Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages

AbstractHow the innate and adaptive host immune system miscommunicate to worsen COVID-19 immunopathology has not been fully elucidated. Here, we perform single-cell deep-immune profiling of bronchoalveolar lavage (BAL) samples from 5 patients with mild and 26 with critical COVID-19 in comparison to BALs from non-COVID-19 pneumonia and normal lung. We use pseudotime inference to build T-cell and monocyte-to-macrophage trajectories and model gene expression changes along them. In mild COVID-19, CD8+ resident-memory (TRM) and CD4+ T-helper-17 (TH17) cells undergo active (presumably antigen-driven) expansion towards the end of the trajectory, and are characterized by good effector functions, while in critical COVID-19 they remain more naïve. Vice versa, CD4+ T-cells with T-helper-1 characteristics (TH1-like) and CD8+ T-cells expressing exhaustion markers (TEX-like) are enriched halfway their trajectories in mild COVID-19, where they also exhibit good effector functions, while in critical COVID-19 they show evidence of inflammation-associated stress at the end of their trajectories. Monocyte-to-macrophage trajectories show that chronic hyperinflammatory monocytes are enriched in critical COVID-19, while alveolar macrophages, otherwise characterized by anti-inflammatory and antigen-presenting characteristics, are depleted. In critical COVID-19, monocytes contribute to an ATP-purinergic signaling-inflammasome footprint that could enable COVID-19 associated fibrosis and worsen disease-severity. Finally, viral RNA-tracking reveals infected lung epithelial cells, and a significant proportion of neutrophils and macrophages that are involved in viral clearance.

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Early Lung Carcinogenesis and Tumor Microenvironment Observed by Single-Cell Transcriptome Analysis

10.21203/rs.3.rs-735382/v1 ◽

2021 ◽

Author(s):

Eun Young Kim ◽

Yoon Jin Cha ◽

Sang Hoon Lee ◽

Sukin Jeong ◽

Young Jun Choi ◽

...

Keyword(s):

Lung Cancer ◽

T Cells ◽

Tumor Microenvironment ◽

Single Cell ◽

Early Stage ◽

Lung Epithelial Cells ◽

Normal Lung ◽

Sequencing Analysis ◽

Lung Carcinogenesis ◽

Early Lung Cancer

Abstract Background: Ground-glass nodules (GGNs) are radiologically defined pulmonary nodules characterized by preserved bronchial and vascular structures in the lung window on chest computed tomography. Lung adenocarcinoma present in the form of persistent GGN is a good model for studying early lung carcinogenesis. We sought to decipher the transcriptome of early lung cancer and its tumor microenvironment from nonsmokers.Methods: Eleven surgical specimens from 6 patients with persistent pure or part-solid GGNs and no smoking or long-term nonsmoking history were obtained and studied by single-cell RNA sequencing analysis.Results: Early lung cancer cells showed enrichment of genes related to small vesicle processing and surfactant homeostasis compared to normal lung epithelial cells, suggesting that the surfactant-related pathway is strongly involved in early lung carcinogenesis. Even in this early stage of lung carcinogenesis, the tumor immune microenvironment was disrupted, with myeloid-derived suppressor cells showing activation of tumor-promoting cytokine pathways, making the tumor microenvironment more permissive for tumor progression and promoting infiltration of regulatory T cells and depletion of CD8+ cytotoxic T cells (TCs) and γδ TCs. Although mucosa-associated lymphoid tissue (MALT) B cells (BCs) and follicular BCs are present in small proportions, they showed increased infiltration in tumor tissues compared to adjacent normal lung tissues. Overexpression of hypoxia-related genes and active suppression of normal angiogenesis were observed in cancer-associated fibroblasts.Conclusions: Changes in the tumor microenvironment that begin very early in lung cancer create an environment prone to immune evasion, suggesting that regulation of such changes is a strategy for inhibiting cancer growth.

