A Distinct Dexamethasone-Dependent Gene Expression Profile in the Lungs of COVID-19 Patients

  1. Ulrik Fahnøe
  2. Andreas Ronit
  3. Ronan M G Berg
  4. Sofie E Jørgensen
  5. Trine H Mogensen
  6. Alexander P Underwood
  7. Troels K H Scheel
  8. Jens Bukh
  9. Ronni R Plovsing

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Abstract

The effects of dexamethasone (DXM) treatment on pulmonary immunity in COVID-19–associated acute respiratory distress syndrome (CARDS) remain insufficiently understood. We performed transcriptomic RNA-seq analysis of bronchoalveolar lavage fluid from 20 mechanically ventilated patients: 12 with CARDS (with or without DXM) and 8 non–COVID-19 critically ill controls. CARDS with DXM was characterized by upregulation of genes related to B-cell and complement pathway activation, antigen presentation, phagocytosis, and FC-γ receptor signaling. Most interferon-stimulated genes were upregulated in CARDS, particularly in CARDS without DXM. In conclusion, DXM treatment was not associated with regulation of proinflammatory pathways in CARDS but with regulation of other local immune responses.

Clinical Trials Registration. NCT04354584.

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  1. Version published to 10.1093/infdis/jiac218
  2. ScreenIT

    SciScore for 10.1101/2022.01.12.22269048: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Unrelated data from these healthy individuals have been presented elsewhere.13,14 All patients (CARDS and non-COVID-19) were sedated and unable to provide oral and written informed consent, which was therefore obtained from the next of kin.
    IRB: 5 The study was approved by the Regional Ethics Committee of Copenhagen (H-20023159/H-22011021/H-22009131) and the Knowledge Center for Data Review of Copenhagen (P-2020-399) and registered at ClinicalTrials.gov (NCT04354584).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    19 IFN autoantibodies: IFN autoantibodies were measured in BALF by enzyme-linked immunosorbent assay (ELISA), as previously described for serum.20 Briefly, ELISA plates were coated with 1 μg/mL IFN-α (Miltenyi Biotec, Bergish Gladbach, Germany) and IFN-ω (ThermoFisher Scientific) overnight at 4°C followed by blocking in 5% skimmed milk.
    IFN-ω
    suggested: None
    Bound autoantibodies were detected with HRP-conjugated goat anti-human IgG, IgA, IgM (Fc specific)(Nordic-MUbio, Susteren, Netherlands) and HRP substrate KPL SureBlue (Seracare Life Sciences, Milford, MA, US).
    anti-human IgG
    suggested: None
    IgA, IgM
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    All non-COVID-19 patients had ARDS and/or sepsis according to Berlin criteria11 and The Third International Consensus Definition for Sepsis and Septic Shock,12 respectively.
    Berlin criteria11
    suggested: None
    Software and Algorithms
    SentencesResources
    RNA yield and integrity were assessed using Qubit (ThemoFisher Scientific) and Bioanalyzer 2100 (Agilent, Santa Clara, CA, US) using the RNA nano chip.
    ThemoFisher Scientific
    suggested: None
    Sequence analysis: Reads from the two flow cells were de-multiplexed, pooled and mapped by Hisat2 v2.1.0 to the human reference genome GRCh38 obtained from Ensembl.
    Hisat2
    suggested: (HISAT2, RRID:SCR_015530)
    Ensembl
    suggested: (Ensembl, RRID:SCR_002344)
    Gene expression profiles were obtained from the sorted bam files using featureCounts v2.0.0 and the Ensembl annotation GRCh38.103.
    featureCounts
    suggested: (featureCounts, RRID:SCR_012919)
    Differential analysis was performed in R, as described previously.15 Briefly, we used the Limma-voom and DeSeq2 package for pre-processing and principal component (PC) analysis, respectively, and figures were produced using the ggplot2 package.
    DeSeq2
    suggested: (DESeq2, RRID:SCR_015687)
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    Gene ontology (GO) analysis was performed using Goseq on up and downregulated genes separately for each contrast.
    Goseq
    suggested: (Goseq, RRID:SCR_017052)

    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: 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: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT04354584CompletedCompartmental Inflammation in Mechanically Ventilated Patien…

    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

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  3. Version published to 10.1101/2022.01.12.22269048v1 on medRxiv