Single-Cell RNA Sequencing Reveals the Expansion of Cytotoxic CD4+ T Lymphocytes and a Landscape of Immune Cells in Primary Sjögren’s Syndrome

ObjectivePrimary Sjögren’s syndrome (pSS) is a systemic autoimmune disease, and its pathogenetic mechanism is far from being understood. In this study, we aimed to explore the cellular and molecular mechanisms that lead to pathogenesis of this disease.MethodsWe applied single-cell RNA sequencing (scRNA-seq) to 57,288 peripheral blood mononuclear cells (PBMCs) from five patients with pSS and five healthy controls. The immune cell subsets and susceptibility genes involved in the pathogenesis of pSS were analyzed. Flow cytometry was preformed to verify the result of scRNA-seq.ResultsWe identified two subpopulations significantly expand in pSS patients. The one highly expressing cytotoxicity genes is named as CD4+ CTLs cytotoxic T lymphocyte, and another highly expressing T cell receptor (TCR) variable gene is named as CD4+ TRAV13-2+ T cell. Flow cytometry results showed the percentages of CD4+ CTLs, which were profiled with CD4+ and GZMB+ staining; the total T cells of 10 patients with pSS were significantly higher than those of 10 healthy controls (P= 0.008). The expression level of IL-1β in macrophages, TCL1A in B cells, as well as interferon (IFN) response genes in most cell subsets was upregulated in the patients with pSS. Susceptibility genes including HLA-DRB5, CTLA4, and AQP3 were highly expressed in patients with pSS.ConclusionsOur data revealed disease-specific immune cell subsets and provided some potential new targets of pSS. Specific expansion of CD4+ CTLs may be involved in the pathogenesis of pSS, which might give valuable insights for therapeutic interventions of pSS.

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VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data

Bioinformatics ◽

10.1093/bioinformatics/btz610 ◽

2019 ◽

Vol 36 (2) ◽

pp. 546-551 ◽

Cited By ~ 3

Author(s):

Kyungsoo Kim ◽

Sunmo Yang ◽

Sang-Jun Ha ◽

Insuk Lee

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Cell Differentiation ◽

T Cell ◽

Single Cell ◽

Rna Sequencing ◽

Immune Cell ◽

Signaling Molecules ◽

Single Cell Rna Sequencing ◽

Functional States

Abstract Motivation The immune system has diverse types of cells that are differentiated or activated via various signaling pathways and transcriptional regulation upon challenging conditions. Immunophenotyping by flow and mass cytometry are the major approaches for identifying key signaling molecules and transcription factors directing the transition between the functional states of immune cells. However, few proteins can be evaluated by flow cytometry in a single experiment, preventing researchers from obtaining a comprehensive picture of the molecular programs involved in immune cell differentiation. Recent advances in single-cell RNA sequencing (scRNA-seq) have enabled unbiased genome-wide quantification of gene expression in individual cells on a large scale, providing a new and versatile analytical pipeline for studying immune cell differentiation. Results We present VirtualCytometry, a web-based computational pipeline for evaluating immune cell differentiation by exploiting cell-to-cell variation in gene expression with scRNA-seq data. Differentiating cells often show a continuous spectrum of cellular states rather than distinct populations. VirtualCytometry enables the identification of cellular subsets for different functional states of differentiation based on the expression of marker genes. Case studies have highlighted the usefulness of this subset analysis strategy for discovering signaling molecules and transcription factors for human T-cell exhaustion, a state of T-cell dysfunction, in tumor and mouse dendritic cells activated by pathogens. With more than 226 scRNA-seq datasets precompiled from public repositories covering diverse mouse and human immune cell types in normal and disease tissues, VirtualCytometry is a useful resource for the molecular dissection of immune cell differentiation. Availability and implementation www.grnpedia.org/cytometry

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The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing

Cell Discovery ◽

10.1038/s41421-020-00225-2 ◽

2020 ◽

Vol 6 (1) ◽

Cited By ~ 3

Author(s):

