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Abstract
Background
The tumor microenvironment in colorectal cancer (CRC) significantly influences disease progression and immune responses, particularly the role of macrophages in regulating immune evasion requires further investigation.
Methods
This study integrated data from the TCGA-COAD dataset with the GEO database, along with single-cell RNA sequencing data, to systematically analyze key genes in colorectal cancer. R software was utilized for data normalization and differential analysis, with criteria set at ∣log2FoldChange ∣ > 1 and adjusted p-value < 0.05 for gene selection. The Seurat package was employed for clustering single-cell data, while the “Monocle2” algorithm was used to perform pseudo-time analysis on the differentiation trajectory of macrophages. Additionally, non-negative matrix factorization (NMF) was applied for subtype classification of CRC patients, and various machine learning algorithms (such as LASSO and random forest models) were utilized to identify key pathogenic genes. Finally, PCR was employed to validate the expression of these key genes, and immune analysis software was used to assess their impact on immune cells, alongside pathway enrichment analysis.
Results
Through the integration of multi-omics data, we identified significant differential expression of VSIG4, CYBBC3AR1, and FCGR1A in CRC patients. LASSO and random forest models selected these three genes as critical pathogenic factors for CRC, with AUC values exceeding 0.8 across multiple machine learning models, demonstrating their high diagnostic efficacy. PCR validation further supported the differential expression of VSIG4 and other genes in CRC. Single-cell transcriptomic analysis revealed that VSIG4 was highly enriched in specific macrophage subpopulations and significantly influenced the tumor microenvironment by regulating CD8 + T cell immune exhaustion. Pseudo-time analysis indicated that the differentiation trajectory of macrophages during tumor progression was closely associated with VSIG4 expression. Additionally, cell communication analysis.
highlighted the important role of VSIG4 in the interactions between macrophages and endothelial cells. Pathway enrichment analysis demonstrated that VSIG4 expression was closely linked to the regulation of the JAK-STAT pathway and metabolic pathways such as the TCA cycle.
Conclusion
This study provides the first evidence that VSIG4, CYBBC3AR1, and FCGR1A play critical roles in the immune microenvironment of colorectal cancer, particularly emphasizing the immunoregulatory function of VSIG4 in macrophage activity and CD8 + T cell immune exhaustion. PCR validation further confirmed the differential expression of these genes. These findings offer new insights into the molecular mechanisms of CRC and provide a potential theoretical basis for targeting VSIG4 in immunotherapy.