Single-cell transcriptome of bronchoalveolar lavage fluid reveals sequential change of macrophages during SARS-CoV-2 infection in ferrets
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Abstract
Few studies have used a longitudinal approach to describe the immune response to SARS-CoV-2 infection. Here, we perform single-cell RNA sequencing of bronchoalveolar lavage fluid cells longitudinally obtained from SARS-CoV-2-infected ferrets. Landscape analysis of the lung immune microenvironment shows distinct changes in cell proportions and characteristics compared to uninfected control, at 2 and 5 days post-infection (dpi). Macrophages are classified into 10 distinct subpopulations with transcriptome changes among monocyte-derived infiltrating macrophages and differentiated M1/M2 macrophages, notably at 2 dpi. Moreover, trajectory analysis reveals gene expression changes from monocyte-derived infiltrating macrophages toward M1 or M2 macrophages and identifies a macrophage subpopulation that has rapidly undergone SARS-CoV-2-mediated activation of inflammatory responses. Finally, we find that M1 or M2 macrophages show distinct patterns of gene modules downregulated by immune-modulatory drugs. Overall, these results elucidate fundamental aspects of the immune response dynamics provoked by SARS-CoV-2 infection.
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SciScore for 10.1101/2020.11.18.388280: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Virus and Cells: SARS-CoV-2 strain NMC-nCoV02 (reference, Cell host & Microbe) was propagated in Vero cells in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Grand Island, NY) supplemented with 1% penicillin/streptomycin (GIBCO) and TPCK-treated trypsin (0.5 μg/mL; Worthington Biochemical, Lakewood, NJ) in a 37°C incubator with 5% CO2 for 72 h. Verosuggested: NoneSoftware and Algorithms Sentences Resources Slides were viewed using an Olympus IX 71 (Olympus, Tokyo, Japan) microscope, and images were captured using DP controller software. scRNA-Seq Analysis: Basic Quality Control: … SciScore for 10.1101/2020.11.18.388280: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Virus and Cells: SARS-CoV-2 strain NMC-nCoV02 (reference, Cell host & Microbe) was propagated in Vero cells in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Grand Island, NY) supplemented with 1% penicillin/streptomycin (GIBCO) and TPCK-treated trypsin (0.5 μg/mL; Worthington Biochemical, Lakewood, NJ) in a 37°C incubator with 5% CO2 for 72 h. Verosuggested: NoneSoftware and Algorithms Sentences Resources Slides were viewed using an Olympus IX 71 (Olympus, Tokyo, Japan) microscope, and images were captured using DP controller software. scRNA-Seq Analysis: Basic Quality Control: Reference sequence and gene information were downloaded from the Ensembl database (MusPutFur1.0, under accession number GCF_000215625.1), and then annotated with human ortholog genes using the same database (Biomart database, GRCh38). Ensemblsuggested: (Ensembl, RRID:SCR_002344)Lastly, the cells were clustered by unsupervised clustering, using the default pipeline of the Seurat package (resolution = 0.4 for whole cell types, 0.3 for NK cells, 0.2 for CD8 T lymphocytes, and 0.6 for monocytes/macrophages). Seuratsuggested: (SEURAT, RRID:SCR_007322)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.
- 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.
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