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1.
Viruses ; 14(1)2021 12 28.
Article in English | MEDLINE | ID: covidwho-1715736

ABSTRACT

Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) infection induces elevated levels of inflammatory cytokines, which are mainly produced by the innate response to the virus. The role of NK cells, which are potent producers of IFN-γ and cytotoxicity, has not been sufficiently studied in the setting of SARS-CoV-2 infection. We confirmed a different distribution of NK cell subsets in hospitalized COVID-19 patients despite their NK cell deficiency. The impairment of this innate defense is mainly focused on the cytotoxic capacity of the CD56dim NK cells. On the one hand, we found an expansion of the CD56dimCD16neg NK subset, lower cytotoxic capacities, and high frequencies of inhibitory 2DL1 and 2DL1/S1 KIR receptors in COVID-19 patients. On the other hand, the depletion of CD56dimCD16dim/bright NK cell subsets, high cytotoxic capacities, and high frequencies of inhibitory 2DL1 KIR receptors were found in COVID-19 patients. In contrast, no differences in the distribution of CD56bright NK cell subsets were found in this study. These alterations in the distribution and phenotype of NK cells might enhance the impairment of this crucial innate line of defense during COVID-19 infection.


Subject(s)
COVID-19/immunology , Killer Cells, Natural/metabolism , Lymphocyte Subsets/metabolism , Receptors, KIR/metabolism , Aged , CD56 Antigen/metabolism , COVID-19/blood , Female , GPI-Linked Proteins/metabolism , Hospitalization , Humans , Inflammation , Male , Middle Aged , Receptors, IgG/metabolism , SARS-CoV-2
2.
Genome Med ; 14(1): 16, 2022 02 17.
Article in English | MEDLINE | ID: covidwho-1690882

ABSTRACT

BACKGROUND: Understanding the host genetic architecture and viral immunity contributes to the development of effective vaccines and therapeutics for controlling the COVID-19 pandemic. Alterations of immune responses in peripheral blood mononuclear cells play a crucial role in the detrimental progression of COVID-19. However, the effects of host genetic factors on immune responses for severe COVID-19 remain largely unknown. METHODS: We constructed a computational framework to characterize the host genetics that influence immune cell subpopulations for severe COVID-19 by integrating GWAS summary statistics (N = 969,689 samples) with four independent scRNA-seq datasets containing healthy controls and patients with mild, moderate, and severe symptom (N = 606,534 cells). We collected 10 predefined gene sets including inflammatory and cytokine genes to calculate cell state score for evaluating the immunological features of individual immune cells. RESULTS: We found that 34 risk genes were significantly associated with severe COVID-19, and the number of highly expressed genes increased with the severity of COVID-19. Three cell subtypes that are CD16+monocytes, megakaryocytes, and memory CD8+T cells were significantly enriched by COVID-19-related genetic association signals. Notably, three causal risk genes of CCR1, CXCR6, and ABO were highly expressed in these three cell types, respectively. CCR1+CD16+monocytes and ABO+ megakaryocytes with significantly up-regulated genes, including S100A12, S100A8, S100A9, and IFITM1, confer higher risk to the dysregulated immune response among severe patients. CXCR6+ memory CD8+ T cells exhibit a notable polyfunctionality including elevation of proliferation, migration, and chemotaxis. Moreover, we observed an increase in cell-cell interactions of both CCR1+ CD16+monocytes and CXCR6+ memory CD8+T cells in severe patients compared to normal controls among both PBMCs and lung tissues. The enhanced interactions of CXCR6+ memory CD8+T cells with epithelial cells facilitate the recruitment of this specific population of T cells to airways, promoting CD8+T cell-mediated immunity against COVID-19 infection. CONCLUSIONS: We uncover a major genetics-modulated immunological shift between mild and severe infection, including an elevated expression of genetics-risk genes, increase in inflammatory cytokines, and of functional immune cell subsets aggravating disease severity, which provides novel insights into parsing the host genetic determinants that influence peripheral immune cells in severe COVID-19.


