Manuscript Detail

Title: Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans.
Authors: Arunachalam, Prabhu S et al
Abstract: COVID-19 represents a global crisis, yet major knowledge gaps remain about human immunity to SARS-CoV-2. We analyzed immune responses in 76 COVID-19 patients and 69 healthy individuals from Hong Kong and Atlanta. In PBMCs of COVID-19 patients, there was reduced expression of HLA-DR and pro-inflammatory cytokines by myeloid cells, and impaired mTOR-signaling and IFN-α production by plasmacytoid DCs. In contrast, there were enhanced plasma levels of inflammatory mediators, including EN-RAGE, TNFSF14, and oncostatin-M, which correlated with disease severity and increased bacterial products in human plasma. Single-cell transcriptomics revealed no type-I IFN, reduced HLA-DR in myeloid cells of severe patients, and transient expression of IFN-stimulated genes. This was consistent with bulk PBMC transcriptomics, and transient, low plasma IFN-α levels during infection. These results reveal mechanisms and potential therapeutic targets for COVID-19.
Journal: Science
Curator: Kenneth Smith
Reviewer: Aris Floratos
Author-provided data: ?

paper: Arunachalam, P. S., Wimmers, F., Mok, C. K. P., Perera, R. A., Scott, M., Hagan, T., ... & Pulendran B. (2020). Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science, 369(6508), 1210-1220. Chicago
contributor: Bali Pulendran
contributor_organization: Stanford
contributor_email: bpulend@stanford.edu

 

    • description: Genes differentially expressed in COVID-19 patients compared to healthy controls
    • exact_source: Fig. 4, Table S4 Tab "DEG_healthy_vs_covid-19"
    • tissue: PBMC
    • immune_exposure: SARS-CoV-2 infection
    • cohort: Adults (38 - 90)
    • comparison: COVID-19 vs healthy
    • repository_id: GSE155673
    • platform: CITE-seq
    • response_components:
    • response_behavior: Up or down
        • description: Interferon-stimulated genes in COVID-19 patients
        • exact_source: Fig. 4G and supplementary fig. 15A
        • tissue: PBMC
        • immune_exposure: SARS-CoV-2 infection
        • cohort: Adults (38 - 90)
        • comparison: COVID-19 vs healthy
        • repository_id: GSE152418
        • platform: Bulk RNAseq
        • response_components:
        • response_behavior: Up
            • description:
            • exact_source:
            • tissue:
            • immune_exposure:
            • cohort:
            • comparison:
            • repository_id:
            • platform:
            • response_components:
            • response_behavior:
                • description:
                • exact_source:
                • tissue:
                • immune_exposure:
                • cohort:
                • comparison:
                • repository_id:
                • platform:
                • response_components:
                • response_behavior:

 

Spreadsheet: Link to curation spreadsheet