Gang Xu ◽

Furong Qi ◽

Hanjie Li ◽

Qianting Yang ◽

Haiyan Wang ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Single Cell ◽

Rna Sequencing ◽

Mononuclear Cells ◽

Immune Cell ◽

Close Association ◽

T Cell Subsets ◽

Peripheral T Cells ◽

Single Cell Rna Sequencing

Abstract Understanding the mechanism that leads to immune dysfunction in severe coronavirus disease 2019 (COVID-19) is crucial for the development of effective treatment. Here, using single-cell RNA sequencing, we characterized the peripheral blood mononuclear cells (PBMCs) from uninfected controls and COVID-19 patients and cells in paired broncho-alveolar lavage fluid (BALF). We found a close association of decreased dendritic cells (DCs) and increased monocytes resembling myeloid-derived suppressor cells (MDSCs), which correlated with lymphopenia and inflammation in the blood of severe COVID-19 patients. Those MDSC-like monocytes were immune-paralyzed. In contrast, monocyte-macrophages in BALFs of COVID-19 patients produced massive amounts of cytokines and chemokines, but secreted little interferons. The frequencies of peripheral T cells and NK cells were significantly decreased in severe COVID-19 patients, especially for innate-like T and various CD8+ T cell subsets, compared to healthy controls. In contrast, the proportions of various activated CD4+ T cell subsets among the T cell compartment, including Th1, Th2, and Th17-like cells were increased and more clonally expanded in severe COVID-19 patients. Patients’ peripheral T cells showed no sign of exhaustion or augmented cell death, whereas T cells in BALFs produced higher levels of IFNG, TNF, CCL4, CCL5, etc. Paired TCR tracking indicated abundant recruitment of peripheral T cells to the severe patients’ lung. Together, this study comprehensively depicts how the immune cell landscape is perturbed in severe COVID-19.

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Integrative single cell RNA-sequencing descrambles a substantial divergence of adaptive immune cell identities and transcriptional programs in mouse and human atherosclerosis

European Heart Journal ◽

10.1093/eurheartj/ehab724.3411 ◽

2021 ◽

Vol 42 (Supplement_1) ◽

Author(s):

H Horstmann ◽

N Anto Michel ◽

X S Sheng ◽

S Hansen ◽

A Lindau ◽

...

Keyword(s):

T Cell ◽

Single Cell ◽

Rna Sequencing ◽

Immune Cells ◽

Immune Cell ◽

Atherosclerotic Plaques ◽

Cell Repertoire ◽

Single Cell Rna Sequencing ◽

Human Atherosclerosis ◽

Human Immune

Abstract Aims The distinct function of immune cells in human atherosclerosis has been mostly defined by preclinical mouse studies. Contrastingly, the immune cell composition of human atherosclerotic plaques and their contribution to disease progression is only poorly understood. It remains uncertain whether genetic animal models allow for valuable translational approaches. Methods and results We performed single cell RNA-sequencing (scRNAseq) to define the immune cell landscape in human carotid atherosclerotic plaques. The human immune cell repertoire was dominated by T cells with a considerable inter-patient variability and an unexpected heterogeneity. We performed bioinformatical integration with 7 mouse data sets and discovered a total of 38 cellular identities, of which some were not conserved between species and exclusively found in mice or humans. Locations, frequencies, and transcriptional programs of immune cells in preclinical mouse models did not resemble the immune cell landscape in human atherosclerosis. In contrast to mice, human plaques were not myeloid- and B cell-dominated and instead contained several T cell phenotypes with hallmarks of T cell memory, dysregulation, exhaustion, and activation. Human immune cells were predominantly enriched for transcriptional programs of hypoxia, glucose, and autoimmunity. In a validation cohort of 43 patients activated immune cell subsets defined by multi-colour flow cytometry associated with cerebral ischemia and coronary artery disease. Conclusion Here, we uncover yet undefined immune cell types associating with clinical disease. This leukocyte atlas of human atherosclerosis builds the conceptual basis for subsequent identification of cellular targets for clinical immunomodulatory therapies and risk prediction. FUNDunding Acknowledgement Type of funding sources: Public grant(s) – National budget only. Main funding source(s): ERC Starting Grant

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MBRS-46. CHARTING NEOPLASTIC AND IMMUNE CELL HETEROGENEITY IN HUMAN AND GEM MODELS OF MEDULLOBLASTOMA USING scRNAseq

Neuro-Oncology ◽

10.1093/neuonc/noaa222.555 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii406-iii406

Author(s):

Andrew Donson ◽

Kent Riemondy ◽

Sujatha Venkataraman ◽

Ahmed Gilani ◽

Bridget Sanford ◽

...