Subject(s)
CD8-Positive T-Lymphocytes/virology , COVID-19/genetics , COVID-19/pathology , Monocytes/virology , Single-Cell Analysis/methods , COVID-19/immunology , Computational Biology/methods , GPI-Linked Proteins/metabolism , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Megakaryocyte Progenitor Cells/immunology , Megakaryocyte Progenitor Cells/virology , Monocytes/metabolism , Quantitative Trait Loci , Receptors, CCR1/immunology , Receptors, CCR1/metabolism , Receptors, CXCR6/immunology , Receptors, CXCR6/metabolism , Receptors, IgG/metabolism , Sequence Analysis, RNA , Severity of Illness Index
3.
Sci Adv ; 8(5): eabl8920, 2022 02 04.
Article in English | MEDLINE | ID: covidwho-1673337

ABSTRACT

Dexamethasone is widely used as an immunosuppressive therapy and recently as COVID-19 treatment. Here, we demonstrate that dexamethasone sensitizes to ferroptosis, a form of iron-catalyzed necrosis, previously suggested to contribute to diseases such as acute kidney injury, myocardial infarction, and stroke, all of which are triggered by glutathione (GSH) depletion. GSH levels were significantly decreased by dexamethasone. Mechanistically, we identified that dexamethasone up-regulated the GSH metabolism regulating protein dipeptidase-1 (DPEP1) in a glucocorticoid receptor (GR)-dependent manner. DPEP1 knockdown reversed the phenotype of dexamethasone-induced ferroptosis sensitization. Ferroptosis inhibitors, the DPEP1 inhibitor cilastatin, or genetic DPEP1 inactivation reversed the dexamethasone-induced increase in tubular necrosis in freshly isolated renal tubules. Our data indicate that dexamethasone sensitizes to ferroptosis by a GR-mediated increase in DPEP1 expression and GSH depletion. Together, we identified a previously unknown mechanism of glucocorticoid-mediated sensitization to ferroptosis bearing clinical and therapeutic implications.


Subject(s)
Dexamethasone/pharmacology , Dipeptidases/genetics , Ferroptosis/drug effects , Ferroptosis/genetics , Gene Expression Regulation/drug effects , Glutathione/metabolism , Receptors, Glucocorticoid/metabolism , Carbolines/adverse effects , Carbolines/pharmacology , Cell Line , Dipeptidases/metabolism , Fluorescent Antibody Technique , GPI-Linked Proteins/genetics , GPI-Linked Proteins/metabolism , Gene Knockdown Techniques , Humans , Immunophenotyping , Oxidation-Reduction/drug effects , Piperazines/adverse effects , Piperazines/pharmacology
4.
Front Immunol ; 12: 799558, 2021.
Article in English | MEDLINE | ID: covidwho-1662582

ABSTRACT

The poor outcome of the coronavirus disease-2019 (COVID-19), caused by SARS-CoV-2, is associated with systemic hyperinflammatory response and immunopathology. Although inflammasome and oxidative stress have independently been implicated in COVID-19, it is poorly understood whether these two pathways cooperatively contribute to disease severity. Herein, we found an enrichment of CD14highCD16- monocytes displaying inflammasome activation evidenced by caspase-1/ASC-speck formation in severe COVID-19 patients when compared to mild ones and healthy controls, respectively. Those cells also showed aberrant levels of mitochondrial superoxide and lipid peroxidation, both hallmarks of the oxidative stress response, which strongly correlated with caspase-1 activity. In addition, we found that NLRP3 inflammasome-derived IL-1ß secretion by SARS-CoV-2-exposed monocytes in vitro was partially dependent on lipid peroxidation. Importantly, altered inflammasome and stress responses persisted after short-term patient recovery. Collectively, our findings suggest oxidative stress/NLRP3 signaling pathway as a potential target for host-directed therapy to mitigate early COVID-19 hyperinflammation and also its long-term outcomes.


Subject(s)
COVID-19/metabolism , Inflammasomes/metabolism , Lipopolysaccharide Receptors/metabolism , Monocytes/metabolism , Oxidative Stress/physiology , Receptors, IgG/metabolism , Aged , COVID-19/pathology , Caspase 1/metabolism , Female , GPI-Linked Proteins/metabolism , Humans , Interleukin-1beta/metabolism , Male , Middle Aged , Mitochondria/metabolism , Mitochondria/pathology , Monocytes/pathology , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , SARS-CoV-2/metabolism , Signal Transduction/physiology
5.
ChemistryOpen ; 10(11): 1133-1141, 2021 11.
Article in English | MEDLINE | ID: covidwho-1520270

ABSTRACT

We present in this work a first X-ray Absorption Spectroscopy study of the interactions of Zn with human BST2/tetherin and SARS-CoV-2 orf7a proteins as well as with some of their complexes. The analysis of the XANES region of the measured spectra shows that Zn binds to BST2, as well as to orf7a, thus resulting in the formation of BST2-orf7a complexes. This structural information confirms the the conjecture, recently put forward by some of the present Authors, according to which the accessory orf7a (and possibly also orf8) viral protein are capable of interfering with the BST2 antiviral activity. Our explanation for this behavior is that, when BST2 gets in contact with Zn bound to the orf7a Cys15 ligand, it has the ability of displacing the metal owing to the creation of a new disulfide bridge across the two proteins. The formation of this BST2-orf7a complex destabilizes BST2 dimerization, thus impairing the antiviral activity of the latter.


