Pneumocytes are distinguished by highly elevated expression of the ER stress biomarker GRP78, a co-receptor for SARS-CoV-2, in COVID-19 autopsies

  1. Andrii Puzyrenko
  2. Elizabeth R. Jacobs
  3. Yunguang Sun
  4. Juan C. Felix
  5. Yuri Sheinin
  6. Linna Ge
  7. Shuping Lai
  8. Qiang Dai
  9. Benjamin N. Gantner
  10. Rahul Nanchal
  11. Paula E. North
  12. Pippa M. Simpson
  13. Hallgeir Rui
  14. Ivor J. Benjamin

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Abstract

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  1. Version published to 10.1007/s12192-021-01230-4
  2. ScreenIT

    SciScore for 10.1101/2021.06.17.21259098: (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

    Antibodies
    SentencesResources
    ) Rabbit mAb; Cell Signaling, Danvers, MA; Cat#3177; 1:200) and Envision Plus polymer (Agilent/DAKO) were used with magenta chromogen for visualization. Immunohistochemistry for SARS-CoV-2 Nucleocapsid protein was performed using an affinity-purified polyclonal rabbit antibody (affinity-purified rabbit IgG; ProSci, Poway, CA; Cat# 9099; 0.04 µg/ml).
    rabbit IgG
    suggested: None
    Antibody stripping was accomplished using the Omnis (Dako/Agilent) low (CD68 and SARS-CoV-2 Nucleocapsid) or high (GRP78) pH antigen retrieval protocol.
    GRP78
    suggested: None
    Nucleocapsid (ProSci, Poway, CA; Cat# 9099; 0.01 µg/ml) was visualized using the TSA Plus Cyanine-5 System (Perkin Elmer Cat# NEL745001KT); macrophages were identified using CD68 (CD68 Monoclonal Antibody KP1, Thermo Fisher Scientific, Grand Island, NY; Cat# 14-0688-82; 1:10,000 dilution) and visualized using the TSA Plus Cyanine-7 System (Perkin Elmer, Cat# CUSM03644000EA).
    CD68
    suggested: (Thermo Fisher Scientific Cat# 14-0688-82, RRID:AB_11151139)
    Iterative primary antibody stripping was accomplished using the Omnis (Dako/Agilent) low (pH 6; CD68 and SARS-CoV-2 Nucleocapsid) or high (pH 9; GRP78) antigen retrieval protocols.
    antigen retrieval protocols .
    suggested: None
    Pneumocytes were identified using anti-pan-cytokeratin antibody (mouse monoclonal AE1/AE3 blend, Cat# M3515
    anti-pan-cytokeratin
    suggested: (Agilent Cat# M3515, RRID:AB_2132885)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 29. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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 10.1101/2021.06.17.21259098v1 on medRxiv