Global absence and targeting of protective immune states in severe COVID-19

  1. Alexis J. Combes
  2. Tristan Courau
  3. Nicholas F. Kuhn
  4. Kenneth H. Hu
  5. Arja Ray
  6. William S. Chen
  7. Nayvin W. Chew
  8. Simon J. Cleary
  9. Divyashree Kushnoor
  10. Gabriella C. Reeder
  11. Alan Shen
  12. Jessica Tsui
  13. Kamir J. Hiam-Galvez
  14. Priscila Muñoz-Sandoval
  15. Wandi S. Zhu
  16. David S. Lee
  17. Yang Sun
  18. Ran You
  19. Mélia Magnen
  20. Lauren Rodriguez
  21. K. W. Im
  22. Nina K. Serwas
  23. Aleksandra Leligdowicz
  24. Colin R. Zamecnik
  25. Rita P. Loudermilk
  26. Michael R. Wilson
  27. Chun J. Ye
  28. Gabriela K. Fragiadakis
  29. Mark R. Looney
  30. Vincent Chan
  31. Alyssa Ward
  32. Sidney Carrillo
  33. The UCSF COMET Consortium
  34. Cai Cathy
  35. Jenny Zhan
  36. Bushra Samad
  37. Suzanna Chak
  38. Rajani Ghale
  39. Jeremy Giberson
  40. Ana Gonzalez
  41. Alejandra Jauregui
  42. Deanna Lee
  43. Viet Nguyen
  44. Kimberly Yee
  45. Yumiko Abe-Jones
  46. Logan Pierce
  47. Priya Prasad
  48. Pratik Sinha
  49. Alexander Beagle
  50. Tasha Lea
  51. Armond Esmalii
  52. Austin Sigman
  53. Gabriel M. Ortiz
  54. Kattie Raffel
  55. Chayse Jones
  56. Kathleen Liu
  57. Walter Eckalbar
  58. Michael Matthay
  59. David J. Erle
  60. Prescott G. Woodruff
  61. Charles Langelier
  62. Kirsten Kangelaris
  63. Carolyn M. Hendrickson
  64. Carolyn Calfee
  65. Arjun Arkal Rao
  66. Matthew F. Krummel

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Abstract

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  1. Version published to 10.1038/s41586-021-03234-7
  2. ScreenIT

    SciScore for 10.1101/2020.10.28.359935: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Patients, or a designated surrogate, provided informed consent to participate in the study.
    IRB: The study is approved by the Institutional Review board: IRB#
    RandomizationThe average expression of the genes in each signature are compared to a background list of randomly selected from the bins and used to generate a score per cell for each signature.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Samples were harvested and unconjugated AffiniPure Fab Fragment Goat anti-human IgG (H+L) (Jackson Immunoresearch; #109-007-003) and Human TruStain FcX block (BioLegend; #422302) were used to block pre-bound antibodies and Fc receptors.
    anti-human IgG
    suggested: (Jackson ImmunoResearch Labs Cat# 109-007-003, RRID:AB_2337555)
    After washing the cells with FACS buffer, cell-bound antibodies were detected using an AffiniPure Donkey anti-human IgG-Alexa Fluor 647 antibody (Jackson Immunoresearch; #709-605-149), which was incubated with the cells for 30 min on ice.
    anti-human IgG-Alexa Fluor 647
    suggested: None
    The following antibodies were used for flow cytometric analysis: anti-human CD3-BB700 (clone SK7; BD Biosciences;
    anti-human CD3-BB700
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    The supernatant was collected and viral titer was quantified using a plaque assay in Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    Bulk RNASeq library preparation for Genotyping: RNA was extracted from aliquots of 250K Peripheral Blood Mononuclear Cells (PBMCs) utilizing the ZYMO Research Quick RNA MagBead kit (R2133) on a Thermofisher KingFisher Flex system following manufacturer’s procedures.
    Thermofisher KingFisher
    suggested: None
    Computational Processing for Genotyping: Sequencing reads were aligned to the human reference genome and Ensembl annotation (GRCh38 genome build, Ensembl annotation version 95) using STAR v2.7.5c (PMID: 23104886) with the following parameters: --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000.
    Ensembl
    suggested: (Ensembl, RRID:SCR_002344)
    STAR
    suggested: (STAR, RRID:SCR_015899)
    Duplicate reads were removed and read groups assigned by individual for variant calling using Picard Tools v2.23.3 (
    Picard
    suggested: (Picard, RRID:SCR_006525)
    Nucleotide variants were identified from the resulting bam files using the Genome Analysis Tool Kit (GATK, v4.0.11.0) following the best practices for RNA-seq variant calling (PMID: 25431634; PMID: 21478889).
    GATK
    suggested: (GATK, RRID:SCR_001876)
    Processed, annotated Seurat objects were processed using the DoubletFinder package (8).
    DoubletFinder
    suggested: (DoubletFinder, RRID:SCR_018771)
    The R package EnrichR were used to generate volcano plot from differential gene expression using FindMarkers function in Seurat.
    EnrichR
    suggested: (Enrichr, RRID:SCR_001575)
    20 μL each of plasma collected from the COMET patient cohort (21 COVID-19 positive, 13 COVID-19 negative, and 14 healthy individuals) were analyzed using the Olink® Target 96 Inflammation panel, which is a set of 92 inflammation-related protein biomarkers.
    COMET
    suggested: (CoMet, RRID:SCR_011925)
    After surface staining and addition of fixable live/dead violet dye (ThermoFisher; #L34955), intracellular detection of IFITM3 was done using the eBioscience Foxp3 /
    ThermoFisher
    suggested: (ThermoFisher; SL 8; Centrifuge, RRID:SCR_020809)
    Samples were harvested and unconjugated AffiniPure Fab Fragment Goat anti-human IgG (H+L) (Jackson Immunoresearch; #109-007-003) and Human TruStain FcX block (BioLegend; #422302) were used to block pre-bound antibodies and Fc receptors.
    BioLegend
    suggested: (BioLegend, RRID:SCR_001134)
    Statistical Analysis and Data visualization: Statistical analyses were performed using GraphPad prism or the R software package.
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    The R packages Seurat, ggplot2
    Seurat
    suggested: (SEURAT, RRID:SCR_007322)
    2 (version 3.1.0) (Wickham, 2016) GraphPad Prism and Adobe Illustrator were used to generate figures.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Adobe Illustrator
    suggested: (Adobe Illustrator, RRID:SCR_010279)

    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. Version published to 10.1101/2020.10.28.359935v1 on bioRxiv
  4. Version published to 10.21203/rs.3.rs-97042/v1 on Research Square