Identification of potential coagulation pathway abnormalities in SARS-Cov-2 infection; insights from bioinformatics analysis

  1. Sareh Arjmand
  2. Nazanin Hosseinkhan

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Abstract

Abnormal coagulation parameters have been explored in a significant number of severe COVID-19 patients, linked to poor prognosis and increased risk of organ failure. Here, to uncover the potential abnormalities in coagulation pathways, we analyzed the RNA-seq data (GEO147507) obtained from the treatment of three pulmonary epithelial cell lines with SARS-CoV-2. The significant differentially expressed genes (DEGs) were subjected to Enrichr database for KEGG pathway enrichment analysis and gene ontology (GO) functional annotation. The STRING database was used to generate PPI networks for identified DEGs. We found three upregulated procoagulant genes (SERPINE1, SERPINA5, and SERPINB2) belong to the serine protease inhibitor (serpin) superfamily that inhibit tissue plasminogen activator (t-PA) and urokinase plasminogen activator (u-PA) in the fibrinolysis process. In conclusion, we suggest the fibrinolysis process, especially the blockage of t-PA and u-PA inhibitors, a potential target for more study in treating coagulopathy in severe COVID-19 cases.

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    SciScore for 10.1101/2020.12.07.414631: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Trimming of FASTQ files was then carried out using Trimmomatic algorithm.
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    GO and KEGG enrichment analysis: The significant DEGs were mapped into Enrichr database for KEGG pathway enrichment analysis and GO functional annotation.
    KEGG
    suggested: (KEGG, RRID:SCR_012773)
    Enrichr
    suggested: (Enrichr, RRID:SCR_001575)
    PPI network investigation: The STRING database was used to predict the interaction relationship between DEGs corresponding to coagulation.
    STRING
    suggested: (STRING, RRID:SCR_005223)
    The integrated PPI network was visualized and analyzed using cytoscape v3.8.2.
    cytoscape
    suggested: (Cytoscape, RRID:SCR_003032)

    Results from OddPub: Thank you for sharing your data.

    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 10.1101/2020.12.07.414631v1 on bioRxiv