Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses

AbstractThe severity and outcome of respiratory viral infections is partially determined by the cellular response mounted by infected lung epithelial cells. Disease prevention and treatment is dependent on our understanding of the shared and unique responses elicited by diverse viruses, yet few studies compare host responses to different viruses while controlling other experimental parameters. We compared changes in gene expression of murine lung epithelial cells infected individually by three respiratory viruses causing mild (rhinovirus, RV1B), moderate (coronavirus, MHV-1), and severe (influenza A virus, PR8) disease in mice. RV1B infection caused numerous gene expression changes, but the differential effect peaked at 12 hours post-infection. PR8 altered an intermediate number of genes whose expression continued to change through 24 hours. MHV-1 had comparatively few effects on host gene expression. The viruses elicited highly overlapping responses in antiviral genes, though MHV-1 induced a lower type I interferon response than the other two viruses. Signature genes were identified for each virus and included host defense genes for PR8, tissue remodeling genes for RV1B, and transcription factors for MHV-1. Our comparative approach identified universal and specific transcriptional signatures of virus infection that can be used to discover mechanisms of pathogenesis in the respiratory tract.

Download Full-text

Regulation of Indoleamine-3,5-dioxygenase 1 (IDO1) in Lung Epithelial Cells by Coronaviruses (SARS-CoV) and Cytokine Signaling

10.21203/rs.3.rs-871230/v1 ◽

2021 ◽

Author(s):

Ramana Chilakamarti

Keyword(s):

Gene Expression ◽

Epithelial Cells ◽

Inflammatory Cytokines ◽

Proinflammatory Cytokines ◽

Human Lung ◽

Respiratory Viruses ◽

Lung Epithelial Cells ◽

Type I ◽

Lung Epithelial ◽

Rna Levels

Abstract Interferons (IFNs) and proinflammatory cytokines play an important role in the innate immune response to respiratory viruses, including coronaviruses (SARS-CoV). Metabolic profiling in the serum samples of coronavirus disease-19 (COVID-19) patients revealed altered cholesterol and tryptophan metabolism. Indoleamine-3,5-dioxygenase (IDO1) is the key enzyme involved in the tryptophan catabolism and induced by interferons and inflammatory cytokines. The regulation of IDO1 in immune cells and cancer was extensively studied. In this study, IDO1 regulation in human lung epithelial cells by coronaviruses and respiratory viruses as well as inflammatory cytokines was investigated. SARS-CoV-2 was a potent inducer of IFN–regulated metabolic enzymes such as IDO1, Cholesterol-25-hydroxylase (CH25H), Spermidine acetyltransferase (SAT1), and Sterile alpha motif and histidine/aspartic acid domain-containing protein (SAMHD1) at RNA levels in Calu-3 cells. Reconstitution of A549 lung epithelial cells with Angiotensin-converting enzyme 2 (ACE2) was necessary and sufficient to induce IDO1 at RNA levels. Influenza A virus (IAV) suppressed IDO1 RNA levels in a non-structural protein (NS1)-dependent manner in NHBE cells. In contrast, IDO1 RNA levels were dramatically induced in the lungs of mice infected with a reconstructed 1918 H1N1 influenza virus. Treatment of A549 cells with either type I or type II interferon induced IDO1 RNA levels. Furthermore, IDO1 levels were significantly higher in the lung tissues of COVID-19 patients in comparison with healthy controls. A mix of proinflammatory cytokines dramatically induced IDO1 and chemokine RNA levels in lung epithelial cells in a cell culture model, simulating the gene expression pattern in the lung tissue samples of COVID-19 patients. Furthermore, hypertonic saline solution (HTS) dramatically abrogated the gene expression induced by cytokine mix in human lung cells. The IDO1 protein interaction network included transcription factors STAT1 and STAT3. These studies suggest that IDO1 inhibition may be a potential therapeutic target in the treatment of viral and inflammatory diseases.

