Fig. 5

A Using niche-DE marker genes in macrophages near tumor as input, pathway enrichment analysis finds ECM organization, metabolism, and lipid metabolism as top processes in macrophages in the presence of tumor cells. B Ligand-receptor pairs found between macrophages and tumor via niche-LR include C5/C5AR1, SPP1/ITGA4, and TF/TFRC.C Lists of niche-DE-positive and negative tumor-associated macrophage marker genes. D Overlap of niche-DE marker genes with lists found by Sathe et al. [39]. E From top to bottom. Top Two: Spatial heatmaps of SPP1 and CD74 confirm differential expression of marker genes in the region of the tissue containing tumor and hepatocytes respectively. Bottom: Differential spatial colocalization plots of macrophages near tumor and macrophages near hepatocytes. Larger values shown in red correspond to regions that contain macrophages near tumor and smaller values shown in blue correspond to regions that contain macrophages near hepatocytes. Regions in yellow correspond to regions with no macrophages or regions with macrophages that have a similar amount of tumor cells and hepatocytes in their effective niche. F From top to bottom. Top Two: Feature plot of module scores for the set of niche-DE tumor-associated macrophage markers finds enrichment in the region of the UMAP corresponding to lipid-associated macrophages. Feature plot of module scores for the set of niche-DE normal macrophage markers finds depletion in the region of the UMAP corresponding to lipid-associated macrophages. Bottom: UMAP of scrna-seq from Wu et al. [40]. Cells were filtered to only include macrophages, monocytes, and dendritic cells. G Using niche-DE marker genes in macrophages near tumor relative to hepatocytes as input, pathway analysis finds interferon signaling, cytokine signaling, and lipid metabolism among enriched processes