Subject(s)
Antigens, CD/metabolism , SARS-CoV-2/chemistry , Viral Proteins/metabolism , Zinc/metabolism , Cysteine/chemistry , GPI-Linked Proteins/metabolism , Histidine/chemistry , Humans , Molecular Dynamics Simulation , Protein Binding , X-Ray Absorption Spectroscopy
6.
Dis Markers ; 2021: 5566826, 2021.
Article in English | MEDLINE | ID: covidwho-1341351

ABSTRACT

An excess formation of neutrophil extracellular traps (NETs), previously shown to be strongly associated with cytokine storm and acute respiratory distress syndrome (ARDS) with prevalent endothelial dysfunction and thrombosis, has been postulated to be a central factor influencing the pathophysiology and clinical presentation of severe COVID-19. A growing number of serological and morphological evidence has added to this assumption, also in regard to potential treatment options. In this study, we used immunohistochemistry and histochemistry to trace NETs and their molecular markers in autopsy lung tissue from seven COVID-19 patients. Quantification of key immunomorphological features enabled comparison with non-COVID-19 diffuse alveolar damage. Our results strengthen and extend recent findings, confirming that NETs are abundantly present in seriously damaged COVID-19 lung tissue, especially in association with microthrombi of the alveolar capillaries. In addition, we provide evidence that low-density neutrophils (LDNs), which are especially prone to NETosis, contribute substantially to COVID-19-associated lung damage in general and vascular blockages in particular.


Subject(s)
COVID-19/pathology , Extracellular Traps , Lung Injury/pathology , Neutrophils/pathology , Aged , Aged, 80 and over , Antigens, CD/metabolism , Autopsy , Cell Adhesion Molecules/metabolism , Extracellular Traps/virology , Female , GPI-Linked Proteins/metabolism , Humans , Immunohistochemistry , Lung/pathology , Lung/virology , Lung Injury/virology , Male , Neutrophils/metabolism , Neutrophils/virology , Peroxidase/metabolism
7.
Front Immunol ; 12: 665773, 2021.
Article in English | MEDLINE | ID: covidwho-1264333

ABSTRACT

The COVID-19 pandemic has caused more than three million deaths globally. The severity of the disease is characterized, in part, by a dysregulated immune response. CD16+ monocytes are innate immune cells involved in inflammatory responses to viral infections, and tissue repair, among other functions. We characterized the transcriptional changes in CD16+ monocytes from PBMC of people with COVID-19, and from healthy individuals using publicly available single cell RNA sequencing data. CD16+ monocytes from people with COVID-19 compared to those from healthy individuals expressed transcriptional changes indicative of increased cell activation, and induction of a migratory phenotype. We also analyzed COVID-19 cases based on severity of the disease and found that mild cases were characterized by upregulation of interferon response and MHC class II related genes, whereas the severe cases had dysregulated expression of mitochondrial and antigen presentation genes, and upregulated inflammatory, cell movement, and apoptotic gene signatures. These results suggest that CD16+ monocytes in people with COVID-19 contribute to a dysregulated host response characterized by decreased antigen presentation, and an elevated inflammatory response with increased monocytic infiltration into tissues. Our results show that there are transcriptomic changes in CD16+ monocytes that may impact the functions of these cells, contributing to the pathogenesis and severity of COVID-19.


