Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons

  1. Nils Rother
  2. Cansu Yanginlar
  3. Rik G.H. Lindeboom
  4. Siroon Bekkering
  5. Mandy M.T. van Leent
  6. Baranca Buijsers
  7. Inge Jonkman
  8. Mark de Graaf
  9. Marijke Baltissen
  10. Lieke A. Lamers
  11. Niels P. Riksen
  12. Zahi A. Fayad
  13. Willem J.M. Mulder
  14. Luuk B. Hilbrands
  15. Leo A.B. Joosten
  16. Mihai G. Netea
  17. Michiel Vermeulen
  18. Johan van der Vlag
  19. Raphaël Duivenvoorden

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Abstract

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  1. Version published to 10.1016/j.xcrm.2020.100146
  2. ScreenIT

    SciScore for 10.1101/2020.06.08.20122143: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Human Subjects: For in vitro studies on human PBMCs and monocytes, buffy coats from healthy donors were obtained from Sanquin blood bank, Nijmegen after written informed consent.
    IRB: The study was approved by the local medical ethics committee of the Radboudumc under reference number: 2020–6359.
    RandomizationFor unsupervised computation analysis, FCS files were randomly down sampled to 20,000 events of the pre-processed files and subsequently concatenated to a single file containing all events.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Antibodies and dilutions used are CD45-BV510 (Biolegend, 1:100), CD14-PC7 (eBioscience, 1:100), CD16-FITC (eBioscience, 1:100), CD3-APC750 (Beckman Coulter, 1:50), CD19-APC-R700 (Becton Dickinson, 1:100), CD56-APC (Beckman Coulter, 1:50), HLADR-PE (Beckman Coulter, 1:20), CD11b-BV785 (Biolegend, 1:100), CCR2-BV421 (Becton Dickinson, 1:50), CX3CR1-BV650 (Biolegend, 1:50) and Live/Dead FVS620 (Becton Dickinson, according to manufacturers’ instructions).
    CD14-PC7
    suggested: (Beckman Coulter Cat# A22331, RRID:AB_10639528)
    CD16-FITC
    suggested: None
    CD11b-BV785
    suggested: None
    CX3CR1-BV650
    suggested: None
    In short, 500,000 cells were incubated overnight with 1 μg H3K4me3 or H3K27Ac antibody (Diagenode) and protein A magnetic beads at 4 °C.
    H3K4me3
    suggested: None
    H3K27Ac
    suggested: None
    Software and Algorithms
    SentencesResources
    Unsupervised clustering was performed on the expression values of all markers using the tSNE plugin in FlowJo (Becton Dickinson, version 10.6.2), using 1000 iterations and a perplexity of 30.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Library preparation and sequencing of ChIP samples: ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to manufacturer’s protocol, with the following modifications.
    ChIP-seq
    suggested: (ChIP-seq, RRID:SCR_001237)
    Data was analyzed using GraphPad Prism 5.0.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    RNA-seq data analysis: RNA-sequencing reads were aligned with Hisat2 version 2.0.4 to the provided and pre-indexed hg38 transcript assembly from UCSC, with alignment tailoring for transcript assemblers enabled44.
    Hisat2
    suggested: (HISAT2, RRID:SCR_015530)
    Samtools was used to filter reads with a quality score lower than 20, and PCR duplicates were removed with Picard45.
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    The ‘rlogTransformation’ function in DESeq2 was used to normalize, transform and noise-stabilize the expression data for visualization purposes.
    DESeq2
    suggested: (DESeq, RRID:SCR_000154)
    A union of all identified peaks was generated with BEDTools, which was used to count reads per peak in each sample53.
    BEDTools
    suggested: (BEDTools, RRID:SCR_006646)
    Figures were generated in R with the ggplot2 and ComplexHeatmap R packages47–49.
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    ComplexHeatmap
    suggested: (ComplexHeatmap, RRID:SCR_017270)

    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: 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.

    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 10.1101/2020.06.08.20122143v1 on medRxiv