Fig. 7: Downregulation of MHC-II and upstream transcriptional regulators in severe COVID-19 CD1c⁺ DCs of the discovery set.

a, Dot plot distribution of HLA-II-related genes at the patient level within the CD1c⁺ DC subset; expression levels are colour-coded, and the percentage of cells expressing the respective gene is size-coded. b, Violin plot distribution of HLA-II and the upstream regulatorsʼ (HLAII_Regulators) module scores among the three severity groups within the CD1c⁺ DC subset; severity groups are colour-coded, each dot represents a cell and the horizontal line displays the mean value of the enrichment score of each given pathway. The violin plots were designed using the total CD1c⁺ DC subsets from the discovery set obtained from n = 2 HC, n = 4 moderate and n = 6 severe samples. Comparative analysis was performed using the two-sided Wilcoxon rank-sum test. P values were adjusted to multiple testings using ‘Bonferroni’ correction. Asterisks above severe indicate P values for severe versus control; asterisks above moderate indicate significance of moderate versus control. *P < 0.05, **P < 0.01, ***P < 0.001; NS, not significant. c, Heatmap representation of top 50 highly variable TF activities between CD1c⁺ DC severity groups; the z-score of activity scores is colour-coded. d, Pseudotime inference tree on UMAP embeddings (left) of the CD1c⁺ DC subset using Monocle3; pseudotime values are colour-coded (right). e, UMAP representation of density scores for the top genes contributing to the pseudotime tree initially inferred in d. Density scores were computed using Nebulosa and are colour-coded. All statistical tests displayed in this figure were performed using the discovery set, comprising a total of 12 samples (n = 2 controls, n = 4 moderate and n = 6 samples) collected from seven patients and two healthy donors.