Download Full-text

Lung Epithelial Regulation of BCL2 Related Protein A1 (BCL2A1) by Coronaviruses (SARS-CoV) and Type I Interferon Signaling

10.1101/2021.07.21.453244 ◽

2021 ◽

Author(s):

Ramana Chilakamarti

Keyword(s):

Epithelial Cells ◽

Human Lung ◽

Type I Interferon ◽

Respiratory Viruses ◽

Lung Epithelial Cells ◽

Type I ◽

Related Protein ◽

Interferon Signaling ◽

Lung Epithelial ◽

Human Lung Epithelial Cells

Highly pathogenic respiratory viruses such as 1918 influenza (HIN1) and coronavirus (SARS-CoV-2) induce significant lung injury with diffuse alveolar damage, capillary leak, and extensive cell death resulting in acute respiratory distress syndrome (ARDS). Direct effects of the virus, as well as host immune response such as proinflammatory cytokine production, contribute to programmed cell death or apoptosis. Alveolar lung epithelial type II (AT2) cells play a major role in the clearance of respiratory viruses, secretion of surfactant proteins and antimicrobial substances into the bronchoalveolar fluid as well as repair of lung injury. Gene expression in AT2 cells is regulated in a tissue and cell-specific manner and in a temporal fashion. The availability of tissue and cell-specific RNA datasets in Human Protein Atlas led to the identification of localized expression patterns of BCL-2 family members such as BCL2 related protein A1 (BCL2A1) in AT2 cells and immune cells of the lung. BCL2A1 expression was regulated by multiple stimuli including Toll-like receptor (TLR) ligands, interferons (IFNs), inflammatory cytokines, and inhibited by the steroid dexamethasone. In this study, regulation of BCL2A1 gene expression in human lung epithelial cells by several respiratory viruses and type I interferon signaling was investigated. SARS-CoV-2 infection significantly induced BCL2A1 expression in human lung epithelial cells within 24 hours that required the expression of Angiotensin-converting enzyme 2 (ACE2). BCL2A1 mRNA induction by SARS-CoV-2 was correlated with the induced expression of IFN-β and IFN-regulated transcription factor mRNA. BCL2A1 was induced by IFN-β treatment or by infection with influenza virus lacking the non-structural protein1(NS1) in NHBE cells. Furthermore, bioinformatics revealed that a subset of BCL-2 family members involved in the control of apoptosis and transcription such as BCL2A1, BCL2L14, BCL3, and BCL6 were regulated in the lung epithelial cells by coronaviruses and in the lung tissue samples of COVID-19 patients. Transcriptomic data also suggested that these genes were differentially regulated by the steroid drug dexamethasone.

Download Full-text

The NS1 Protein of Influenza A Virus Blocks RIG-I-Mediated Activation of the Noncanonical NF-κB Pathway and p52/RelB-Dependent Gene Expression in Lung Epithelial Cells

Journal of Virology ◽

10.1128/jvi.00323-12 ◽

2012 ◽

Vol 86 (18) ◽

pp. 10211-10217 ◽

Cited By ~ 43

Author(s):

Andrea Rückle ◽

Emanuel Haasbach ◽

Ilkka Julkunen ◽

Oliver Planz ◽

Christina Ehrhardt ◽

...

Keyword(s):

Gene Expression ◽

Epithelial Cells ◽

Influenza A Virus ◽

Influenza A ◽

Target Gene ◽

Lung Epithelial Cells ◽

Ns1 Protein ◽

Antiviral Immune Response ◽

Lung Epithelial ◽

Infected Cells

Influenza A virus (IAV) infection of epithelial cells activates NF-κB transcription factors via the canonical NF-κB signaling pathway, which modulates both the antiviral immune response and viral replication. Since almost nothing is known so far about a function of noncanonical NF-κB signaling after IAV infection, we tested infected cells for activation of p52 and RelB. We show that the viral NS1 protein strongly inhibits RIG-I-mediated noncanonical NF-κB activation and expression of the noncanonical target gene CCL19.