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OX40L–OX40 Signaling in Atopic Dermatitis

Journal of Clinical Medicine ◽

10.3390/jcm10122578 ◽

2021 ◽

Vol 10 (12) ◽

pp. 2578

Author(s):

Masutaka Furue ◽

Mihoko Furue

Keyword(s):

T Cells ◽

Atopic Dermatitis ◽

Memory T Cells ◽

Effector Memory ◽

T Helper ◽

T Helper 1 ◽

Therapeutic Success ◽

T Helper 2 ◽

Promising Target ◽

Antigen Presenting

OX40 is one of the co-stimulatory molecules expressed on T cells, and it is engaged by OX40L, primarily expressed on professional antigen-presenting cells such as dendritic cells. The OX40L–OX40 axis is involved in the sustained activation and expansion of effector T and effector memory T cells, but it is not active in naïve and resting memory T cells. Ligation of OX40 by OX40L accelerates both T helper 1 (Th1) and T helper 2 (Th2) effector cell differentiation. Recent therapeutic success in clinical trials highlights the importance of the OX40L–OX40 axis as a promising target for the treatment of atopic dermatitis.

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Development of Autologous, Oligoclonal, Poorly Functioning T Lymphocytes in a Patient With Autosomal Recessive Severe Combined Immunodeficiency Caused by Defects of the Jak3 Tyrosine Kinase

Blood ◽

10.1182/blood.v91.3.949 ◽

1998 ◽

Vol 91 (3) ◽

pp. 949-955 ◽

Cited By ~ 32

Author(s):

Duilio Brugnoni ◽

Luigi D. Notarangelo ◽

Alessandra Sottini ◽

Paolo Airò ◽

Marta Pennacchio ◽

...

Keyword(s):

T Cells ◽

T Lymphocytes ◽

Tyrosine Kinase ◽

Cd4 T Cells ◽

Severe Combined Immunodeficiency ◽

Combined Immunodeficiency ◽

T Helper ◽

T Helper 1 ◽

In Vitro Susceptibility ◽

And Function

Abstract Defects of the common gamma chain subunit of the cytokine receptors (γc) or of Jak3, a tyrosine kinase required for γc signal transduction, result in T−B+ severe combined immunodeficiency (SCID). However, atypical cases, characterized by progressive development of T lymphocytes, have been also reported. We describe a child with SCID caused by Jak3 gene defects, which strongly but not completely affect Jak3 protein expression and function, who developed a substantial number (>3,000/μL) of autologous CD3+CD4+ T cells. These cells showed a primed/activated phenotype (CD45R0+ Fas+HLA-DR+ CD62Llo), defective secretion of T-helper 1 and T-helper 2 cytokines, reduced proliferation to mitogens, and a high in vitro susceptibility to spontaneous (caused by downregulation of bcl-2 expression) as well as activation-induced cell death. A restricted T-cell receptor repertoire was observed, with oligoclonal expansion within each of the dominant segments. These features resemble those observed in γc-/y and in Jak3−/−mice, in which a population of activated, anergic T cells (predominantly CD4+) also develops with age. These results suggest that residual Jak3 expression and function or other Jak3-independent signals may also permit the generation of CD4+ T cells that undergo in vivo clonal expansion in humans; however, these mechanisms do not allow development of CD8+ T cells, nor do they fully restore the functional properties of CD4+ T lymphocytes.

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Proliferation through activation: hemophagocytic lymphohistiocytosis in hematologic malignancy

Blood Advances ◽

10.1182/bloodadvances.2017005561 ◽

2017 ◽

Vol 1 (12) ◽

pp. 779-791 ◽

Cited By ~ 9

Author(s):

Eric J. Vick ◽

Kruti Patel ◽

Philippe Prouet ◽

Mike G. Martin

Keyword(s):

