Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement

  1. Eric Song
  2. Christopher M. Bartley
  3. Ryan D. Chow
  4. Thomas T. Ngo
  5. Ruoyi Jiang
  6. Colin R. Zamecnik
  7. Ravi Dandekar
  8. Rita P. Loudermilk
  9. Yile Dai
  10. Feimei Liu
  11. Isobel A. Hawes
  12. Bonny D. Alvarenga
  13. Trung Huynh
  14. Lindsay McAlpine
  15. Nur-Taz Rahman
  16. Bertie Geng
  17. Jennifer Chiarella
  18. Benjamin Goldman-Israelow
  19. Chantal B.F. Vogels
  20. Nathan D. Grubaugh
  21. Arnau Casanovas-Massana
  22. Brett S. Phinney
  23. Michelle Salemi
  24. Jessa Alexander
  25. Juan A. Gallego
  26. Todd Lencz
  27. Hannah Walsh
  28. Carolina Lucas
  29. Jon Klein
  30. Tianyang Mao
  31. Jieun Oh
  32. Aaron Ring
  33. Serena Spudich
  34. Albert I. Ko
  35. Steven H. Kleinstein
  36. Joseph L. DeRisi
  37. Akiko Iwasaki
  38. Samuel J. Pleasure
  39. Michael R. Wilson
  40. Shelli F. Farhadian

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Abstract

One third of COVID-19 patients develop significant neurological symptoms, yet SARS-CoV-2 is rarely detected in central nervous system (CNS) tissue, suggesting a potential role for parainfectious processes, including neuroimmune responses. We therefore examined immune parameters in cerebrospinal fluid (CSF) and blood samples from a cohort of patients with COVID-19 and significant neurological complications. We found divergent immunological responses in the CNS compartment, including increased levels of IL-12 and IL-12-associated innate and adaptive immune cell activation. Moreover, we found increased proportions of B cells in the CSF relative to the periphery and evidence of clonal expansion of CSF B cells, suggesting a divergent intrathecal humoral response to SARS-CoV-2. Indeed, all COVID-19 cases examined had anti-SARS-CoV-2 IgG antibodies in the CSF whose target epitopes diverged from serum antibodies. We directly examined whether CSF resident antibodies target self-antigens and found a significant burden of CNS autoimmunity, with the CSF from most patients recognizing neural self-antigens. Finally, we produced a panel of monoclonal antibodies from patients’ CSF and show that these target both anti-viral and anti-neural antigens—including one mAb specific for the spike protein that also recognizes neural tissue. This exploratory immune survey reveals evidence of a compartmentalized and self-reactive immune response in the CNS meriting a more systematic evaluation of neurologically impaired COVID-19 patients.

One Sentence Summary

A subset of COVID-19 patients with neurologic impairment show cerebrospinal fluid-specific immune alterations that point to both neuroinvasion and anti-neural autoimmunity as potential causes of impairment.

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  1. ScreenIT

    SciScore for 10.1101/2020.09.11.293464: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIACUC: All procedures used in this study (sex-matched, age-matched) complied with federal guidelines and the institutional policies of the Yale School of Medicine Animal Care and Use Committee.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Plates were washed three times with PBS-T (PBS with 0.1% Tween-20) and 50μl of mouse IgG-specific secondary antibody (BioLegend #405306, 1:10,000) diluted in dilution solution added to each well.
    mouse IgG-specific
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Generation of SARS-CoV-2 virus: To generate SARS-CoV-2 viral stocks, Huh7.5 cells were inoculated with SARS-CoV-2 isolate USA-WA1/2020 (BEI Resources #NR-52281) to generate a P1 stock.
    Huh7.5
    suggested: RRID:CVCL_7927)
    Virus titer was determined by plaque assay using Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Experimental Models: Organisms/Strains
    SentencesResources
    Cytokine assays: Soluble chemokines and cytokines were assessed in CSF supernatant and paired plasma using the HD71 Human Cytokine Array/Chemokine Array (Eve Technologies, Calgary, AB).
    AB
    suggested: RRID:BDSC_203)
    Software and Algorithms
    SentencesResources
    To identify potential intercellular interactions between different cell types in the scRNA-seq data, we utilized CellPhoneDB v2(10)
    CellPhoneDB
    suggested: (CellPhoneDB, RRID:SCR_017054)
    Assignments of V(D)J sequences were performed using IgBLAST v.
    IgBLAST
    suggested: (IgBLAST, RRID:SCR_002873)
    Statistical methods: All statistical analyses were performed using commercially available software (Prism or Excel).
    Prism or Excel
    suggested: None
    Human Monoclonal antibodies: Data availability: Gene expression and repertoire data in the study are available in the NCBI repository SRAxxxx Raw mass spectrometry files and data analysis output are available from MassIVE (https://massive.ucsd.edu/) and Proteome Exchange (http://www.proteomexchange.org/) under MassIVE dataset identifier # and Proteome Exchange # Competing Interests: None of the authors declare interests related to the manuscript.
    MassIVE
    suggested: None
    http://www.proteomexchange.org/
    suggested: (ProteomeXchange, RRID:SCR_004055)

    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.

  2. Version published to 10.1101/2020.09.11.293464 on bioRxiv