Figure 4: scRNA-seq demonstrates that COVID-19 VAP is associated with early impaired anti-bacterial immune signaling in lower respiratory tract monocytes, macrophages and neutrophils.

A) UMAP of single cell RNA-seq data from patients that do or do not develop VAP at the “early” time-point, annotated by cell type. B) Cell type proportions in single cell RNA-seq from VAP and No-VAP patients at the “early” time-point. Bars represent the median with IQR. Statistical significance was determined by Mann-Whitney tests. None of the cell types were significantly different with a p-value <0.05. The p-values for each cell type are as follows: B cells: 0.073; Neutrophils: 0.28; T/NK cells: 0.21; Secretory: 0.46; Ciliated: 0.94, and Mono/Mac: 0.81. C) Volcano plot displaying the differentially expressed genes between VAP and No-VAP patients in monocytes and macrophages. D) Ingenuity Pathway Analysis (IPA) of key canonical pathways and upstream cytokines based on differential gene expression analysis in monocytes and macrophages of patients who develop VAP versus those who do not, with adjusted p-values < 0.05. Only significant pathways (IPA Z-score of >2 or <−2 and overlap p-value <0.05) are shown. E) Volcano plot displaying the differentially expressed genes between VAP and No-VAP patients in neutrophils. F) IPA of canonical pathways and upstream cytokines based on differential gene expression analysis in neutrophils of patients who develop VAP versus those who do not, with adjusted p-values < 0.05. Only significant pathways (IPA Z-score of >2 or <−2 and overlap p-value <0.05) are shown. All pathways and cytokines are shown in Supplementary data files 5 and 6.