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Immune Cell ◽

Genetically Engineered ◽

Cellular Heterogeneity ◽

Cell Heterogeneity ◽

Transcriptomic Data ◽

Single Cell Rna Sequencing ◽

Transcript Profiles

Abstract We explored cellular heterogeneity in medulloblastoma using single-cell RNA sequencing (scRNAseq), immunohistochemistry and deconvolution of bulk transcriptomic data. Over 45,000 cells from 31 patients from all main subgroups of medulloblastoma (2 WNT, 10 SHH, 9 GP3, 11 GP4 and 1 GP3/4) were clustered using Harmony alignment to identify conserved subpopulations. Each subgroup contained subpopulations exhibiting mitotic, undifferentiated and neuronal differentiated transcript profiles, corroborating other recent medulloblastoma scRNAseq studies. The magnitude of our present study builds on the findings of existing studies, providing further characterization of conserved neoplastic subpopulations, including identification of a photoreceptor-differentiated subpopulation that was predominantly, but not exclusively, found in GP3 medulloblastoma. Deconvolution of MAGIC transcriptomic cohort data showed that neoplastic subpopulations are associated with major and minor subgroup subdivisions, for example, photoreceptor subpopulation cells are more abundant in GP3-alpha. In both GP3 and GP4, higher proportions of undifferentiated subpopulations is associated with shorter survival and conversely, differentiated subpopulation is associated with longer survival. This scRNAseq dataset also afforded unique insights into the immune landscape of medulloblastoma, and revealed an M2-polarized myeloid subpopulation that was restricted to SHH medulloblastoma. Additionally, we performed scRNAseq on 16,000 cells from genetically engineered mouse (GEM) models of GP3 and SHH medulloblastoma. These models showed a level of fidelity with corresponding human subgroup-specific neoplastic and immune subpopulations. Collectively, our findings advance our understanding of the neoplastic and immune landscape of the main medulloblastoma subgroups in both humans and GEM models.

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Abstract AP29: A SINGLE CELL RNA-SEQUENCING APPROACH TO UNCOVERING HUMAN OVARIAN TUMOR AND IMMUNE CELL HETEROGENEITY, AND THEIR RESPONSE TO MULLERIAN INHIBITING SUBSTANCE USING PATIENT ASCITES SAMPLES

10.1158/1557-3265.ovcasymp18-ap29 ◽

2019 ◽

Author(s):

Raghav Mohan ◽

Motohiro Kano ◽

Hatice Saatcioglu ◽

Nobuhiro Takahashi ◽

LiHua Zhang ◽

...

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Ovarian Tumor ◽

Immune Cell ◽

Cell Heterogeneity ◽

Müllerian Inhibiting Substance ◽

Single Cell Rna Sequencing ◽

Mullerian Inhibiting Substance

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Localization of migraine susceptibility genes in human brain by single-cell RNA sequencing

Cephalalgia ◽

10.1177/0333102418762476 ◽

2018 ◽

Vol 38 (13) ◽

pp. 1976-1983 ◽

Cited By ~ 5

Author(s):

William Renthal

Keyword(s):