Hemophagocytic Lymphohistiocytosis ◽

Hematologic Malignancy ◽

Lymphocytic Infiltration ◽

Hematologic Malignancies ◽

Interferon Γ ◽

Host Immune System ◽

T Helper ◽

T Helper 1 ◽

Factor Α ◽

Necrosis Factor

AbstractHemophagocytic lymphohistiocytosis (HLH) is a syndrome of cytokine-driven immune activation. Cardinal features include fever, hemophagocytosis, hepatosplenomegaly, lymphocytic infiltration, and hypercytokinemia that result in multisystem organ dysfunction and failure. Familial HLH is genetically driven, whereas secondary HLH (SHL) is caused by drugs, autoimmune disease, infection, or cancer. SHL is associated with worse outcomes, with a median overall survival typically of less than 1 year. This reflects difficulty in both diagnostic accuracy and in establishing reliable treatments, especially in cases of malignancy-induced SHL, which have significantly worse outcomes. Malignancy-induced HLH is seen almost exclusively with hematologic malignancies, constituting 97% of cases in the literature over the past 2 years. In these situations, the native immune response driven by CD8 T cells produces an overabundance of T helper 1 cytokines, notably interferon-γ, tumor necrosis factor-α, and interleukin-6, which establish a positive feedback loop of inflammation, enhancing replication of hematologic malignancies while leaving the host immune system in disarray. In this paper, we present 2 case studies of secondary HLH driven by HM, followed by a review of the literature discussing the cytokines driving HLH, diagnostic criteria, and current treatments used or undergoing investigation.

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CD4+T Cells: Differentiation and Functions

Clinical and Developmental Immunology ◽

10.1155/2012/925135 ◽

2012 ◽

Vol 2012 ◽

pp. 1-12 ◽

Cited By ~ 341

Author(s):

Rishi Vishal Luckheeram ◽

Rui Zhou ◽

Asha Devi Verma ◽

Bing Xia

Keyword(s):

T Cells ◽

Transcription Factors ◽

T Cell ◽

Cytokine Signaling ◽

T Helper ◽

T Helper 1 ◽

T Helper 17 ◽

Differentiated Cells ◽

Follicular Helper ◽

Follicular Helper T Cell

CD4+T cells are crucial in achieving a regulated effective immune response to pathogens. Naive CD4+T cells are activated after interaction with antigen-MHC complex and differentiate into specific subtypes depending mainly on the cytokine milieu of the microenvironment. Besides the classical T-helper 1 and T-helper 2, other subsets have been identified, including T-helper 17, regulatory T cell, follicular helper T cell, and T-helper 9, each with a characteristic cytokine profile. For a particular phenotype to be differentiated, a set of cytokine signaling pathways coupled with activation of lineage-specific transcription factors and epigenetic modifications at appropriate genes are required. The effector functions of these cells are mediated by the cytokines secreted by the differentiated cells. This paper will focus on the cytokine-signaling and the network of transcription factors responsible for the differentiation of naive CD4+T cells.

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Adoptive cell therapy with CD4+ T helper 1 cells and CD8+ cytotoxic T cells enhances complete rejection of an established tumour, leading to generation of endogenous memory responses to non-targeted tumour epitopes

Clinical & Translational Immunology ◽

10.1038/cti.2017.37 ◽

2017 ◽

Vol 6 (10) ◽

pp. e160 ◽

Cited By ~ 6

Author(s):

Kunyu Li ◽

Braeden Donaldson ◽

Vivienne Young ◽

Vernon Ward ◽

Christopher Jackson ◽

...

Keyword(s):

T Cells ◽

Cell Therapy ◽

Cytotoxic T Cells ◽

Adoptive Cell Therapy ◽

T Helper ◽

T Helper 1 ◽

Complete Rejection ◽

T Helper 1 Cells

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Pathogenic Autoimmunity in Atherosclerosis Evolves From Initially Protective Apolipoprotein B 100 –Reactive CD4 + T-Regulatory Cells

Circulation ◽

10.1161/circulationaha.119.042863 ◽

2020 ◽

Vol 142 (13) ◽

pp. 1279-1293 ◽

Cited By ~ 5

Author(s):

Dennis Wolf ◽

Teresa Gerhardt ◽

Holger Winkels ◽

Nathaly Anto Michel ◽

Akula Bala Pramod ◽

...

