Integrative single-cell and spatial transcriptomic analysis reveals lipid metabolism–mediated macrophage heterogeneity during colorectal cancer liver metastasis progression

Colorectal cancer liver metastasis (CRLM) is a leading cause of cancer-related death in patients with colorectal cancer (CRC) and remains a major clinical challenge. Emerging evidence indicates that metabolic reprogramming within the tumor microenvironment profoundly influences immune cell behavior and disease progression, yet the specific role of lipid metabolism in macrophage heterogeneity during CRLM is still unclear. We integrated single-cell RNA sequencing and spatial transcriptomics to characterize lipid metabolic states, differentiation trajectories, intercellular communication, and spatial distribution of macrophages across normal colon, primary CRC (pCRC), and CRLM. Lipid metabolic activity was quantified using multiple scoring algorithms, pseudotime analysis was performed with the “Monocle” R package, cell–cell communication was evaluated using the “CellChat” R package, and spatial localization was inferred using the RCTD method and the “MISTy” R package. Macrophages exhibited the highest lipid metabolic activity among immune cells, and this activity was significantly elevated in CRLM compared with pCRC. Subclustering analysis identified three lipid metabolism–related macrophage subsets (CD1C⁺, CXCL10⁺, CX3CR1⁺) enriched in CRLM, among which CD1C⁺ and CXCL10⁺ subsets displayed distinct differentiation dynamics. Cell–cell communication analysis revealed metastasis-specific remodeling, including diversified VEGF signaling in CD1C⁺ macrophages and enhanced SPP1-integrin and C3–(ITGAX + ITGB2) interactions in CXCL10⁺ macrophages. Spatial transcriptomics analysis showed that lipid metabolism activity was highest in macrophage-rich regions of the normal colon, higher in epithelial and tumor regions of pCRC than in fibroblast regions, and highest in hepatocyte regions of CRLM. Moreover, CD1C⁺ macrophages predominantly localized to tumor regions in both pCRC and CRLM and maintained close associations with other immune cells. Lipid metabolism shapes macrophage heterogeneity and function states during CRLM progression, with CD1C⁺ populations emerging as key macrophage subsets linked to metastatic niche remodeling.