Subject(s)
COVID-19/virology , Monocytes/virology , Receptors, IgG/metabolism , SARS-CoV-2/pathogenicity , Transcription, Genetic , Transcriptome , Adult , Aged , Apoptosis Regulatory Proteins/genetics , Apoptosis Regulatory Proteins/metabolism , COVID-19/genetics , COVID-19/immunology , COVID-19/metabolism , Case-Control Studies , Cytokines/genetics , Cytokines/metabolism , Female , GPI-Linked Proteins/metabolism , Gene Expression Profiling , Host-Pathogen Interactions , Humans , Inflammation Mediators/metabolism , Interferon Regulatory Factors/genetics , Interferon Regulatory Factors/metabolism , Male , Middle Aged , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Monocytes/immunology , Monocytes/metabolism , RNA-Seq , SARS-CoV-2/immunology , Severity of Illness Index , Single-Cell Analysis , Young Adult
8.
IUBMB Life ; 73(6): 843-854, 2021 06.
Article in English | MEDLINE | ID: covidwho-1219298

ABSTRACT

The 78 kDa glucose-regulated protein (GRP78) is an endoplasmic reticulum (ER)-resident molecular chaperone. GRP78 is a member of the 70 kDa heat shock family of proteins involved in correcting and clearing misfolded proteins in the ER. In response to cellular stress, GRP78 escapes from the ER and moves to the plasma membrane where it (a) functions as a receptor for many ligands, and (b) behaves as an autoantigen for autoantibodies that contribute to human disease and cancer. Cell surface GRP78 (csGRP78) associates with the major histocompatibility complex class I (MHC-I), and is the port of entry for several viruses, including the predictive binding of the novel SARS-CoV-2. Furthermore, csGRP78 is found in association with partners as diverse as the teratocarcinoma-derived growth factor 1 (Cripto), the melanocortin-4 receptor (MC4R) and the DnaJ-like protein MTJ-1. CsGRP78 also serves as a receptor for a large variety of ligands including activated α2 -macroglobulin (α2 M*), plasminogen kringle 5 (K5), microplasminogen, the voltage-dependent anion channel (VDAC), tissue factor (TF), and the prostate apoptosis response-4 protein (Par-4). In this review, we discuss the mechanisms involved in the translocation of GRP78 from the ER to the cell surface, and the role of secreted GRP78 and its autoantibodies in cancer and neurological disorders.


Subject(s)
Autoimmune Diseases of the Nervous System/immunology , COVID-19/transmission , Heat-Shock Proteins/physiology , Neoplasm Proteins/physiology , Nerve Tissue Proteins/physiology , Receptors, Cell Surface/physiology , Receptors, Virus/physiology , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Autoantibodies/immunology , Autoantigens/immunology , Autoimmune Diseases of the Nervous System/metabolism , Cell Survival , Endoplasmic Reticulum Stress/physiology , Exosomes , GPI-Linked Proteins/metabolism , Heat-Shock Proteins/chemistry , Heat-Shock Proteins/immunology , Humans , Ligands , Neoplasm Invasiveness , Neoplasm Proteins/immunology , Nerve Tissue Proteins/immunology , Protein Domains , Protein Transport , Signal Transduction , Tumor Microenvironment , Unfolded Protein Response/physiology , Virus Internalization
9.
Front Immunol ; 12: 651656, 2021.
Article in English | MEDLINE | ID: covidwho-1211812

ABSTRACT

Although immune dysfunction is a key feature of coronavirus disease 2019 (COVID-19), the metabolism-related mechanisms remain elusive. Here, by reanalyzing single-cell RNA sequencing data, we delineated metabolic remodeling in peripheral blood mononuclear cells (PBMCs) to elucidate the metabolic mechanisms that may lead to the progression of severe COVID-19. After scoring the metabolism-related biological processes and signaling pathways, we found that mono-CD14+ cells expressed higher levels of glycolysis-related genes (PKM, LDHA and PKM) and PPP-related genes (PGD and TKT) in severe patients than in mild patients. These genes may contribute to the hyperinflammation in mono-CD14+ cells of patients with severe COVID-19. The mono-CD16+ cell population in COVID-19 patients showed reduced transcription levels of genes related to lysine degradation (NSD1, KMT2E, and SETD2) and elevated transcription levels of genes involved in OXPHOS (ATP6V1B2, ATP5A1, ATP5E, and ATP5B), which may inhibit M2-like polarization. Plasma cells also expressed higher levels of the OXPHOS gene ATP13A3 in COVID-19 patients, which was positively associated with antibody secretion and survival of PCs. Moreover, enhanced glycolysis or OXPHOS was positively associated with the differentiation of memory B cells into plasmablasts or plasma cells. This study comprehensively investigated the metabolic features of peripheral immune cells and revealed that metabolic changes exacerbated inflammation in monocytes and promoted antibody secretion and cell survival in PCs in COVID-19 patients, especially those with severe disease.


