Identification of potential key genes for SARS-CoV-2 infected human bronchial organoids based on bioinformatics analysis

  1. Hanming Gu
  2. Gongsheng Yuan

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Abstract

There is an urgent need to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) that leads to COVID-19 and respiratory failure. Our study is to discover differentially expressed genes (DEGs) and biological signaling pathways by using a bioinformatics approach to elucidate their potential pathogenesis. The gene expression profiles of the GSE150819 datasets were originally produced using an Illumina NextSeq 500 (Homo sapiens). KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) were utilized to identify functional categories and significant pathways. KEGG and GO results suggested that the Cytokine-cytokine receptor interaction, P53 signaling pathway, and Apoptosis are the main signaling pathways in SARS-CoV-2 infected human bronchial organoids (hBOs). Furthermore, NFKBIA, C3, and CCL20 may be key genes in SARS-CoV-2 infected hBOs. Therefore, our study provides further insights into the therapy of COVID-19.

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  1. ScreenIT

    SciScore for 10.1101/2020.08.18.256735: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    resources: Gene expression profile dataset GSE150819 was downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/).
    http://www.ncbi.nlm.nih.gov/geo/
    suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
    GO analysis and KEGG pathway enrichment analysis of DEGs in this study were performed by the Database for Annotation, Visualization, and Integrated Discovery (DAVID) (http://david.ncifcrf.gov/) online tools.
    KEGG
    suggested: (KEGG, RRID:SCR_012773)
    DAVID
    suggested: (DAVID, RRID:SCR_001881)
    The significant modules were from the constructed PPI network using MCODE from Cytoscape software (https://cytoscape.org/). the functional and pathway enrichment analyses were performed using DAVID (http://david.ncifcrf.gov/) online tools.
    Cytoscape
    suggested: (Cytoscape, RRID:SCR_003032)

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • No funding statement was detected.
    • No protocol registration statement was detected.

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  2. Version published to 10.1101/2020.08.18.256735v2 on bioRxiv
  3. Version published to 10.1101/2020.08.18.256735v1 on bioRxiv