Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung

  1. Marian Kalocsay
  2. Zoltan Maliga
  3. Ajit J. Nirmal
  4. Robyn J. Eisert
  5. Gary A. Bradshaw
  6. Isaac H Solomon
  7. Yu-An Chen
  8. Roxanne J. Pelletier
  9. Connor A. Jacobson
  10. Julian Mintseris
  11. Robert F. Padera
  12. Amanda J. Martinot
  13. Dan H. Barouch
  14. Sandro Santagata
  15. Peter K. Sorger

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Abstract

Normal tissue physiology and repair depends on communication with the immune system. Understanding this communication at the molecular level in intact tissue requires new methods. The consequences of SARS-CoV-2 infection, which can result in acute respiratory distress, thrombosis and death, has been studied primarily in accessible liquid specimens such as blood, sputum and bronchoalveolar lavage, all of which are peripheral to the primary site of infection in the lung. Here, we describe the combined use of multiplexed deep proteomics with multiplexed imaging to profile infection and its sequelae directly in fixed lung tissue specimens obtained from necropsy of infected animals and autopsy of human decedents. We characterize multiple steps in disease response from cytokine accumulation and protein phosphorylation to activation of receptors, changes in signaling pathways, and crosslinking of fibrin to form clots. Our data reveal significant differences between naturally resolving SARS-CoV-2 infection in rhesus macaques and lethal COVID-19 in humans. The approach we describe is broadly applicable to other tissues and diseases.

Summary

Proteomics of infected tissue reveals differences in inflammatory and thrombotic responses between resolving and lethal COVID-19.

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  1. ScreenIT

    SciScore for 10.1101/2020.10.14.339952: (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

    Antibodies
    SentencesResources
    Immunofluorescence with a DNA stain and antibodies against PANCK, CD45 were used to visualize tissue, with area of interest (AOI) guided by staining of SARS-N and DNA staining in an adjacent stained tissue section.
    antibodies against PANCK, CD45
    suggested: None
    Software and Algorithms
    SentencesResources
    Proteomics raw data and search results were deposited in the PRIDE archive56 and can be accessed under ProteomeXchange accession numbers: PXD021453, PXD021456 and PXD021459.
    PRIDE
    suggested: (Pride-asap, RRID:SCR_012052)
    ProteomeXchange
    suggested: (ProteomeXchange, RRID:SCR_004055)
    The raw images were corrected for uneven illumination using the BaSiC tool72 and images from multiple rounds of scanning of the same tissue were stitched and aligned using ASHLAR.73.
    BaSiC
    suggested: (BaSiC, RRID:SCR_016371)

    Results from OddPub: Thank you for sharing your data.

    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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  2. Version published to 10.1101/2020.10.14.339952v1 on bioRxiv