Subject(s)
COVID-19/immunology , Glycolysis/genetics , Lysine/metabolism , Monocytes/metabolism , Single-Cell Analysis/methods , Adenosine Triphosphatases/blood , Adenosine Triphosphatases/genetics , Antibodies/metabolism , COVID-19/metabolism , COVID-19/physiopathology , Databases, Genetic , GPI-Linked Proteins/metabolism , Gene Ontology , Hematopoiesis/genetics , Humans , Inflammation/genetics , Inflammation/immunology , Inflammation/metabolism , Leukocytes, Mononuclear/immunology , Leukocytes, Mononuclear/metabolism , Leukocytes, Mononuclear/pathology , Lipopolysaccharide Receptors/metabolism , Lysine/genetics , Membrane Transport Proteins/blood , Membrane Transport Proteins/genetics , Metabolic Networks and Pathways/genetics , Metabolic Networks and Pathways/physiology , Monocytes/immunology , Monocytes/pathology , Oxidative Phosphorylation , RNA-Seq , Receptors, IgG/metabolism , Signal Transduction/genetics , Signal Transduction/immunology , Transcriptome/genetics
10.
Med Hypotheses ; 144: 110012, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-997289

ABSTRACT

The most serious health issue today is the rapid outbreak of Coronavirus Disease 2019 (COVID-19). More than 6,973,427 confirmed cases were diagnosed in nearly 213 countries and territories around the world and two international conveyances, causing globally over 400,000 deaths. Epidemiology, risk factors, and clinical characteristics of COVID-19 patients have been identified, but the factors influencing the immune system against COVID-19 have not been well established. Upon infection or cell damage, high amounts of adenosine triphosphate (ATP) are released from damaged cells, which serve as mediators of inflammation through purinergic cell surface receptor signaling. As a protective mechanism to prevent excessive damage to host tissue, adenosine counteracts ATP's effects by adenosine receptor stimulation to suppress the pro-inflammatory response. Adenosine is seen as a major obstacle to the efficacy of immune therapies, and the adenosinergic axis components are critical therapeutic targets for cancer and microbial infections. Pharmacologic inhibitors or antibodies specific to adenosinergic pathway components or adenosine receptors in microbial and tumor therapy have shown efficacy in pre-clinical studies and are entering the clinical arena. In this review, we provide a novel hypothesis explaining the potential for improving the efficiency of innate and adaptive immune systems by targeting adenosinergic pathway components and adenosine A2A receptor signaling for the treatment of COVID-19.


Subject(s)
Adenosine A2 Receptor Antagonists/therapeutic use , COVID-19/drug therapy , Pandemics , Receptor, Adenosine A2A/physiology , 5'-Nucleotidase/metabolism , Adaptive Immunity/drug effects , Adenosine A2 Receptor Antagonists/pharmacology , Adenosine Triphosphate/metabolism , Apyrase/metabolism , COVID-19/epidemiology , COVID-19/immunology , COVID-19/metabolism , GPI-Linked Proteins/metabolism , Humans , Immunity, Innate/drug effects , Interferon-beta/physiology , Models, Immunological , Molecular Targeted Therapy , SARS Virus/immunology , SARS-CoV-2/immunology , Signal Transduction/drug effects , Virus Replication/drug effects
11.
Front Immunol ; 11: 580250, 2020.
Article in English | MEDLINE | ID: covidwho-918140

ABSTRACT

Little is known about the time-dependent immune responses in severe COVID-19. Data of 15 consecutive patients were sequentially recorded from intensive care unit admission. Lymphocyte subsets and total monocyte and subsets counts were monitored as well as the expression of HLA-DR. For 5 patients, SARS-CoV-2-specific T-cell polyfunctionality was assessed against Spike and Nucleoprotein SARS-CoV-2 peptides. Non-specific inflammation markers were increased in all patients. Median monocyte HLA-DR expression was below the 8,000 AB/C threshold defining acquired immunodepression. A "V" trend curve for lymphopenia, monocyte numbers, and HLA-DR expression was observed with a nadir between days 11 and 14 after symptoms' onset. Intermediate CD14++CD16+ monocytes increased early with a reduction in classic CD14++CD16- monocytes. Polyfunctional SARS-Cov-2-specific CD4 T-cells were present and functional, whereas virus-specific CD8 T-cells were less frequent and not efficient. We report a temporal variation of both innate and adaptive immunity in severe COVID-19 patients, helpful in guiding therapeutic decisions (e.g. anti-inflammatory vs. immunostimulatory ones). We describe a defect in virus-specific CD8 T-cells, a potential biomarker of clinical severity. These combined data also provide helpful knowledge for vaccine design. CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/, identifier NCT04386395.