Download Full-text

Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses

PLoS ONE ◽

10.1371/journal.pone.0178408 ◽

2017 ◽

Vol 12 (6) ◽

pp. e0178408 ◽

Cited By ~ 9

Author(s):

James T. VanLeuven ◽

Benjamin J. Ridenhour ◽

Andres J. Gonzalez ◽

Craig R. Miller ◽

Tanya A. Miura

Keyword(s):

Gene Expression ◽

Epithelial Cells ◽

Respiratory Viruses ◽

Lung Epithelial Cells ◽

Lung Epithelial ◽

Shared Gene

Download Full-text

Regulation of Lysosome-Associated Membrane Protein 3 (LAMP3) in Lung Epithelial Cells by Coronaviruses (SARS-CoV-1/2) and Type I Interferon Signaling

10.1101/2021.04.28.441840 ◽

2021 ◽

Author(s):

Chilakamarti V. Ramana

Keyword(s):

Epithelial Cells ◽

Viral Entry ◽

Human Lung ◽

Type I Interferon ◽

Respiratory Viruses ◽

Lung Epithelial Cells ◽

Type I ◽

Type Ii ◽

Interferon Signaling ◽

Lung Epithelial

AbstractSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is a major risk factor for mortality and morbidity in critical care hospitals around the world. Lung epithelial type II cells play a major role in several physiological processes, including recognition and clearance of respiratory viruses as well as repair of lung injury in response to environmental toxicants. Gene expression profiling of lung epithelial type II-specific genes led to the identification of lysosomal-associated membrane protein 3 (LAMP3). Intracellular locations of LAMP3 include plasma membrane, endosomes, and lysosomes. These intracellular organelles are involved in vesicular transport and facilitate viral entry and release of the viral RNA into the host cell cytoplasm. In this study, regulation of LAMP3 expression in human lung epithelial cells by several respiratory viruses and type I interferon signaling was investigated. Coronaviruses including SARS-CoV-1 and SARS-CoV-2 significantly induced LAMP3 expression in lung epithelial cells within 24 hours after infection that required the presence of ACE2 viral entry receptor. Time-course experiments revealed that the induced expression of LAMP3 by SARS-CoV-2 was correlated with the induced expression of interferon-beta1 (IFNB1) and signal transducers and activator of transcription 1 (STAT1) mRNA levels. LAMP3 was also induced by direct IFN-beta treatment or by infection with influenza virus lacking the non-structural protein1(NS1) in NHBE bronchial epithelial cells. LAMP3 expression was induced in human lung epithelial cells by several respiratory viruses, including respiratory syncytial virus (RSV) and the human parainfluenza virus 3 (HPIV3). Location in lysosomes and endosomes as well as induction by respiratory viruses and type I Interferon suggests that LAMP3 may have an important role in inter-organellar regulation of innate immunity and a potential target for therapeutic modulation in health and disease. Furthermore, bioinformatics revealed that a subset of lung type II cell genes were differentially regulated in the lungs of COVID-19 patients.

Download Full-text

SARS-CoV-2 triggers an MDA-5-dependent interferon response which is unable to control replication in lung epithelial cells

Journal of Virology ◽

10.1128/jvi.02415-20 ◽

2021 ◽

Cited By ~ 2

Author(s):

Antoine Rebendenne ◽

Ana Luiza Chaves Valadão ◽

Marine Tauziet ◽

Ghizlane Maarifi ◽

Boris Bonaventure ◽

...

