1
|
Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID-19) diagnosis and treatment using microarray dataset and bioinformatics methods. 3 Biotech 2020; 10:422. [PMID: 33251083 PMCID: PMC7679428 DOI: 10.1007/s13205-020-02406-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/20/2020] [Indexed: 12/15/2022] Open
Abstract
The goal of the present investigation is to identify the differentially expressed genes (DEGs) between SARS-CoV-2 infected and normal control samples to investigate the molecular mechanisms of infection with SARS-CoV-2. The microarray data of the dataset E-MTAB-8871 were retrieved from the ArrayExpress database. Pathway and Gene Ontology (GO) enrichment study, protein–protein interaction (PPI) network, modules, target gene–miRNA regulatory network, and target gene–TF regulatory network have been performed. Subsequently, the key genes were validated using an analysis of the receiver operating characteristic (ROC) curve. In SARS-CoV-2 infection, a total of 324 DEGs (76 up- and 248 down-regulated genes) were identified and enriched in a number of associated SARS-CoV-2 infection pathways and GO terms. Hub and target genes such as TP53, HRAS, MAPK11, RELA, IKZF3, IFNAR2, SKI, TNFRSF13C, JAK1, TRAF6, KLRF2, CD1A were identified from PPI network, target gene–miRNA regulatory network, and target gene–TF regulatory network. Study of the ROC showed that ten genes (CCL5, IFNAR2, JAK2, MX1, STAT1, BID, CD55, CD80, HAL-B, and HLA-DMA) were substantially involved in SARS-CoV-2 patients. The present investigation identified key genes and pathways that deepen our understanding of the molecular mechanisms of SARS-CoV-2 infection, and could be used for SARS-CoV-2 infection as diagnostic and therapeutic biomarkers.
Collapse
|
2
|
Ben Haij N, Planès R, Leghmari K, Serrero M, Delobel P, Izopet J, BenMohamed L, Bahraoui E. HIV-1 Tat Protein Induces Production of Proinflammatory Cytokines by Human Dendritic Cells and Monocytes/Macrophages through Engagement of TLR4-MD2-CD14 Complex and Activation of NF-κB Pathway. PLoS One 2015; 10:e0129425. [PMID: 26090662 PMCID: PMC4474861 DOI: 10.1371/journal.pone.0129425] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/10/2015] [Indexed: 11/18/2022] Open
Abstract
We recently reported that the human immunodeficiency virus type-1 (HIV-1) Tat protein induced the expression of programmed death ligand-1 (PD-L1) on dendritic cells (DCs) through a TLR4 pathway. However, the underlying mechanisms by which HIV-1 Tat protein induces the abnormal hyper-activation of the immune system seen in HIV-1 infected patients remain to be fully elucidated. In the present study, we report that HIV-1 Tat protein induced the production of significant amounts of the pro-inflammatory IL-6 and IL-8 cytokines by DCs and monocytes from both healthy and HIV-1 infected patients. Such production was abrogated in the presence of anti-TLR4 blocking antibodies or soluble recombinant TLR4-MD2 as a decoy receptor, suggesting TLR4 was recruited by Tat protein. Tat-induced murine IL-6 and CXCL1/KC a functional homologue of human IL-8 was abolished in peritoneal macrophages derived from TLR4 KO but not from Wt mice, confirming the involvement of the TLR4 pathway. Furthermore, the recruitment of TLR4-MD2-CD14 complex by Tat protein was demonstrated by the activation of TLR4 downstream pathways including NF-κB and SOCS-1 and by down-modulation of cell surface TLR4 by endocytosis in dynamin and lipid-raft-dependent manners. Collectively, these findings demonstrate, for the first time, that HIV-1 Tat interacts with TLR4-MD2-CD14 complex and activates the NF-κB pathway, leading to overproduction of IL-6 and IL-8 pro-inflammatory cytokines by myeloid cells from both healthy and HIV-1 infected patients. This study reveals a novel mechanism by which HIV-1, via its early expressed Tat protein, hijacks the TLR4 pathway, hence establishing abnormal hyper-activation of the immune system.