Subject(s)
CD4-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , COVID-19/immunology , Monocytes/immunology , SARS-CoV-2/immunology , Severity of Illness Index , Aged , Biomarkers , COVID-19/virology , Female , GPI-Linked Proteins/metabolism , HLA-DR Antigens/immunology , Humans , Immunity, Cellular , Lipopolysaccharide Receptors/metabolism , Longitudinal Studies , Male , Middle Aged , Prospective Studies , Receptors, IgG/metabolism , SARS-CoV-2/genetics
12.
Nat Immunol ; 21(9): 1107-1118, 2020 09.
Article in English | MEDLINE | ID: covidwho-710376

ABSTRACT

In coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the relationship between disease severity and the host immune response is not fully understood. Here we performed single-cell RNA sequencing in peripheral blood samples of 5 healthy donors and 13 patients with COVID-19, including moderate, severe and convalescent cases. Through determining the transcriptional profiles of immune cells, coupled with assembled T cell receptor and B cell receptor sequences, we analyzed the functional properties of immune cells. Most cell types in patients with COVID-19 showed a strong interferon-α response and an overall acute inflammatory response. Moreover, intensive expansion of highly cytotoxic effector T cell subsets, such as CD4+ effector-GNLY (granulysin), CD8+ effector-GNLY and NKT CD160, was associated with convalescence in moderate patients. In severe patients, the immune landscape featured a deranged interferon response, profound immune exhaustion with skewed T cell receptor repertoire and broad T cell expansion. These findings illustrate the dynamic nature of immune responses during disease progression.


Subject(s)
Antigens, CD/metabolism , Antigens, Differentiation, T-Lymphocyte/metabolism , Betacoronavirus/immunology , Coronavirus Infections/immunology , Interferon Type I/metabolism , Pneumonia, Viral/immunology , Receptors, Immunologic/metabolism , Adolescent , Adult , Aged , Antigens, CD/genetics , Antigens, CD/immunology , Antigens, Differentiation, T-Lymphocyte/genetics , Antigens, Differentiation, T-Lymphocyte/immunology , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/metabolism , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , COVID-19 , Cohort Studies , Coronavirus Infections/blood , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Female , GPI-Linked Proteins/genetics , GPI-Linked Proteins/immunology , GPI-Linked Proteins/metabolism , Humans , Interferon Type I/genetics , Interferon Type I/immunology , Killer Cells, Natural/immunology , Killer Cells, Natural/metabolism , Male , Middle Aged , Pandemics , Pneumonia, Viral/blood , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , RNA-Seq , Receptors, Immunologic/genetics , Receptors, Immunologic/immunology , SARS-CoV-2 , Severity of Illness Index , Single-Cell Analysis
13.
Exp Cell Res ; 395(2): 112204, 2020 10 15.
Article in English | MEDLINE | ID: covidwho-680000

ABSTRACT

BACKGROUND: SARS-CoV2, the agent responsible for the current pandemic, is also causing respiratory distress syndrome (RDS), hyperinflammation and high mortality. It is critical to dissect the pathogenetic mechanisms in order to reach a targeted therapeutic approach. METHODS: In the present investigation, we evaluated the effects of SARS-CoV2 on human bronchial epithelial cells (HBEC). We used RNA-seq datasets available online for identifying SARS-CoV2 potential genes target on human bronchial epithelial cells. RNA expression levels and potential cellular gene pathways have been analyzed. In order to identify possible common strategies among the main pandemic viruses, such as SARS-CoV2, SARS-CoV1, MERS-CoV, and H1N1, we carried out a hypergeometric test of the main genes transcribed in the cells of the respiratory tract exposed to these viruses. RESULTS: The analysis showed that two mechanisms are highly regulated in HBEC: the innate immunity recruitment and the disassembly of cilia and cytoskeletal structure. The granulocyte colony-stimulating factor (CSF3) and dynein heavy chain 7, axonemal (DNAH7) represented respectively the most upregulated and downregulated genes belonging to the two mechanisms highlighted above. Furthermore, the carcinoembryonic antigen-related cell adhesion molecule 7 (CEACAM7) that codifies for a surface protein is highly specific of SARS-CoV2 and not for SARS-CoV1, MERS-CoV, and H1N1, suggesting a potential role in viral entry. In order to identify potential new drugs, using a machine learning approach, we highlighted Flunisolide, Thalidomide, Lenalidomide, Desoximetasone, xylazine, and salmeterol as potential drugs against SARS-CoV2 infection. CONCLUSIONS: Overall, lung involvement and RDS could be generated by the activation and down regulation of diverse gene pathway involving respiratory cilia and muscle contraction, apoptotic phenomena, matrix destructuration, collagen deposition, neutrophil and macrophages recruitment.


