No evidence that plasmablasts transdifferentiate into developing neutrophils in severe COVID‐19 disease

  1. José Alquicira‐Hernandez
  2. Joseph E Powell
  3. Tri Giang Phan

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Abstract

Objectives

A recent single‐cell RNA sequencing study by Wilk et al . suggested that plasmablasts can transdifferentiate into ‘developing neutrophils’ in patients with severe COVID‐19 disease. We explore the evidence for this.

Methods

We downloaded the original data and code used by the authors in their study to replicate their findings and explore the possibility that regressing out variables may have led the authors to overfit their data.

Results

The lineage relationship between plasmablasts and developing neutrophils breaks down when key features are not regressed out, and the data are not overfitted during the analysis.

Conclusion

Plasmablasts do not transdifferentiate into developing neutrophils. The single‐cell RNA sequencing is a powerful technique for biological discovery and hypothesis generation. However, caution should be exercised in the bioinformatic analysis and interpretation of the data and findings cross‐validated by orthogonal techniques.

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  1. Version published to 10.1002/cti2.1308
  2. ScreenIT

    SciScore for 10.1101/2020.09.27.312538: (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

    No key resources detected.

    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

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  3. Version published to 10.1101/2020.09.27.312538v1 on bioRxiv