Collapse
Affiliation(s)
- Nawal Ben Haij
- INSERM, U1043, Toulouse, France, CNRS, U5282, Toulouse, France
- Université Paul Sabatier Toulouse, Toulouse, France
- Department of Infectious Diseases, Toulouse University Hospital, Toulouse, France
| | - Rémi Planès
- INSERM, U1043, Toulouse, France, CNRS, U5282, Toulouse, France
- Université Paul Sabatier Toulouse, Toulouse, France
- Department of Infectious Diseases, Toulouse University Hospital, Toulouse, France
| | - Kaoutar Leghmari
- INSERM, U1043, Toulouse, France, CNRS, U5282, Toulouse, France
- Université Paul Sabatier Toulouse, Toulouse, France
- Department of Infectious Diseases, Toulouse University Hospital, Toulouse, France
| | - Manutea Serrero
- INSERM, U1043, Toulouse, France, CNRS, U5282, Toulouse, France
- Université Paul Sabatier Toulouse, Toulouse, France
- Department of Infectious Diseases, Toulouse University Hospital, Toulouse, France
| | - Pierre Delobel
- INSERM, U1043, Toulouse, France, CNRS, U5282, Toulouse, France
- Université Paul Sabatier Toulouse, Toulouse, France
- Department of Infectious Diseases, Toulouse University Hospital, Toulouse, France
| | - Jacques Izopet
- INSERM, U1043, Toulouse, France, CNRS, U5282, Toulouse, France
- Université Paul Sabatier Toulouse, Toulouse, France
- Department of Infectious Diseases, Toulouse University Hospital, Toulouse, France
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, 92697, United States of America
- Institute for Immunology, Irvine, CA, 92697, United States of America
- Department of Molecular Biology & Biochemistry, University of California Irvine, School of Medicine, Irvine, CA, 92697, United States of America
| | - Elmostafa Bahraoui
- INSERM, U1043, Toulouse, France, CNRS, U5282, Toulouse, France
- Université Paul Sabatier Toulouse, Toulouse, France
- Department of Infectious Diseases, Toulouse University Hospital, Toulouse, France
- * E-mail:
| |
Collapse
|
3
|
Sciaraffia E, Riccomi A, Lindstedt R, Gesa V, Cirelli E, Patrizio M, De Magistris MT, Vendetti S. Human monocytes respond to extracellular cAMP through A2A and A2B adenosine receptors. J Leukoc Biol 2014; 96:113-22. [PMID: 24652540 DOI: 10.1189/jlb.3a0513-302rr] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In this study, we test the hypothesis that cAMP, acting as an extracellular mediator, affects the physiology and function of human myeloid cells. The cAMP is a second messenger recognized as a universal regulator of several cellular functions in different organisms. Many studies have shown that extracellular cAMP exerts regulatory functions, acting as first mediator in multiple tissues. However, the impact of extracellular cAMP on cells of the immune system has not been fully investigated. We found that human monocytes exposed to extracellular cAMP exhibit higher expression of CD14 and lower amount of MHC class I and class II molecules. When cAMP-treated monocytes are exposed to proinflammatory stimuli, they exhibit an increased production of IL-6 and IL-10 and a lower amount of TNF-α and IL-12 compared with control cells, resembling the features of the alternative-activated macrophages or M2 macrophages. In addition, we show that extracellular cAMP affects monocyte differentiation into DCs, promoting the induction of cells displaying an activated, macrophage-like phenotype with reduced capacity of polarized, naive CD4(+) T cells into IFN-γ-producing lymphocytes compared with control cells. The effects of extracellular cAMP on monocytes are mediated by CD73 ecto-5'-nucleotidase and A2A and A2B adenosine receptors, as selective antagonists could reverse its effects. Of note, the expression of CD73 molecules has been found on the membrane of a small population of CD14(+)CD16(+) monocytes. These findings suggest that an extracellular cAMP-adenosine pathway is active in cells of the immune systems.
