The co-location of MARCO+ tumor-associated macrophages and CTSE+ tumor cells determined the poor prognosis in intrahepatic cholangiocarcinoma

BACKGROUND AND AIMS: Intratumor immune infiltration plays a crucial role in interacting with tumor cells in intrahepatic cholangiocarcinoma (ICC). However, the specific phenotypes of immune cells and their spatial distribution within the tumor microenvironment remain unclear. This study aimed to address these limitations by providing a detailed analysis of immune infiltration patterns in ICC using combined spatial and single-cell transcriptomic data. APPROACH AND RESULTS: We analyzed 29,632 spots from 6 spatial transcriptomic samples and 21,158 cells from 35 single-cell samples of ICC. Two distinct immune infiltration patterns were identified: macrophage+ (characterized by CD68 and macrophage receptor with collagenous structure [MARCO]) and plasma cell+ (characterized by IGHG1 and JCHAIN). These patterns showed contrasting impacts on patient survival, with macrophage+ infiltration associated with poorer outcomes and plasma cell+ infiltration linked to better survival. MARCO+ tumor-associated macrophages (TAMs) were the predominant cell type in macrophage+ samples, indicative of an immune-resistant microenvironment. In MARCO+ TAMs, elevated epithelial-mesenchymal transition activity, angiogenesis, and hypoxia were observed. Spatial transcriptomics and bulk data also revealed co-location of MARCO+ TAMs with cathepsin E (CTSE+) tumor cells, a finding validated by multiplex immunofluorescence in 20 ICC samples. The co-location area was enriched with protumorigenic pathways and suppressed immune responses, and CTSE expression was associated with intrahepatic metastasis and vascular invasion. High infiltration of both MARCO+ TAMs and CTSE+ tumor cells correlated with the poorest survival outcomes. Within the co-location area, the galectin signaling pathway, particularly the LGALS9-CD44 ligand-receptor pair, was highly active in cell-cell communication. CONCLUSIONS: This study identifies 2 intratumor immune infiltration patterns, macrophage+ and plasma cell+, in ICC. Furthermore, the co-location of MARCO+ TAMs and CTSE+ tumor cells contributes to an immune-resistant microenvironment, highlighting potential targets for therapeutic intervention in ICC.