Fig. 2: Unsupervised analysis of CD4+ T cells and their characterization. | Nature Communications

Fig. 2: Unsupervised analysis of CD4+ T cells and their characterization.

From: Marked T cell activation, senescence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia

Fig. 2

a Uniform Manifold Approximation and Projection (UMAP) representation of the CD4+ T cell landscape. b Heat map representing different CD4+ T cell clusters identified by FlowSOM, with relative identity and percentages in healthy controls and COVID-19 patients. The colors in the heat map represent the median of the arcsinh, 0–1 transformed marker expression calculated over cells from all the samples, varying from blue for lower expression to red for higher expression. The dendrogram on the left represents the hierarchical similarity between the metaclusters (metric: Euclidean distance; linkage: average). Each cluster has a unique color assigned (bar on the left). Barplot along the rows (clusters) and values on the right indicate the relative sizes of clusters. c Differential analysis between controls (bar color: salmon; n = 13) and COVID-19 (emerald; n = 21). The heat represents arcsine-square-root transformed cell frequencies that were subsequently normalized per cluster (rows) to mean of zero and standard deviation of one. The color of the heat varies from blue indicating relative under-representation to orange indicating relative over-representation. Bar and numbers at the right indicate significant differentially abundant clusters (green) and adjusted p values. Clusters are sorted according to adjusted p values, so that the cluster at the top shows the most significant abundance changes between the two conditions. d Representative dot plots related to the expression of different chemokine receptors and lineage-specifying transcription factors in gated CD4+ T from a control (upper) and a patient (lower panel). Numbers indicate the percentage in each quadrant. Two experiments (one for the control group, one for patients) out of 13 are shown. Numbers indicate the percentage in each quadrant. The gating strategy for the identification of CD4+ T cells is reported in Supplementary Fig. 1. e Percentages of different CD4+ T cell subpopulations in controls (n = 6) and patients (n = 7), obtained by manual gating. Data represent individual values (dots), mean (centre bar) ± SEM (upper and lower bars). Statistical analysis is performed by two-sided Mann–Whitney nonparametric test; if not indicated, p value is not significant. Source data are provided as a Source Data file.

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