Collapse
Affiliation(s)
- Ester Sciaraffia
- Department of Infectious, Parasitic and Immune-Mediated Diseases, and
| | - Antonella Riccomi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, and
| | - Ragnar Lindstedt
- Department of Infectious, Parasitic and Immune-Mediated Diseases, and
| | - Valentina Gesa
- Department of Infectious, Parasitic and Immune-Mediated Diseases, and
| | - Elisa Cirelli
- Department of Infectious, Parasitic and Immune-Mediated Diseases, and Animal Breeding Department, University of Rome "Tor Vergata", Rome, Italy
| | - Mario Patrizio
- Department of Drug Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy; and
| | | | - Silvia Vendetti
- Department of Infectious, Parasitic and Immune-Mediated Diseases, and
| |
Collapse
|
4
|
Rinaldo CR. HIV-1 Trans Infection of CD4(+) T Cells by Professional Antigen Presenting Cells. SCIENTIFICA 2013; 2013:164203. [PMID: 24278768 PMCID: PMC3820354 DOI: 10.1155/2013/164203] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/09/2013] [Indexed: 06/02/2023]
Abstract
Since the 1990s we have known of the fascinating ability of a complex set of professional antigen presenting cells (APCs; dendritic cells, monocytes/macrophages, and B lymphocytes) to mediate HIV-1 trans infection of CD4(+) T cells. This results in a burst of virus replication in the T cells that is much greater than that resulting from direct, cis infection of either APC or T cells, or trans infection between T cells. Such APC-to-T cell trans infection first involves a complex set of virus subtype, attachment, entry, and replication patterns that have many similarities among APC, as well as distinct differences related to virus receptors, intracellular trafficking, and productive and nonproductive replication pathways. The end result is that HIV-1 can sequester within the APC for several days and be transmitted via membrane extensions intracellularly and extracellularly to T cells across the virologic synapse. Virus replication requires activated T cells that can develop concurrently with the events of virus transmission. Further research is essential to fill the many gaps in our understanding of these trans infection processes and their role in natural HIV-1 infection.
Collapse
Affiliation(s)
- Charles R. Rinaldo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
| |
Collapse
|
5
|
Abstract
Tuberculosis (TB) and HIV co-infections place an immense burden on health care systems and pose particular diagnostic and therapeutic challenges. Infection with HIV is the most powerful known risk factor predisposing for Mycobacterium tuberculosis infection and progression to active disease, which increases the risk of latent TB reactivation 20-fold. TB is also the most common cause of AIDS-related death. Thus, M. tuberculosis and HIV act in synergy, accelerating the decline of immunological functions and leading to subsequent death if untreated. The mechanisms behind the breakdown of the immune defense of the co-infected individual are not well known. The aim of this review is to highlight immunological events that may accelerate the development of one of the two diseases in the presence of the co-infecting organism. We also review possible animal models for studies of the interaction of the two pathogens, and describe gaps in knowledge and needs for future studies to develop preventive measures against the two diseases.
Collapse
|
6
|
Exogenous control of the expression of Group I CD1 molecules competent for presentation of microbial nonpeptide antigens to human T lymphocytes. Clin Dev Immunol 2011; 2011:790460. [PMID: 21603161 PMCID: PMC3095450 DOI: 10.1155/2011/790460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/12/2011] [Accepted: 01/19/2011] [Indexed: 12/21/2022]
Abstract
Group I CD1 (CD1a, CD1b, and CD1c) glycoproteins expressed on immature and mature dendritic cells present nonpeptide antigens (i.e., lipid or glycolipid molecules mainly of microbial origin) to T cells. Cytotoxic CD1-restricted T lymphocytes recognizing mycobacterial lipid antigens were found in tuberculosis patients. However, thanks to a complex interplay between mycobacteria and CD1 system, M. tuberculosis possesses a successful tactic based, at least in part, on CD1 downregulation to evade CD1-dependent immunity. On the ground of these findings, it is reasonable to hypothesize that modulation of CD1 protein expression by chemical, biological, or infectious agents could influence host's immune reactivity against M. tuberculosis-associated lipids, possibly affecting antitubercular resistance. This scenario prompted us to perform a detailed analysis of the literature concerning the effect of external agents on Group I CD1 expression in order to obtain valuable information on the possible strategies to be adopted for driving properly CD1-dependent immune functions in human pathology and in particular, in human tuberculosis.
