Fig. 2: SARS-CoV-2 infection causes massive death of lung-resident cells at the early stage. | Cell Discovery

Fig. 2: SARS-CoV-2 infection causes massive death of lung-resident cells at the early stage.

From: Single-cell spatiotemporal analysis of the lungs reveals Slamf9+ macrophages involved in viral clearance and inflammation resolution

Fig. 2

a UMAP projection of AM and monocyte/macrophage showing 15 cell subpopulations. b The expression of selected genes defining key tissue-resident AM and monocyte/macrophage subpopulations. c The temporal distribution of AM and monocyte/macrophage subpopulations. Ro/e > 1, enrichment; Ro/e < 1, depletion. d Detection rates of SARS-CoV-2 genes in AM-Cd36. Given a viral gene gv, the detection rate is defined as the ratio of the number of gv+ cells to the total cells of the specific cell type and then normalized by the gene length in the SARS-CoV-2 genome and multiplied by 106. e Volcano plot of differentially expressed genes between virus-positive and virus-negative cells in AM-Cd36 (cutoff: (|Log2FC| > 0.5, Padj < 0.05)). f Gene ontology (GO) terms enriched in upregulated genes in virus-positive AM-Cd36. GO terms related with cell death are indicated by dashed line. g Spatial distribution of cell death-related genes (death signal) and AMs, represented by three lung sections at d2. Scale bars, 2 mm. h Boxplot showing the proportion of AM-Cd36 and proliferating AM-Cd36 in total Stereo-seq bin80-bins of nine lung slides at each timepoint. Center line, median; box bounds, first and third quartiles; whiskers, 1.5 times the interquartile range. Data are represented as mean ± SEM (n = 9 slides per timepoint). Kruskal–Wallis test. i Spatial distribution of viral genes and death signals, represented by three lung sections at d2. Scale bars, 2 mm. j Boxplot showing the spatial correlation of different cell types and death-related genes at d0, d2, d5, and d7. Data are represented as mean ± SEM (n = 9 slides per timepoint). Center line, median; box bounds, first and third quartiles; whiskers, 1.5 times the interquartile range. Kruskal–Wallis test was performed to calculate the P value across different timepoints. Pearson correlation was performed to calculate the P value of all spots within each slide. Black dots: P < 0.05; gray dots: P ≥ 0.05. Red dotted line represents the correlation value of 0.

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