Integrated Single-Cell Analysis Reveals the Heterogeneity of Tumor-Associated Macrophages and Their Implications for Immunotherapy in Colorectal Cancer.

Background: Tumor-associated macrophages (TAMs) are one of the predominant cell components within the colorectal cancer (CRC) microenvironment, which display prominent and multifaceted roles in modulating tumor biology. The systematic subtypes and function analysis of TAMs remain elusive in CRC.

Methods: We performed an integrated single-cell atlas of three American studies (GSE178341, GSE200997, and GSE231559) to establish the TAM subtypes in the CRC microenvironment. We adopted unsupervised clustering and manual cell annotation to categorize macrophage subtypes accurately, performed enrichment analysis and developmental trajectory analysis for three TAM subsets, and explored the cell-to-cell crosstalk of different TAM subsets with other cell types. Finally, we further performed an integrated single-cell atlas of five Asian studies (GSE132257, GSE132465, GSE144735, GSE221575, and GSE245552) to validate these characteristics of different TAM subtypes.

Results: We identified three TAM subtypes, including CCL20⁺ TAMs with proinflammatory and anti-tumor properties, APOE⁺ TAMs with lipid-metabolism and pro-tumor properties, and SLC40A1⁺ TAMs with immunosuppressive and pro-tumor properties. APOE⁺ TAMs might be intermediate state during macrophage polarization and foster a desmoplastic niche by the fibroblast-derived collagen pathways. SLC40A1⁺ TAMs might play an immunosuppressive role by the fibroblast-derived MIF pathways and the high expression of LGALS9. CRC with enriched CCL20⁺ and APOE⁺ TAMs were characterized by high prevalence of deficient-mismatch repair (27.9%) and might achieve more benefit from immunotherapy.

Conclusion: This single-cell study established an accurate classification system of CRC TAMs, unveiling their diverse roles in modulating tumor biology and assisting in treatment options of CRC patients.