells were enriched in LR-CHL when compared to the other subtypes and specifically, all four naïve B-cell clusters were quantitatively dominated by cells derived from the LR-CHL samples. T follicular helper (TFH) cells support antibody response and differentiation of B cells. Our data show the preferential enrichment of TFH in LR-CHL as compared to other CHL subtypes, but TFH cells were still less frequent compared to RLN. Of note, Chemokine C-X-C motif ligand 13 (CXCL13) was identified as the most up-regulated gene in LR compared to RLN. CXCL13, which is a ligand of C-X-C motif receptor 5 (CXCR5) is well known as a B-cell attractant via the CXCR5-CXCL13 axis. Analyzing co-expression patterns on the single cell level revealed that the majority of CXCL13+ T cells co-expressed PD-1 and ICOS, which is known as a universal TFH marker, but co-expression of CXCR5, another common TFH marker, was variable. Notably, classical TFH cells co-expressing CXCR5 and PD-1 were significantly enriched in RLN, whereas PD-1+ CXCL13+ CXCR5- CD4+ T cells were significantly enriched in LR-CHL. These co-expression patterns were validated using flow cytometry. Moreover, the expression of CXCR5 on naïve B cells in the TME was increased in LR-CHL compared to the other CHL subtypes We next sought to understand the spatial relationship between CXCL13+ T cells and malignant HRS cells. IHC of all cases revealed that CXCL13+ T cells were significantly enriched in the LR-CHL TME compared to other subtypes of CHL, and 46% of the LR-CHL cases showed CXCL13+ T cell rosettes closely surrounding HRS cells. Since PD-1+ T cell rosettes are known as a specific feature of LR-CHL, we confirmed co-expression of PD-1 in the rosetting cells by IHC in these cases. Conclusions: Our results reveal a unique TME composition in LR-CHL. LR-CHL seems to be distinctly characterized among the CHL subtypes by enrichment of CXCR5+ naïve B cells and CD4+ CXCL13+ PD-1+ T cells, indicating the importance of the CXCR5-CXCL13 axis in the pathogenesis of LR-CHL. Figure Disclosures Savage: BeiGene: Other: Steering Committee; Merck, BMS, Seattle Genetics, Gilead, AstraZeneca, AbbVie: Honoraria; Roche (institutional): Research Funding; Merck, BMS, Seattle Genetics, Gilead, AstraZeneca, AbbVie, Servier: Consultancy. Scott:Janssen: Consultancy, Research Funding; Celgene: Consultancy; NanoString: Patents & Royalties: Named inventor on a patent licensed to NanoString, Research Funding; NIH: Consultancy, Other: Co-inventor on a patent related to the MCL35 assay filed at the National Institutes of Health, United States of America.; Roche/Genentech: Research Funding; Abbvie: Consultancy; AstraZeneca: Consultancy. Steidl:AbbVie: Consultancy; Roche: Consultancy; Curis Inc: Consultancy; Juno Therapeutics: Consultancy; Bayer: Consultancy; Seattle Genetics: Consultancy; Bristol-Myers Squibb: Research Funding.

scholarly journals High-dimensional cytometric analysis of colorectal cancer reveals novel mediators of antitumour immunity

Gut ◽  
2019 ◽  
Vol 69 (4) ◽  
pp. 691-703 ◽  
Author(s):  
Natasja L de Vries ◽  
Vincent van Unen ◽  
Marieke E Ijsselsteijn ◽  
Tamim Abdelaal ◽  
Ruud van der Breggen ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
T Cells ◽  
Lymph Nodes ◽  
Single Cell ◽  
Immune Cell ◽  
Γδ T Cells ◽  
High Dimensional ◽  
Hla Dr ◽  
Healthy Mucosa ◽  
Immune Contexture