Keyword(s):

T Cells ◽

Single Cell ◽

Rna Sequencing ◽

Apolipoprotein B ◽

T Helper Cell ◽

Helper Cell ◽

Cell Type ◽

T Helper ◽

Single Cell Rna Sequencing ◽

Helper Cell Type

Background: Throughout the inflammatory response that accompanies atherosclerosis, autoreactive CD4 + T-helper cells accumulate in the atherosclerotic plaque. Apolipoprotein B 100 (apoB), the core protein of low-density lipoprotein, is an autoantigen that drives the generation of pathogenic T-helper type 1 (T H 1) cells with proinflammatory cytokine secretion. Clinical data suggest the existence of apoB-specific CD4 + T cells with an atheroprotective, regulatory T cell (T reg ) phenotype in healthy individuals. Yet, the function of apoB-reactive T regs and their relationship with pathogenic T H 1 cells remain unknown. Methods: To interrogate the function of autoreactive CD4 + T cells in atherosclerosis, we used a novel tetramer of major histocompatibility complex II to track T cells reactive to the mouse self-peptide apo B 978-993 (apoB + ) at the single-cell level. Results: We found that apoB + T cells build an oligoclonal population in lymph nodes of healthy mice that exhibit a T reg -like transcriptome, although only 21% of all apoB + T cells expressed the T reg transcription factor FoxP3 (Forkhead Box P3) protein as detected by flow cytometry. In single-cell RNA sequencing, apoB + T cells formed several clusters with mixed T H signatures that suggested overlapping multilineage phenotypes with pro- and anti-inflammatory transcripts of T H 1, T helper cell type 2 (T H 2), and T helper cell type 17 (T H 17), and of follicular-helper T cells. ApoB + T cells were increased in mice and humans with atherosclerosis and progressively converted into pathogenic T H 1/T H 17-like cells with proinflammatory properties and only a residual T reg transcriptome. Plaque T cells that expanded during progression of atherosclerosis consistently showed a mixed T H 1/T H 17 phenotype in single-cell RNA sequencing. In addition, we observed a loss of FoxP3 in a fraction of apoB + T regs in lineage tracing of hyperlipidemic Apoe –/– mice. In adoptive transfer experiments, converting apoB + T regs failed to protect from atherosclerosis. Conclusions: Our results demonstrate an unexpected mixed phenotype of apoB-reactive autoimmune T cells in atherosclerosis and suggest an initially protective autoimmune response against apoB with a progressive derangement in clinical disease. These findings identify apoB autoreactive T regs as a novel cellular target in atherosclerosis.

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Heterogeneity of T Cells in Atherosclerosis Defined by Single-Cell RNA-Sequencing and Cytometry by Time of Flight

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvbaha.120.312137 ◽

2020 ◽

Author(s):

Holger Winkels ◽

Dennis Wolf

Keyword(s):

T Cells ◽

T Cell ◽

Single Cell ◽

Rna Sequencing ◽

T Regulatory Cells ◽

Foam Cell ◽

Regulatory Cells ◽

T Helper ◽

Antigen Specificity ◽

Single Cell Rna Sequencing

The infiltration and accumulation of pro- and anti-inflammatory leukocytes within the intimal layer of the arterial wall is a hallmark of developing and progressing atherosclerosis. While traditionally perceived as macrophage- and foam cell-dominated disease, it is now established that atherosclerosis is a partial autoimmune disease that involves the recognition of peptides from ApoB (apolipoprotein B), the core protein of LDL (low-density lipoprotein) cholesterol particles, by CD4 + T-helper cells and autoantibodies against LDL and ApoB. Autoimmunity in the atherosclerotic plaque has long been understood as a pathogenic T-helper type-1 driven response with proinflammatory cytokine secretion. Recent developments in high-parametric cell immunophenotyping by mass cytometry, single-cell RNA-sequencing, and in tools exploring antigen-specificity have established the existence of several unforeseen layers of T cell diversity with mixed T H 1 and T regulatory cells transcriptional programs and unpredicted fates. These findings suggest that pathogenic ApoB-reactive T cells evolve from atheroprotective and immunosuppressive CD4 + T regulatory cells that lose their protective properties over time. Here, we discuss T cell heterogeneity in atherosclerosis with a focus on plasticity, antigen-specificity, exhaustion, maturation, tissue residency, and its potential use in clinical prediction.

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