Interaction network of SARS-CoV-2 with host receptome through spike protein

  1. Yunqing Gu
  2. Jun Cao
  3. Xinyu Zhang
  4. Hai Gao
  5. Yuyan Wang
  6. Jia Wang
  7. Jinlan Zhang
  8. Guanghui Shen
  9. Xiaoyi Jiang
  10. Jie Yang
  11. Xichen Zheng
  12. Jianqing Xu
  13. Cheng Cheng Zhang
  14. Fei Lan
  15. Di Qu
  16. Yun Zhao
  17. Guoliang Xu
  18. Youhua Xie
  19. Min Luo
  20. Zhigang Lu

Reviewed by

Read the full article See related articles

Discuss this preprint

Start a discussion What are Sciety discussions?

Listed in

Log in to save this article

Abstract

Host cellular receptors are key determinants of virus tropism and pathogenesis. Virus utilizes multiple receptors for attachment, entry, or specific host responses. However, other than ACE2, little is known about SARS-CoV-2 receptors. Furthermore, ACE2 cannot easily interpret the multi-organ tropisms of SARS-CoV-2 nor the clinical differences between SARS-CoV-2 and SARS-CoV. To identify host cell receptors involved in SARS-CoV-2 interactions, we performed genomic receptor profiling to screen almost all human membrane proteins, with SARS-CoV-2 capsid spike (S) protein as the target. Twelve receptors were identified, including ACE2. Most receptors bind at least two domains on S protein, the receptor-binding-domain (RBD) and the N-terminal-domain (NTD), suggesting both are critical for virus-host interaction. Ectopic expression of ASGR1 or KREMEN1 is sufficient to enable entry of SARS-CoV-2, but not SARS-CoV and MERS-CoV. Analyzing single-cell transcriptome profiles from COVID-19 patients revealed that virus susceptibility in airway epithelial ciliated and secretory cells and immune macrophages highly correlates with expression of ACE2, KREMEN1 and ASGR1 respectively, and A CE2/A S GR1/K R EMEN1 (ASK) together displayed a much better correlation than any individual receptor. Based on modeling of systemic SARS-CoV-2 host interactions through S receptors, we revealed ASK correlation with SARS-CoV-2 multi-organ tropism and provided potential explanations for various COVID-19 symptoms. Our study identified a panel of SARS-CoV-2 receptors with diverse binding properties, biological functions, and clinical correlations or implications, including ASGR1 and KREMEN1 as the alternative entry receptors, providing insights into critical interactions of SARS-CoV-2 with host, as well as a useful resource and potential drug targets for COVID-19 investigation.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.09.09.287508: (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.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Supernatant was discarded after centrifugation and washed once with PBS/2%FBS, the cells were then labelled with Anti-hFc-APC (Jackson Lab) antibody for 20min, and washed once with PBS/2%FBS.
    Anti-hFc-APC (Jackson Lab)
    suggested: None
    Beads were washed three times with the RIPA buffer, and the samples were prepared for western blot with anti-hFc or anti-FLAG antibodies.
    anti-hFc
    suggested: None
    anti-FLAG
    suggested: None
    SARS-CoV-2 replication was examined by immuno-fluorescence and flow cytometry with anti SARS-CoV-2 N protein antibody.
    anti SARS-CoV-2 N protein
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Cell culture and transfection: Vero E6 cells and HEK293T cells were cultured in DMEM supplemented with 10% FBS at 37°C in 5% CO2 and the normal level of O2.
    HEK293T
    suggested: None
    HEK293e cells were cultured in serum-free FreeStyle 293 Medium (Invitrogen) with 120 rpm rotation at 37°C in 5% CO2 and the normal level of O2.
    HEK293e
    suggested: None
    ACE2 knockout 293T stable cell line: ACE2 small guide RNA was constructed into pSLQ1651 (Addgene #51024) (44) with a targeting sequence of CTTGGCCTGTTCCTCAATGGTGG.
    293T
    suggested: None
    ACE2 KO 293T stable cell line were obtained by single cell dilution.
    ACE2 KO 293T
    suggested: None
    Authentic SARS-CoV-2 generation and infection: SARS-CoV-2/MT020880.1 were expanded in Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    The flow data were analyzed with FlowJo software.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Data analysis and statistics: Gene Ontology Enrichment Analysis was performed by R bioconductor.
    bioconductor
    suggested: (Bioconductor, RRID:SCR_006442)

    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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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.

  2. Version published to 10.1101/2020.09.09.287508 on bioRxiv