ObjectiveA comprehensive understanding of anticancer immune responses is paramount for the optimal application and development of cancer immunotherapies. We unravelled local and systemic immune profiles in patients with colorectal cancer (CRC) by high-dimensional analysis to provide an unbiased characterisation of the immune contexture of CRC.DesignThirty-six immune cell markers were simultaneously assessed at the single-cell level by mass cytometry in 35 CRC tissues, 26 tumour-associated lymph nodes, 17 colorectal healthy mucosa and 19 peripheral blood samples from 31 patients with CRC. Additionally, functional, transcriptional and spatial analyses of tumour-infiltrating lymphocytes were performed by flow cytometry, single-cell RNA-sequencing and multispectral immunofluorescence.ResultsWe discovered that a previously unappreciated innate lymphocyte population (Lin–CD7+CD127–CD56+CD45RO+) was enriched in CRC tissues and displayed cytotoxic activity. This subset demonstrated a tissue-resident (CD103+CD69+) phenotype and was most abundant in immunogenic mismatch repair (MMR)-deficient CRCs. Their presence in tumours was correlated with the infiltration of tumour-resident cytotoxic, helper and γδ T cells with highly similar activated (HLA-DR+CD38+PD-1+) phenotypes. Remarkably, activated γδ T cells were almost exclusively found in MMR-deficient cancers. Non-activated counterparts of tumour-resident cytotoxic and γδ T cells were present in CRC and healthy mucosa tissues, but not in lymph nodes, with the exception of tumour-positive lymph nodes.ConclusionThis work provides a blueprint for the understanding of the heterogeneous and intricate immune landscape of CRC, including the identification of previously unappreciated immune cell subsets. The concomitant presence of tumour-resident innate and adaptive immune cell populations suggests a multitargeted exploitation of their antitumour properties in a therapeutic setting.

scholarly journals Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Guohe Song ◽  
Yang Shi ◽  
Meiying Zhang ◽  
Shyamal Goswami ◽  
Saifullah Afridi ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
T Cell Subsets ◽  
M2 Macrophage ◽  
Advanced Hcc ◽  
Immune Cell Subsets

AbstractDiverse immune cells in the tumor microenvironment form a complex ecosystem, but our knowledge of their heterogeneity and dynamics within hepatocellular carcinoma (HCC) still remains limited. To assess the plasticity and phenotypes of immune cells within HBV/HCV-related HCC microenvironment at single-cell level, we performed single-cell RNA sequencing on 41,698 immune cells from seven pairs of HBV/HCV-related HCC tumors and non-tumor liver tissues. We combined bio-informatic analyses, flow cytometry, and multiplex immunohistochemistry to assess the heterogeneity of different immune cell subsets in functional characteristics, transcriptional regulation, phenotypic switching, and interactions. We identified 29 immune cell subsets of myeloid cells, NK cells, and lymphocytes with unique transcriptomic profiles in HCC. A highly complex immunological network was shaped by diverse immune cell subsets that can transit among different states and mutually interact. Notably, we identified a subset of M2 macrophage with high expression of CCL18 and transcription factor CREM that was enriched in advanced HCC patients, and potentially participated in tumor progression. We also detected a new subset of activated CD8+ T cells highly expressing XCL1 that correlated with better patient survival rates. Meanwhile, distinct transcriptomic signatures, cytotoxic phenotypes, and evolution trajectory of effector CD8+ T cells from early-stage to advanced HCC were also identified. Our study provides insight into the immune microenvironment in HBV/HCV-related HCC and highlights novel macrophage and T-cell subsets that could be further exploited in future immunotherapy.

scholarly journals Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data with ImmClassifier

2020 ◽  
Author(s):  
Xuan Liu ◽  
Sara J.C. Gosline ◽  
Lance T. Pflieger ◽  
Pierre Wallet ◽  
Archana Iyer ◽  
...  
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
Cell Types ◽  
Effector Memory ◽  
Immune Cell Population ◽  
Fine Grained ◽  
Knowledge Based ◽  
Comparable Performance

