Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response
<p dir="ltr">The global spread of COVID-19, caused by pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for an imminent response from medical research communities to better understand this rapidly spreading infection. Employing multiple bioi...
محفوظ في:
| المؤلف الرئيسي: | |
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| مؤلفون آخرون: | , |
| منشور في: |
2020
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| الموضوعات: | |
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إضافة وسم
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| _version_ | 1864513514028138496 |
|---|---|
| author | Radhakrishnan Vishnubalaji (3563306) |
| author2 | Hibah Shaath (5599658) Nehad M. Alajez (7397276) |
| author2_role | author author |
| author_facet | Radhakrishnan Vishnubalaji (3563306) Hibah Shaath (5599658) Nehad M. Alajez (7397276) |
| author_role | author |
| dc.creator.none.fl_str_mv | Radhakrishnan Vishnubalaji (3563306) Hibah Shaath (5599658) Nehad M. Alajez (7397276) |
| dc.date.none.fl_str_mv | 2020-07-01T00:00:00Z |
| dc.identifier.none.fl_str_mv | 10.3390/genes11070760 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Protein_Coding_and_Long_Noncoding_RNA_lncRNA_Transcriptional_Landscape_in_SARS-CoV-2_Infected_Bronchial_Epithelial_Cells_Highlight_a_Role_for_Interferon_and_Inflammatory_Response/25904206 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Genetics Biomedical and clinical sciences Cardiovascular medicine and haematology Clinical sciences Oncology and carcinogenesis Bronchial epithelial COVID-19 Gene expressions IFN response Immune response LncRNAs MAPK Pathway analysis SARS-CoV-2 |
| dc.title.none.fl_str_mv | Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">The global spread of COVID-19, caused by pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for an imminent response from medical research communities to better understand this rapidly spreading infection. Employing multiple bioinformatics and computational pipelines on transcriptome data from primary normal human bronchial epithelial cells (NHBE) during SARS-CoV-2 infection revealed activation of several mechanistic networks, including those involved in immunoglobulin G (IgG) and interferon lambda (IFNL) in host cells. Induction of acute inflammatory response and activation of tumor necrosis factor (TNF) was prominent in SARS-CoV-2 infected NHBE cells. Additionally, disease and functional analysis employing ingenuity pathway analysis (IPA) revealed activation of functional categories related to cell death, while those associated with viral infection and replication were suppressed. Several interferon (IFN) responsive gene targets (IRF9, IFIT1, IFIT2, IFIT3, IFITM1, MX1, OAS2, OAS3, IFI44 and IFI44L) were highly upregulated in SARS-CoV-2 infected NBHE cell, implying activation of antiviral IFN innate response. Gene ontology and functional annotation of differently expressed genes in patient lung tissues with COVID-19 revealed activation of antiviral response as the hallmark. Mechanistic network analysis in IPA identified 14 common activated, and 9 common suppressed networks in patient tissue, as well as in the NHBE cell model, suggesting a plausible role for these upstream regulator networks in the pathogenesis of COVID-19. Our data revealed expression of several viral proteins in vitro and in patient-derived tissue, while several host-derived long noncoding RNAs (lncRNAs) were identified. Our data highlights activation of IFN response as the main hallmark associated with SARS-CoV-2 infection in vitro and in human, and identified several differentially expressed lncRNAs during the course of infection, which could serve as disease biomarkers, while their precise role in the host response to SARS-CoV-2 remains to be investigated.</p><h2>Other Information</h2><p dir="ltr">Published in: Genes<br>License: <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.3390/genes11070760" target="_blank">https://dx.doi.org/10.3390/genes11070760</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_7308485fc54d01dacc25e3985ec2f4a6 |
| identifier_str_mv | 10.3390/genes11070760 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/25904206 |
| publishDate | 2020 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory ResponseRadhakrishnan Vishnubalaji (3563306)Hibah Shaath (5599658)Nehad M. Alajez (7397276)Biological sciencesGeneticsBiomedical and clinical sciencesCardiovascular medicine and haematologyClinical sciencesOncology and carcinogenesisBronchial epithelialCOVID-19Gene expressionsIFN responseImmune responseLncRNAsMAPKPathway analysisSARS-CoV-2<p dir="ltr">The global spread of COVID-19, caused by pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for an imminent response from medical research communities to better understand this rapidly spreading infection. Employing multiple bioinformatics and computational pipelines on transcriptome data from primary normal human bronchial epithelial cells (NHBE) during SARS-CoV-2 infection revealed activation of several mechanistic networks, including those involved in immunoglobulin G (IgG) and interferon lambda (IFNL) in host cells. Induction of acute inflammatory response and activation of tumor necrosis factor (TNF) was prominent in SARS-CoV-2 infected NHBE cells. Additionally, disease and functional analysis employing ingenuity pathway analysis (IPA) revealed activation of functional categories related to cell death, while those associated with viral infection and replication were suppressed. Several interferon (IFN) responsive gene targets (IRF9, IFIT1, IFIT2, IFIT3, IFITM1, MX1, OAS2, OAS3, IFI44 and IFI44L) were highly upregulated in SARS-CoV-2 infected NBHE cell, implying activation of antiviral IFN innate response. Gene ontology and functional annotation of differently expressed genes in patient lung tissues with COVID-19 revealed activation of antiviral response as the hallmark. Mechanistic network analysis in IPA identified 14 common activated, and 9 common suppressed networks in patient tissue, as well as in the NHBE cell model, suggesting a plausible role for these upstream regulator networks in the pathogenesis of COVID-19. Our data revealed expression of several viral proteins in vitro and in patient-derived tissue, while several host-derived long noncoding RNAs (lncRNAs) were identified. Our data highlights activation of IFN response as the main hallmark associated with SARS-CoV-2 infection in vitro and in human, and identified several differentially expressed lncRNAs during the course of infection, which could serve as disease biomarkers, while their precise role in the host response to SARS-CoV-2 remains to be investigated.</p><h2>Other Information</h2><p dir="ltr">Published in: Genes<br>License: <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.3390/genes11070760" target="_blank">https://dx.doi.org/10.3390/genes11070760</a></p>2020-07-01T00:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.3390/genes11070760https://figshare.com/articles/journal_contribution/Protein_Coding_and_Long_Noncoding_RNA_lncRNA_Transcriptional_Landscape_in_SARS-CoV-2_Infected_Bronchial_Epithelial_Cells_Highlight_a_Role_for_Interferon_and_Inflammatory_Response/25904206CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/259042062020-07-01T00:00:00Z |
| spellingShingle | Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response Radhakrishnan Vishnubalaji (3563306) Biological sciences Genetics Biomedical and clinical sciences Cardiovascular medicine and haematology Clinical sciences Oncology and carcinogenesis Bronchial epithelial COVID-19 Gene expressions IFN response Immune response LncRNAs MAPK Pathway analysis SARS-CoV-2 |
| status_str | publishedVersion |
| title | Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response |
| title_full | Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response |
| title_fullStr | Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response |
| title_full_unstemmed | Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response |
| title_short | Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response |
| title_sort | Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response |
| topic | Biological sciences Genetics Biomedical and clinical sciences Cardiovascular medicine and haematology Clinical sciences Oncology and carcinogenesis Bronchial epithelial COVID-19 Gene expressions IFN response Immune response LncRNAs MAPK Pathway analysis SARS-CoV-2 |