SLAMF7 engagement super-activates macrophages in acute and chronic inflammation

  1. Daimon P. Simmons
  2. Hung N. Nguyen
  3. Emma Gomez-Rivas
  4. Yunju Jeong
  5. Antonia F. Chen
  6. Jeffrey K. Lange
  7. George S. Dyer
  8. Philip Blazar
  9. Brandon E. Earp
  10. Accelerating Medicines Partnership (AMP) RA/SLE Network
  11. Deepak A. Rao
  12. Edy Y. Kim
  13. Michael B. Brenner

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Abstract

Macrophages regulate protective immune responses to infectious microbes, but aberrant macrophage activation frequently drives pathological inflammation. To identify regulators of vigorous macrophage activation, we analyzed RNA-seq data from synovial macrophages and identified SLAMF7 as a receptor associated with a super-activated macrophage state in rheumatoid arthritis. We implicated IFN-γ as a key regulator of SLAMF7 expression. Engaging this receptor drove an exuberant wave of inflammatory cytokine expression, and induction of TNF-α following SLAMF7 engagement amplified inflammation through an autocrine signaling loop. We observed SLAMF7-induced gene programs not only in macrophages from rheumatoid arthritis patients, but in gut macrophages from active Crohn’s disease patients and lung macrophages from severe COVID-19 patients. This suggests a central role for SLAMF7 in macrophage super-activation with broad implications in pathology.

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  1. ScreenIT

    SciScore for 10.1101/2020.11.05.368647: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Human research: Human subjects research was performed with approval from the Institutional Review Board at Brigham and Women’s Hospital.
    Consent: Patient consent for genomic studies was obtained for all samples used for RNA sequencing.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    antibodies: Recombinant human M-CSF, IFN-β, IFN-γ, IL-1β, IL-6 and TNF-α were from Peprotech.
    antibodies: Recombinant human M-CSF , IFN-β , IFN-γ , IL-1β , IL-6 and TNF-α
    suggested: None
    IFN-β , IFN-γ
    suggested: None
    IL-1β
    suggested: None
    IL-6
    suggested: None
    Anti-TNFR1 (16803) and anti-TNFR2 (22210) were from R&D Systems.
    Anti-TNFR1
    suggested: (Leinco Technologies Cat# T506, RRID:AB_2832006)
    The following antibodies were used for flow cytometry and cell sorting: CD16 (CB16, eBioscience), CD45 (HI30, BioLegend), CD14 (61D3, eBioscience), SLAMF7 (162.1, BioLegend)
    CD16
    suggested: None
    CD45
    suggested: None
    HI30
    suggested: None
    CD14
    suggested: None
    SLAMF7
    suggested: None
    For SLAMF7 stimulation, after 24 h incubation with IFN-γ, macrophages were treated with anti-SLAMF7 antibody or r-SLAMF7 protein.
    IFN-γ
    suggested: None
    r-SLAMF7 protein .
    suggested: None
    For blocking experiments, antibodies were added at 10 μg/ml (TNFR1 and TNFR2) or 20 μg/ml (TNF-α) 30 minutes prior to stimulation with r-SLAMF7. siRNA: Monocytes were cultured in RPMI with 10% FBS and 20 ng/ml M-CSF for 1 week.
    TNFR2
    suggested: None
    TNF-α
    suggested: None
    Software and Algorithms
    SentencesResources
    Data analysis: Flow cytometry data were analyzed using Flowjo version 10.4 (Treestar).
    Flowjo
    suggested: (FlowJo, RRID:SCR_008520)
    Graphical and statistical analysis was done in RStudio version 1.1.383 with R version 3.6.0, JMP Pro version 13.0.0 (JMP Inc), and Prism version 6.0.h (GraphPad).
    RStudio
    suggested: (RStudio, RRID:SCR_000432)
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Heatmaps were generated using pheatmap version 1.0.12.
    pheatmap
    suggested: (pheatmap, RRID:SCR_016418)
    Read quantification was performed using the Broad Institute pipeline, with alignment to GRCh38.83 using STAR version 2.4.2a (68) and quantification with RSEM version 1.2.2.1 (69). 37,414 genes were included for analysis.
    STAR
    suggested: (STAR, RRID:SCR_015899)
    RSEM
    suggested: (RSEM, RRID:SCR_013027)
    Differentially expressed genes for macrophages from inflamed versus non-inflamed tissues from patients with RA or IBD, or healthy versus COVID-19 infected individuals were ordered by the Wald statistic calculated by DESeq2.
    DESeq2
    suggested: (DESeq, RRID:SCR_000154)

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

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  2. Version published to 10.1101/2020.11.05.368647v1 on bioRxiv