AbstractSingle-cell RNA sequencing is an emerging strategy for characterizing the immune cell population in diverse environments including blood, tumor or healthy tissues. While this has traditionally been done with flow or mass cytometry targeting protein expression, scRNA-Seq has several established and potential advantages in that it can profile immune cells and non-immune cells (e.g. cancer cells) in the same sample, identify cell types that lack precise markers for flow cytometry, or identify a potentially larger number of immune cell types and activation states than is achievable in a single flow assay. However, scRNA-Seq is currently limited due to the need to identify the types of each immune cell from its transcriptional profile, which is not only time-consuming but also requires a significant knowledge of immunology. While recently developed algorithms accurately annotate coarse cell types (e.g. T cells vs macrophages), making fine distinctions has turned out to be a difficult challenge. To address this, we developed a machine learning classifier called ImmClassifier that leverages a hierarchical ontology of cell type. We demonstrate that ImmClassifier outperforms other tools (+20% recall, +14% precision) in distinguishing fine-grained cell types (e.g. CD8+ effector memory T cells) with comparable performance on coarse ones. Thus, ImmClassifier can be used to explore more deeply the heterogeneity of the immune system in scRNA-Seq experiments.

scholarly journals Single-Cell RNA Sequencing of Peripheral Blood Reveals Immune Cell Signatures in Alzheimer’s Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Hui Xu ◽  
Jianping Jia
Keyword(s):  
Immune Response ◽  
T Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Peripheral Blood ◽  
Immune Cell ◽  
Adaptive Immune Response ◽  
Immune Repertoire ◽  
Adaptive Immune ◽  
Peripheral Immune Cells

The peripheral immune system is thought to affect the pathology of the central nervous system in Alzheimer’s disease (AD). However, current knowledge is inadequate for understanding the characteristics of peripheral immune cells in AD. This study aimed to explore the molecular basis of peripheral immune cells and the features of adaptive immune repertoire at a single cell level. We profiled 36,849 peripheral blood mononuclear cells from AD patients with amyloid-positive status and normal controls with amyloid-negative status by 5’ single-cell transcriptome and immune repertoire sequencing using the cell ranger standard analysis procedure. We revealed five immune cell subsets: CD4+ T cells, CD8+ T cells, B cells, natural killer cells, and monocytes–macrophages cells, and disentangled the characteristic alterations of cell subset proportion and gene expression patterns in AD. Thirty-one cell type-specific key genes, comprising abundant human leukocyte antigen genes, and multiple immune-related pathways were identified by protein–protein interaction network and pathway enrichment analysis. We also found high-frequency amplification clonotypes in T and B cells and decreased diversity in T cells in AD. As clone amplification suggested the activation of an adaptive immune response against specific antigens, we speculated that the peripheral adaptive immune response, especially mediated by T cells, may have a role in the pathogenesis of AD. This finding may also contribute to further research regarding disease mechanism and the development of immune-related biomarkers or therapy.

scholarly journals Single-cell Map of Diverse Immune Phenotypes Driven by the Tumor Microenvironment

2017 ◽  
Author(s):  
Elham Azizi ◽  
Ambrose J. Carr ◽  
George Plitas ◽  
Andrew E. Cornish ◽  
Catherine Konopacki ◽  
...  
Keyword(s):  
T Cells ◽  
Tumor Microenvironment ◽  
Single Cell ◽  
Cancer Progression ◽  
Immune Cells ◽  
Immune Cell ◽  
Phenotypic Diversity ◽  
Macrophage Polarization ◽  
Sequencing Data ◽  
Significant Similarity

SUMMARYKnowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We created an immune map of breast cancer using single-cell RNA-seq data from 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph node. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. Despite significant similarity between normal and tumor tissue-resident immune cells, we observed continuous tumor-specific phenotypic expansions driven by environmental cues. Analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data from 27,000 additional T cells revealed the combinatorial impact of TCR utilization on phenotypic diversity. Our results support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer, with important implications for characterizing tumor-infiltrating immune cells.

