Fig. 6: Signaling features underlying the COVID-19 symptom difference.
From: Systematic investigation of cytokine signaling activity at the tissue and single-cell levels
a, Sample source sites. We analyzed single-cell RNA-seq datasets from the bronchoalveolar lavage and peripheral blood samples from patients with COVID-19. b, IL-10 activities in macrophages from lavage fluid. Each dot presents a single cell from the COVID-19 study with t-distributed stochastic neighbor embedding (t-SNE) coordinates computed per the original publication45. The color represents the predicted IL-10 activity. Circles highlight the cluster of macrophages. c, Enrichment of IL-10 activities in macrophages from lavage fluid from patients with severe illness. The violin plots present IL-10 activity distributions in different patient groups, smoothed by a kernel density estimator. The color legend is per b. The two-sided Wilcoxon rank-sum P value was computed to compare activities of severe (n = 6) and mild (n = 3) patient groups. d, IFN-I activities in CD8+ T cells from blood. The IFN-I activities in CD8+ T cells (circles) are shown as per b, with uniform manifold approximation and projection (UMAP) coordinates from the original publication46. e, Depletion of IFN-I activities in peripheral blood CD8+ T cells from patients with severe disease. The two-sided Wilcoxon rank-sum P value was computed to compare activities of severe (n = 14) and mild (n = 13) patient groups within each cell type. f, Differential signaling activities in macrophages from lavage fluid. The heat map presents cytokines whose predicted signaling activities were significantly different between individuals with severe disease, those with mild disease and healthy individuals. g, Summary of signaling activities in COVID-19. The heat map includes cell types with significant differences in signaling activities among individuals with severe disease, those with mild disease and healthy individuals. Each cell shows the median value across all individuals in each group. Only cytokines with at least three significant values in at least three cell types were included.
