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Network perturbation analysis in human bronchial epithelial cells following SARS-CoV2 infection.

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.

SUBMITTER: Nunnari G

PROVIDER: S-EPMC7386311 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Network perturbation analysis in human bronchial epithelial cells following SARS-CoV2 infection.

Nunnari Giuseppe G Sanfilippo Cristina C Castrogiovanni Paola P Imbesi Rosa R Li Volti Giovanni G Barbagallo Ignazio I Musumeci Giuseppe G Di Rosa Michelino M

Experimental cell research 20200728 2

<h4>Background</h4>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.<h4>Methods</h4>In the present investigation, we evaluated the effects of SARS-CoV<sub>2</sub> on human bronchial epithelial cells (HBEC). We used RNA-seq datasets available online for identifying SARS-CoV<sub>2</sub> potential ...[more]

PMID: 32735892

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Project description:BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 19 (COVID-19) that was emerged as a new member of coronaviruses since December 2019 in Wuhan, China and then after was spread in all continentals. Since SARS-CoV-2 has shown about 77.5% similarity to SARS-CoV, the transcriptome and immunological regulations of SARS-CoV-2 was expected to have high percentage of overlap with SARS-CoV.ResultsIn this study, we applied the single cell transcriptomics data of human bronchial epithelial cells (2B4 cell line) infected with SARS-CoV, which was annotated in the Expression Atlas database to expand this data to COVID-19. In addition, we employed system biology methods including gene ontology (GO) and Reactome pathway analyses to define functional genes and pathways in the infected cells with SARS-CoV. The transcriptomics analysis on the Expression Atlas database revealed that most genes from infected 2B4 cell line with SARS-CoV were downregulated leading to immune system hyperactivation, induction of signaling pathways, and consequently a cytokine storm. In addition, GO:0016192 (vesicle-mediated transport), GO:0006886 (intracellular protein transport), and GO:0006888 (ER to Golgi vesicle-mediated transport) were shown as top three GOs in the ontology network of infected cells with SARS-CoV. Meanwhile, R-HAS-6807070 (phosphatase and tensin homolog or PTEN regulation) showed the highest association with other Reactome pathways in the network of infected cells with SARS-CoV. PTEN plays a critical role in the activation of dendritic cells, B- and T-cells, and secretion of proinflammatory cytokines, which cooperates with downregulated genes in the promotion of cytokine storm in the COVID-19 patients.ConclusionsBased on the high similarity percentage of the transcriptome of SARS-CoV with SARS-CoV-2, the data of immunological regulations, signaling pathways, and proinflammatory cytokines in SARS-CoV infection can be expanded to COVID-19 to have a valid platform for future pharmaceutical and vaccine studies.

Project description:BackgroundThe SARS-COV2 pandemic has been ongoing worldwide since at least 2 years. In severe cases, this infection triggers acute respiratory distress syndrome and quasi-systemic damage with a wide range of symptoms. Long-term physical and psychological consequences of this infection are therefore naturally present among these patients. The aim of this study was to describe the state of health of these patients at 6 (M6) and 12 months (M12) after infection onset, and compare quality-of-life (QOL) and fatigue at these time-points.MethodsA prospective cohort study was set up at Reims University Hospital. Patients were clinically assessed at M6 and M12. Three scores were calculated to describe patient's status: the modified Medical Research Council score (mMRC) used to determine dyspnoea state, the Fatigue Severity Scale (FSS) and the Short Form 12 (SF12) that was carried out to determine the QOL both mentally and physically (MCS12 and PCS12). Descriptive analysis and comparison of scores between M6 and M12 were made.Results120 patients completed both follow-up consultations. Overall, about 40% of the patients presented dyspnoea symptoms. The median mMRC score was 1 Interquartile ranges (IQR) = [0-2] at the two assessment. Concerning FSS scores, 35% and 44% of patients experienced fatigue at both follow-ups. The two scores of SF12 were lower than the general population standard scores. The mean PCS12 score was 42.85 (95% confidence interval (95% CI [41.05-44.65])) and mean MCS12 score of 46.70 (95% CI [45.34-48.06]) at 6 months. At 12 months, the mean PCS12 score was 42.18 (95% confidence interval (95% CI [40.46-43.89])) and mean MCS12 score of 47.13 (95% CI [45.98-48.28]). No difference was found between SF12 scores at 6 and 12 months.ConclusionsThis study pinpoints the persistence of fatigue and a low mental and physical QOL compared to population norms even after 1 year following infection. It also supports the claims of mental or psychological alterations due to infection by this new virus, hence a lower overall QOL in patients.

Dataset Information

Network perturbation analysis in human bronchial epithelial cells following SARS-CoV2 infection.

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Network perturbation analysis in human bronchial epithelial cells following SARS-CoV2 infection.

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