scholarly journals The ratio of exhausted to resident infiltrating lymphocytes is prognostic for colorectal cancer patient outcome

2020 ◽  
Author(s):  
Momeneh Foroutan ◽  
Ramyar Molania ◽  
Aline Pfefferle ◽  
Corina Behrenbruch ◽  
Axel Kallies ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
T Cells ◽  
Nk Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
Colorectal Cancer Patient ◽  
Colon Adenocarcinoma ◽  
Rna Seq ◽  
Infiltrating Lymphocytes

AbstractImmunotherapy success in colorectal cancer (CRC) is mainly limited to patients whose tumours exhibit high microsatellite instability (MSI). However, there is variability in treatment outcomes within this group, which is in part driven by the frequency and characteristics of tumour infiltrating immune cells. Indeed, the presence of specific infiltrating immune cell subsets has been shown to correlate with immunotherapy responses and is in many cases prognostic of treatment outcome. Tumour-infiltrating lymphocytes (TILs) can undergo distinct differentiation programs such as acquire features of tissue-residency or exhaustion, a process during which T cells upregulate inhibitory receptors such as PD-1 and loose functionality. While residency and exhaustion programs of CD8 T cells are relatively well-studied, these programs have only recently been appreciated in CD4 T cells and remain largely unknown in tumour-infiltrating natural killer (NK) cells. In this study, we use single cell RNA-seq data to identify signatures of residency and exhaustion in CRC infiltrating lymphocytes, including CD8, CD4 and NK cells. We then test these signatures in independent single cell data from tumour and normal tissue infiltrating immune cells. Further, we use versions of these signatures adapted for bulk RNA-seq data to identify a list of tumour intrinsic mutations associated with residency and exhaustion from TCGA data. Finally, using two independent transcriptomic data sets from patients with colon adenocarcinoma, we show that combinations of these signatures, in particular NK signatures, as well as tumour-associated signatures, such as TGF-β signalling, are associated with distinct survival outcomes in colorectal cancer patients.

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.

scholarly journals Single-cell transcriptomic analysis of endometriosis provides insights into fibroblast fates and immune cell heterogeneity

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Junyan Ma ◽  
Liqi Zhang ◽  
Hong Zhan ◽  
Yun Mo ◽  
Zuanjie Ren ◽  
...  
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
Single Cells ◽  
Developmental Trajectory ◽  
Reproductive Age ◽  
Eutopic Endometrium ◽  
Female Population ◽  
Healthy Women

Abstract Background Endometriosis is an oestrogen-dependent disease with an unclear aetiology and pathogenesis affecting 6–10% of the global female population, predominantly those of reproductive age. Herein, we profile the transcriptomes of approximately 55,000 single cells from three groups including ectopic endometrium, eutopic endometrium from women with endometriosis, and eutopic endometrium from healthy women to create a single-cell transcriptome atlas of endometriosis. Results We have identified 9 cell types and performed single-cell analysis of fibroblasts, and determined a potential developmental trajectory associated with endometriosis. We also identified fibroblast subpopulations related to endometriosis development and found that StAR played an important role in this process. Moreover, T cells in endometriosis were less activated or inflammatory with decreased effector CD8 + T cells, while the composition ratio of natural killer cells decreased and the percentage of monocytes/macrophages increased in endometriosis cysts. In addition, the effectiveness of immune cells in endometriosis lesions, eutopic endometrium from women with endometriosis, and eutopic endometrium from healthy women was distinct. Cell–cell interaction analyses highlighted the imbalanced immune environment in endometriosis lesions and immune cells in endometriosis could promote the development of the disease. Conclusion Our study provided a systematic characterisation of endometriosis and insights into the aetiology and pathology of endometriosis.

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