Human Brain ◽

Single Cell ◽

Rna Sequencing ◽

Expression Profiles ◽

Cell Types ◽

Susceptibility Genes ◽

Brain Cell ◽

Cell Type ◽

Single Cell Rna Sequencing ◽

Brain Cell Types

Background Migraine is a debilitating disorder characterized by severe headaches and associated neurological symptoms. A key challenge to understanding migraine has been the cellular complexity of the human brain and the multiple cell types implicated in its pathophysiology. The present study leverages recent advances in single-cell transcriptomics to localize the specific human brain cell types in which putative migraine susceptibility genes are expressed. Methods The cell-type specific expression of both familial and common migraine-associated genes was determined bioinformatically using data from 2,039 individual human brain cells across two published single-cell RNA sequencing datasets. Enrichment of migraine-associated genes was determined for each brain cell type. Results Analysis of single-brain cell RNA sequencing data from five major subtypes of cells in the human cortex (neurons, oligodendrocytes, astrocytes, microglia, and endothelial cells) indicates that over 40% of known migraine-associated genes are enriched in the expression profiles of a specific brain cell type. Further analysis of neuronal migraine-associated genes demonstrated that approximately 70% were significantly enriched in inhibitory neurons and 30% in excitatory neurons. Conclusions This study takes the next step in understanding the human brain cell types in which putative migraine susceptibility genes are expressed. Both familial and common migraine may arise from dysfunction of discrete cell types within the neurovascular unit, and localization of the affected cell type(s) in an individual patient may provide insight into to their susceptibility to migraine.

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Exploring the role of the skin microenvironment in cutaneous T-cell lymphoma using single cell RNA-sequencing

European Journal of Cancer ◽

10.1016/s0959-8049(21)00631-6 ◽

2021 ◽

Vol 156 ◽

pp. S3-S4

Author(s):

Gabor Dobos ◽

Andreea Calugareanu ◽

Laurence Michel ◽

Maxime Battistella ◽

Caroline Ram-Wolff ◽

...

Keyword(s):

T Cell ◽

Single Cell ◽

Rna Sequencing ◽

Cell Lymphoma ◽

T Cell Lymphoma ◽

Cutaneous T Cell Lymphoma ◽

Single Cell Rna Sequencing

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Clonal Hematopoiesis-Driver DNMT3A Mutations Alter Immune Cells in Heart Failure

Circulation Research ◽

10.1161/circresaha.120.317104 ◽

2020 ◽

Cited By ~ 1

Author(s):

Wesley T Abplanalp ◽

Sebastian Cremer ◽

David John ◽

Jedrzej Hoffmann ◽

Bianca Schuhmacher ◽

...

Keyword(s):

Heart Failure ◽

T Cell ◽

Chronic Heart Failure ◽

Single Cell ◽

Rna Sequencing ◽

Immune Cells ◽

Driver Mutations ◽

Clonal Hematopoiesis ◽

Mutation Carriers ◽

Single Cell Rna Sequencing

Rationale: Clonal hematopoiesis (CH) driven by mutations of DNA methyltransferase 3a (DNMT3A) is associated with increased incidence of cardiovascular disease and poor prognosis of patients with chronic heart failure (HF) and aortic stenosis. Although experimental studies suggest that DNMT3A CH-driver mutations may enhance inflammation, specific signatures of inflammatory cells in humans are missing. Objective: To define subsets of immune cells mediating inflammation in humans using single-cell RNA-sequencing. Methods and Results: Transcriptomic profiles of peripheral blood mononuclear cells were analysed in N=6 HF patients harboring DNMT3A CH-driver mutations and N=4 patients with HF and no DNMT3A mutations by single-cell RNA-sequencing. Monocytes of HF patients carrying DNMT3A mutations demonstrated a significantly increased expression of inflammatory genes compared to monocytes derived from HF patients without DNMT3A mutations. Among the specific up-regulated genes were the prototypic inflammatory interleukin (IL) IL1B, IL6, IL8, the inflammasome NLRP3, and the macrophage inflammatory proteins CCL3 and CCL4 as well as resistin, which augments monocyte-endothelial adhesion. Silencing of DNMT3A in monocytes induced a paracrine pro-inflammatory activation and increased adhesion to endothelial cells. Furthermore, the classical monocyte subset of DNMT3A mutation carriers showed increased expression of T-cell stimulating immunoglobulin superfamily members CD300LB, CD83, SIGLEC12, as well as the CD2 ligand and cell adhesion molecule CD58, all of which may be involved in monocyte-T cell interactions. DNMT3A mutation carriers were further characterized by increased expression of the T-cell alpha receptor constant chain and Th1, Th2, Th17, CD8+ effector, CD4+ memory and Treg specific signatures. Conclusions: This study demonstrates that circulating monocytes and T-cells of HF patients harboring CH-driver mutations in DNMT3A exhibit a highly inflamed transcriptome, which may contribute to the aggravation of chronic heart failure.

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

Cell Discovery ◽

10.1038/s41421-020-00214-5 ◽

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.

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