Single cell gene expression profiling of nasal ciliated cells reveals distinctive biological processes related to epigenetic mechanisms in patients with severe COVID-19

  1. Luis Diambra
  2. Andres M. Alonso
  3. Silvia Sookoian
  4. Carlos J. Pirola

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Abstract

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  1. Version published to 10.1016/j.compbiomed.2022.105895
  2. ScreenIT

    SciScore for 10.1101/2021.12.08.21267478: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Single-cell RNA-seq data analysis: We used the single-cell RNA-seq data from nasopharyngeal swabs publicly available for download and visualization via the Single Cell Portal: https://singlecell.broadinstitute.org/, under the identification SCP1289.
    Portal
    suggested: (ProPortal, RRID:SCR_006112)
    COVID-19 M using SEA; and 3) gene-set enrichment tools by the ToppGene Suite available https://toppgene.cchmc.org/.
    ToppGene
    suggested: ( ToppGene Suite , RRID:SCR_005726)
    First, we analyzed the GO (gene ontology) terms for BPs associated with DEG using GSEA (
    GSEA
    suggested: (SeqGSEA, RRID:SCR_005724)
    Next, we performed a cluster analysis of significant BPs by Enrichment Map Cytoscape App 3.3
    Cytoscape
    suggested: (Cytoscape, RRID:SCR_003032)
    To this end, we used the subset of the C3 gene sets (version 7.4, from MSigDB collection) that includes miRNA-targets genes as cataloged by the miRDB v6.0 algorithm [11].
    miRDB
    suggested: (miRDB, RRID:SCR_010848)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    We are aware that our research may have limitations. First, the nature of retrieved metadata and the limited number of patients do not allow us to examine relevant demographic information of the infected patients. Therefore, we did not examine the correlation between the patients’ features, such as age and gender, with deregulated gene expression pathways. Second, the analyzed dataset contains scRNA-seq data from the nasopharyngeal swabs collected within the first three days following admission to the hospital [7], which does not allow any assessment of patient’s follow-up. Hence, further validation of our observations using experimental models either in cell lines or animal models is required. Together, our results may provide novel insights into the cellular and molecular mechanisms that modulate the clinical course of SARS-CoV-2 infection. Based on predicted biological processes and functional enrichment analysis, we detected some relevant mechanisms that may explain the pathogenesis of severe COVID-19. Among these molecular explanations, we found some clues on the importance of post-transcriptional regulation of gene expression by small-non coding RNAs and epigenetic mechanisms of gene transcription regulation, such as DNA and histone methylation and ultimately chromatin remodeling.

    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.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.12.08.21267478v1 on medRxiv