Fig. 2: Identification of anti-tumoral and pro-tumoral macrophage populations.

a Uniform Manifold Approximation and Projection (UMAP) embedding of tumor macrophages. The inset shows the normalized expression level of the CD68 gene (n = 19 patients, n = 42 tumor samples). b Principal component analysis (PCA) plot of cells in scRNA-seq. Single-cell level measurements for each tissue origin were visualized to obtain pseudo-bulk distribution for the PCA analysis, related to the UMAP plot in (a). c Single-cell transcription of selected markers defining tumor macrophage clusters. Transcription levels are color-coded: gray, not expressed; blue, expressed. d Dot plot representing the relative average expression of a subset of marker genes across all clusters. The marker genes in each cluster were identified by log fold change compared with the remaining clusters. e Dot plot showing the relative average expression of a subset of anti-tumoral and pro-tumoral marker genes (y-axis) across the clusters (x-axis). As indicated in the legend, dot size denotes the percentage of cells in a cluster expressing each gene. The dot color represents the relative average expression levels. f Differentially expressed (DE) genes between tumor anti-tumoral and pro-tumoral macrophages; averaged scaled gene expression of all cells in each group.