Fig. 4: Myeloid cell phenotypes in exhausted immune environments indicate inflammation and T cell-suppressive potential.

a Volcano plot showing differential gene expression between myeloid cells of IE1 and IE2 samples in pseudobulk patient-averaged scRNA-seq data. Dashed lines indicate an FDR of 0.1 and a logFC of 0.5. Genes are colored by functional group. b UMAP plot of scRNA-seq data from 26,000 myeloid cells colored by Seurat cluster and annotated by cell type. c Enrichment of cluster frequencies in IE1 and IE2 samples. Two-sided Wilcoxon rank sum test was used for statistical analysis and dashed lines indicate a p value of 0.05. d Heatmap showing normalized average single-cell expression of the top 10 differentially expressed genes for all myeloid cell clusters. Selected genes overexpressed in the respective cluster are indicated in the colored boxes. e Scatterplot of the mean T cell-suppression score versus the mean T cell-attraction score for all myeloid cell clusters. f DotPlot showing expression of main migDC markers across all myeloid cell clusters. g UMAP of cDC subsets and migDCs with Slingshot trajectories overlaid. h Slingshot pseudotime ordering of single cells from the cDC2 and migDC subsets (top) and heatmap showing normalized expression of selected genes along pseudotime using the rolling average expression over 11 cells (bottom). Genes with log counts per million <1.5 in EdgeR analysis were excluded for plots a–d. For scatterplots, Spearman correlation coefficient (two-tailed test) and p value are indicated.