Subject(s)
Bronchi/metabolism , Coronavirus Infections/genetics , Gene Regulatory Networks , Pneumonia, Viral/genetics , Respiratory Mucosa/metabolism , Transcriptome , Bronchi/pathology , COVID-19 , Carcinoembryonic Antigen/genetics , Carcinoembryonic Antigen/metabolism , Coronavirus Infections/metabolism , Drug Discovery/methods , Dyneins/genetics , Dyneins/metabolism , GPI-Linked Proteins/genetics , GPI-Linked Proteins/metabolism , Granulocyte Colony-Stimulating Factor/genetics , Granulocyte Colony-Stimulating Factor/metabolism , Humans , Immunity, Innate , Machine Learning , Pandemics , Pneumonia, Viral/metabolism , Up-Regulation
14.
Nat Microbiol ; 5(11): 1330-1339, 2020 11.
Article in English | MEDLINE | ID: covidwho-676586

ABSTRACT

Zoonotic coronaviruses (CoVs) are substantial threats to global health, as exemplified by the emergence of two severe acute respiratory syndrome CoVs (SARS-CoV and SARS-CoV-2) and Middle East respiratory syndrome CoV (MERS-CoV) within two decades1-3. Host immune responses to CoVs are complex and regulated in part through antiviral interferons. However, interferon-stimulated gene products that inhibit CoVs are not well characterized4. Here, we show that lymphocyte antigen 6 complex, locus E (LY6E) potently restricts infection by multiple CoVs, including SARS-CoV, SARS-CoV-2 and MERS-CoV. Mechanistic studies revealed that LY6E inhibits CoV entry into cells by interfering with spike protein-mediated membrane fusion. Importantly, mice lacking Ly6e in immune cells were highly susceptible to a murine CoV-mouse hepatitis virus. Exacerbated viral pathogenesis in Ly6e knockout mice was accompanied by loss of hepatic immune cells, higher splenic viral burden and reduction in global antiviral gene pathways. Accordingly, we found that constitutive Ly6e directly protects primary B cells from murine CoV infection. Our results show that LY6E is a critical antiviral immune effector that controls CoV infection and pathogenesis. These findings advance our understanding of immune-mediated control of CoV in vitro and in vivo-knowledge that could help inform strategies to combat infection by emerging CoVs.


Subject(s)
Antigens, Surface/metabolism , Coronavirus Infections/immunology , Coronavirus Infections/virology , Coronavirus/physiology , GPI-Linked Proteins/metabolism , Angiotensin-Converting Enzyme 2 , Animals , Antigens, Surface/genetics , Antigens, Surface/immunology , Betacoronavirus/immunology , Betacoronavirus/physiology , COVID-19 , Coronavirus/immunology , Female , GPI-Linked Proteins/genetics , GPI-Linked Proteins/immunology , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Middle East Respiratory Syndrome Coronavirus/immunology , Middle East Respiratory Syndrome Coronavirus/physiology , Pandemics , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , SARS Virus/immunology , SARS Virus/physiology , SARS-CoV-2 , Virus Internalization
15.
Cells ; 9(8)2020 07 22.
Article in English | MEDLINE | ID: covidwho-669617

ABSTRACT

The ectonucleotidases CD39 and CD73 regulate immune responses by balancing extracellular ATP and adenosine in inflammation and are likely to be involved in the pathophysiology of COVID-19. Here, we analyzed CD39 and CD73 on different lymphocyte populations in a small cohort of COVID-19 patients and in healthy individuals. We describe a significantly lower level of expression of CD73 on cytotoxic lymphocyte populations, including CD8+ T, natural killer T (NKT), and natural killer (NK) cells, during COVID-19. Interestingly, the decrease of CD73 on CD8+ T cells and NKT cells correlated with serum ferritin levels. Furthermore, we observed distinct functional differences between the CD73+ and CD73- subsets of CD8+ T cells and NKT cells with regard to cytokine/toxin secretion. In COVID-19 patients, the majority of the CD73-CD8+ T cells were capable of secreting granzyme B, perforin, tumor necrosis factor (TNF-α) or interferon-gamma (IFN-γ). To conclude, in this first study of CD39 and CD73 expression of lymphocytes in COVID-19, we show that CD8+ T cells and NKT cells lacking CD73 possess a significantly higher cytotoxic effector functionality compared to their CD73+ counterparts. Future studies should investigate differences of cellular CD39 and CD73 expression in patients at different disease stages and their potential as prognostic markers or targets for immunomodulatory therapies.