Collapse
|
7
|
Benlahrech A, Gotch F, Kelleher P, Patterson S. Loss of NK stimulatory capacity by plasmacytoid and monocyte-derived DC but not myeloid DC in HIV-1 infected patients. PLoS One 2011; 6:e17525. [PMID: 21408163 PMCID: PMC3050890 DOI: 10.1371/journal.pone.0017525] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 02/03/2011] [Indexed: 11/29/2022] Open
Abstract
Dendritic cells (DC) are potent inducers of natural killer (NK) cells. There are two distinct populations in blood, myeloid (mDC) and plasmacytoid (pDC) but they can also be generated In vitro from monocytes (mdDC). Although it is established that blood DC are lost in HIV-1 infection, the full impact of HIV-1 infection on DC-NK cell interactions remains elusive. We thus investigated the ability of pDC, mDC, and mdDC from viremic and anti-retroviral therapy-treated aviremic HIV-1+ patients to stimulate various NK cell functions. Stimulated pDC and mdDC from HIV-1+ patients showed reduced secretion of IFN-α and IL-12p70 respectively and their capacity to stimulate expression of CD25 and CD69, and IFN-γ secretion in NK cells was also reduced. pDC activation of NK cell degranulation in response to a tumour cell line was severely reduced in HIV-1+ patients but the ability of mDC to activate NK cells was not affected by HIV-1 infection, with the exception of HLA-DR induction. No differences were observed between viremic and aviremic patients indicating that anti-retroviral therapy had minimal effect on restoration on pDC and mdDC-mediated activation of NK cells. Results from this study provide further insight into HIV-1 mediated suppression of innate immune functions.
Collapse
Affiliation(s)
- Adel Benlahrech
- Department of Immunology, Imperial College London, Chelsea and Westminster Hospital, London, United Kingdom
| | - Frances Gotch
- Department of Immunology, Imperial College London, Chelsea and Westminster Hospital, London, United Kingdom
| | - Peter Kelleher
- Department of Immunology, Imperial College London, Chelsea and Westminster Hospital, London, United Kingdom
| | - Steven Patterson
- Department of Immunology, Imperial College London, Chelsea and Westminster Hospital, London, United Kingdom
- * E-mail:
| |
Collapse
|
8
|
Cholera toxin impairs the differentiation of monocytes into dendritic cells, inducing professional antigen-presenting myeloid cells. Infect Immun 2010; 79:1300-10. [PMID: 21149590 DOI: 10.1128/iai.01181-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cholera toxin (CT) is a potent adjuvant for mucosal vaccination; however, its mechanism of action has not been clarified completely. It is well established that peripheral monocytes differentiate into dendritic cells (DCs) both in vitro and in vivo and that monocytes are the in vivo precursors of mucosal CD103(-) proinflammatory DCs. In this study, we asked whether CT had any effects on the differentiation of monocytes into DCs. We found that CT-treated monocytes, in the presence of granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin 4 (IL-4), failed to differentiate into classical DCs (CD14(low) CD1a(high)) and acquired a macrophage-like phenotype (CD14(high) CD1a(low)). Cells differentiated in the presence of CT expressed high levels of major histocompatibility complex class I (MHC-I) and MHC-II and CD80 and CD86 costimulatory molecules and produced larger amounts of IL-1β, IL-6, and IL-10 but smaller amounts of tumor necrosis factor alpha (TNF-α) and IL-12 than did monocytes differentiated into DCs in the absence of CT. The enzymatic activity of CT was found to be important for the skewing of monocytes toward a macrophage-like phenotype (Ma-DCs) with enhanced antigen-presenting functions. Indeed, treatment of monocytes with scalar doses of forskolin (FSK), an activator of adenylate cyclase, induced them to differentiate in a dose-dependent manner into a population with phenotype and functions similar to those found after CT treatment. Monocytes differentiated in the presence of CT induced the differentiation of naïve T lymphocytes toward a Th2 phenotype. Interestingly, we found that CT interferes with the differentiation of monocytes into DCs in vivo and promotes the induction of activated antigen-presenting cells (APCs) following systemic immunization.
Collapse
|
9
|
|