Single-cell Transcriptome of Bronchoalveolar Lavage Fluid Reveals Dynamic Change of Macrophages During SARS-CoV-2 Infection in Ferrets
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Abstract
Although the profile of immune cells changes during the natural course of SARS-CoV-2 inflection in human patients, few studies have used a longitudinal approach to reveal their dynamic features. Here, we performed single-cell RNA sequencing of bronchoalveolar lavage fluid cells longitudinally obtained from SARS-CoV-2-infected ferrets. Landscape analysis of the lung immune microenvironment showed dynamic changes in cell proportions and characteristics in uninfected control, at 2 days post-infection (dpi) (early stage of SARS-CoV-2 infection with peak viral titer), and 5 dpi (resolution phase). NK cells and CD8 + T cells exhibited activated subclusters with interferon-stimulated features, which were peaked at 2 dpi. Intriguingly, macrophages were classified into 10 distinct subpopulations, and their relative proportions changed over the time. We observed prominent transcriptome changes among monocyte-derived infiltrating macrophages and differentiated M1/M2 macrophages, especially at 2 dpi. Moreover, trajectory analysis revealed gene expression changes from monocyte-derived infiltrating macrophages toward M1 or M2 macrophages and identified the distinct macrophage subpopulation that had rapidly undergone SARS-CoV-2-mediated activation of inflammatory responses. Finally, we found that different spectrums of M1 or M2 macrophages showed 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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