Subject(s)
5'-Nucleotidase/metabolism , Apyrase/metabolism , Coronavirus Infections/immunology , Killer Cells, Natural/immunology , Natural Killer T-Cells/immunology , Pneumonia, Viral/immunology , T-Lymphocytes, Cytotoxic/immunology , Adenosine/metabolism , Adult , Aged , Betacoronavirus , COVID-19 , Coronavirus Infections/enzymology , Female , GPI-Linked Proteins/metabolism , Granzymes/metabolism , Humans , Inflammation/enzymology , Inflammation/immunology , Interferon-gamma/metabolism , Male , Middle Aged , Pandemics , Perforin/metabolism , Pneumonia, Viral/enzymology , SARS-CoV-2 , Signal Transduction/immunology , T-Lymphocytes, Cytotoxic/metabolism , Tumor Necrosis Factor-alpha/metabolism
16.
J Virol ; 94(18)2020 08 31.
Article in English | MEDLINE | ID: covidwho-639615

ABSTRACT

C3A is a subclone of the human hepatoblastoma HepG2 cell line with strong contact inhibition of growth. We fortuitously found that C3A was more susceptible to human coronavirus HCoV-OC43 infection than HepG2, which was attributed to the increased efficiency of virus entry into C3A cells. In an effort to search for the host cellular protein(s) mediating the differential susceptibility of the two cell lines to HCoV-OC43 infection, we found that ArfGAP with dual pleckstrin homology (PH) domains 2 (ADAP2), gamma-interferon-inducible lysosome/endosome-localized thiolreductase (GILT), and lymphocyte antigen 6 family member E (LY6E), the three cellular proteins identified to function in interference with virus entry, were expressed at significantly higher levels in HepG2 cells. Functional analyses revealed that ectopic expression of LY6E, but not GILT or ADAP2, in HEK 293 cells inhibited the entry of HCoV-O43. While overexpression of LY6E in C3A and A549 cells efficiently inhibited the infection of HCoV-OC43, knockdown of LY6E expression in HepG2 significantly increased its susceptibility to HCoV-OC43 infection. Moreover, we found that LY6E also efficiently restricted the entry mediated by the envelope spike proteins of other human coronaviruses, including the currently pandemic SARS-CoV-2. Interestingly, overexpression of serine protease TMPRSS2 or amphotericin treatment significantly neutralized the IFN-inducible transmembrane 3 (IFITM3) restriction of human coronavirus (CoV) entry, but did not compromise the effect of LY6E on the entry of human coronaviruses. The work reported herein thus demonstrates that LY6E is a critical antiviral immune effector that controls CoV infection and pathogenesis via a mechanism distinct from other factors that modulate CoV entry.IMPORTANCE Virus entry into host cells is one of the key determinants of host range and cell tropism and is subjected to the control of host innate and adaptive immune responses. In the last decade, several interferon-inducible cellular proteins, including IFITMs, GILT, ADAP2, 25CH, and LY6E, had been identified to modulate the infectious entry of a variety of viruses. Particularly, LY6E was recently identified as a host factor that facilitates the entry of several human-pathogenic viruses, including human immunodeficiency virus, influenza A virus, and yellow fever virus. Identification of LY6E as a potent restriction factor of coronaviruses expands the biological function of LY6E and sheds new light on the immunopathogenesis of human coronavirus infection.


Subject(s)
Antigens, Surface/metabolism , Betacoronavirus/physiology , Coronavirus Infections/metabolism , Coronavirus Infections/virology , Coronavirus/physiology , Host-Pathogen Interactions , Pneumonia, Viral/metabolism , Pneumonia, Viral/virology , Virus Internalization , Amino Acid Sequence , Amphotericin B/pharmacology , Betacoronavirus/drug effects , COVID-19 , Cell Line , Coronavirus/drug effects , Coronavirus Infections/epidemiology , Disease Susceptibility , Evolution, Molecular , GPI-Linked Proteins/metabolism , Humans , Pandemics , Pneumonia, Viral/epidemiology , Protein Sorting Signals , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism
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