Integrated Single-Cell and Spatial Transcriptomic Analysis Reveals the Immunoregulatory Role of MIF Signaling in Colorectal Cancer.

Background

The cellular heterogeneity and spatial organization patterns of the tumor microenvironment (TME) play a crucial role in colorectal cancer (CRC) progression, but their spatial distribution and cellular communication mechanisms require further elucidation. This study aims to systematically dissect the cellular heterogeneity and spatial organization characteristics of the CRC microenvironment by integrating single-cell and spatial transcriptomic data.

Methods

Single-cell RNA sequencing and spatial transcriptomics data of primary CRC were integrated to characterize the TME. Intercellular signaling patterns were elucidated through communication analysis, spatial niche clustering, ligand-receptor pair analysis, and spatial expression mapping. The ESTIMATE algorithm was applied to assess the correlation between TME scores and pathway-associated genes. Drug sensitivity prediction was performed using the oncoPredict.

Results

Single-cell analysis identifies nine major cell types, revealing significant cellular heterogeneity. Intercellular communication analysis demonstrates that the MIF signaling pathway plays a prominent role within the TME communication network, with MIF-(CD74+CD44) and MIF-(CD74+CXCR4) identified as dominant receptor complexes. Spatial transcriptomic analysis reveals distinct spatial functional partitioning of these signaling axes. Signaling flow analysis indicates an immunosuppressive "tumor-immune" axis mediated by MIF signaling from tumor epithelial cells to immune cells. MIF expression is negatively correlated with ImmuneScore, while its receptors CD74, CD44, and CXCR4 are positively correlated. Drug sensitivity analysis reveals potential associations between key genes (MIF, CD74, CD44, and CXCR4) in the MIF pathway and various anti-tumor drugs.

Conclusions

Our study reveals the cellular heterogeneity of the CRC microenvironment from multiple perspectives, elucidates the key mechanisms of the MIF signaling pathway, and provides potential therapeutic targets for CRC treatment.