Direct Exposure to SARS-CoV-2 and Cigarette Smoke Increases Infection Severity and Alters the Stem Cell-Derived Airway Repair Response

  1. Arunima Purkayastha
  2. Chandani Sen
  3. Gustavo Garcia
  4. Justin Langerman
  5. David W. Shia
  6. Luisa K. Meneses
  7. Preethi Vijayaraj
  8. Abdo Durra
  9. Caroline R. Koloff
  10. Delilah R. Freund
  11. Justin Chi
  12. Tammy M. Rickabaugh
  13. Apoorva Mulay
  14. Bindu Konda
  15. Myung S. Sim
  16. Barry R. Stripp
  17. Kathrin Plath
  18. Vaithilingaraja Arumugaswami
  19. Brigitte N. Gomperts

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. Version published to 10.1016/j.stem.2020.11.010
  2. ScreenIT

    SciScore for 10.1101/2020.07.28.226092: (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

    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. ScreenIT

    SciScore for 10.1101/2020.07.28.226092: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementTissues were procured under Institutional Review Board-approved protocols at the David Geffen School of Medicine at UCLA.Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variablenot detected.Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    After several washes of Tris-Buffered Saline and Tween-20 (TBST), secondary antibodies were incubated on samples for 1 hour in darkness, washed, and mounted using Vectashield hardest mounting medium with DAPI (Vector Labs H-1500).
    Vectashield hardest mounting medium with DAPI
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Virus titer was measured in Vero-E6 cells by TCID50 assay.
    Vero-E6
    suggested: None
    Software and Algorithms
    SentencesResources
    Data and Code Availability This study generated a single cell RNA sequencing dataset of ALI cultures that were exposed to cigarette smoke and/or SARS-CoV-2 or neither.
    SARS-CoV-2
    suggested: (Active Motif Cat# 91345, AB_2847847)
    IF images were obtained using an LSM700 or LSM880 Zeiss confocal microscope and composite images generated using ImageJ.
    ImageJ
    suggested: (ImageJ, SCR_003070)
    Cellular suspensions were loaded on a Chromium Controller instrument (10X Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs)
    GEMs
    suggested: (GEMS, SCR_009188)
    Raw sequencing data were filtered by read quality, adapter- and polyA-trimmed, and reads were aligned to a hybrid human hg38-Sars Covid2 transcriptome using the Cell Range software (10X Genomics) and the STAR aligner.
    STAR
    suggested: (STAR, SCR_015899)
    Gene ontology enrichments were determined using the Metascape tool (Zhou et al., 2019).
    Metascape
    suggested: (Metascape, SCR_016620)

    Data from additional tools added to each annotation on a weekly basis.

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2020.07.28.226092v1 on bioRxiv