Keyword(s):

Epithelial Cells ◽

Viral Replication ◽

Mammalian Cells ◽

De Novo ◽

Etiologic Agent ◽

Lung Epithelial Cells ◽

Interferon Response ◽

Lung Cells ◽

Type I ◽

Lung Epithelial

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of coronavirus disease 19 (COVID-19), which ranges from mild respiratory symptoms to acute respiratory distress syndrome, and death in the most severe cases. Immune dysregulation with altered innate cytokine responses is thought to contribute to disease severity. Here, we characterized in depth host cell responses against SARS-CoV-2 in primary human airway epithelia (HAE) and immortalized cell lines. Our results demonstrate that primary HAE and model cells elicit a robust induction of type I and III interferons (IFNs). Importantly, we show for the first time that melanoma differentiation associated gene (MDA)-5 is the main sensor of SARS-CoV-2 in lung cells. IFN exposure strongly inhibited viral replication and de novo production of infectious virions. However, despite high levels of IFNs produced in response to SARS-CoV-2 infection, the IFN response was unable to control viral replication in lung cells, contrary to what was previously reported in intestinal epithelial cells. Altogether, these results highlight the complex and ambiguous interplay between viral replication and the timing of IFN responses. IMPORTANCE Mammalian cells express sensors able to detect specific features of pathogens and induce the interferon response, which is one of the first line of defenses against viruses and help controlling viral replication. The mechanisms and impact of SARS-CoV-2 sensing in lung epithelial cells remained to be deciphered. In this study, we report that despite a high production of type I and III interferons specifically induced by MDA-5-mediated sensing of SARS-CoV-2, primary and immortalized lung epithelial cells are unable to control viral replication. However, exogenous interferons potently inhibited replication, if provided early upon viral exposure. A better understanding of the ambiguous interplay between the interferon response and SARS-CoV-2 replication is essential to guide future therapeutical interventions.

Download Full-text

Nitric oxide increases IL-8 gene transcription and mRNA stability to enhance IL-8 gene expression in lung epithelial cells

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.00165.2004 ◽

2004 ◽

Vol 287 (4) ◽

pp. L764-L773 ◽

Cited By ~ 34

Author(s):

Loretta Sparkman ◽

Vijayakumar Boggaram

Keyword(s):

Gene Expression ◽

Nitric Oxide ◽

Protein Kinase ◽

Epithelial Cells ◽

Gene Transcription ◽

Mrna Stability ◽

Inflammatory Responses ◽

Lung Epithelial Cells ◽

Mrna Levels ◽

Lung Epithelial

Interleukin (IL)-8, a C-X-C chemokine, is a potent chemoattractant and an activator for neutrophils, T cells, and other immune cells. The airway and respiratory epithelia play important roles in the initiation and modulation of inflammatory responses via production of cytokines and surfactant. The association between elevated levels of nitric oxide (NO) and IL-8 in acute lung injury associated with sepsis, acute respiratory distress syndrome, respiratory syncytial virus infection in infants, and other inflammatory diseases suggested that NO may play important roles in the control of IL-8 gene expression in the lung. We investigated the role of NO in the control of IL-8 gene expression in H441 lung epithelial cells. We found that a variety of NO donors significantly induced IL-8 mRNA levels, and the increase in IL-8 mRNA was associated with an increase in IL-8 protein. NO induction of IL-8 mRNA was due to increases in IL-8 gene transcription and mRNA stability. NO induction of IL-8 mRNA levels was not inhibited by 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one and KT-5823, inhibitors of soluble guanylate cyclase and protein kinase G, respectively, and 8-bromo-cGMP did not increase IL-8 mRNA levels. This indicated that NO induces IL-8 mRNA levels independently of changes in the intracellular cGMP levels. NO induction of IL-8 mRNA was significantly reduced by inhibitors of extracellular regulated kinase and protein kinase C. IL-8 induction by NO was also reduced by hydroxyl radical scavengers such as dimethyl sulfoxide and dimethylthiourea, indicating the involvement of hydroxyl radicals in the induction process. NO induction of IL-8 gene expression could be a significant contributing factor in the initiation and induction of inflammatory response in the respiratory epithelium.

Download Full-text