Multi-omics interrogation identifies IRF4 as a causal transcription factor in monocytes that suppresses colorectal cancer progression by remodeling the immune microenvironment and inhibiting EMT

<h4>Background</h4>Although surgery and chemotherapy remain standard treatments for colorectal cancer (CRC), immunotherapy offers a promising avenue for patients with advanced disease. However, the cellular and molecular mechanisms underlying CRC progression and immune evasion are not fully elucidated.<h4>Methods</h4>We integrated single-cell RNA sequencing (GSE161277), bulk transcriptomic data (GEO and TCGA), and Mendelian randomization (MR) analysis to identify key cell subpopulations and transcription factors (TFs) causally associated with CRC. Spatial transcriptomics, multiple immune deconvolution algorithms, and in vitro experiments (including lentiviral-mediated IRF4 modulation, flow cytometry, and ELISA) were performed to validate the expression, immune regulatory function, and prognostic significance of the candidate TF.<h4>Results</h4>Single-cell analysis identified monocytes as the most critical cell subpopulation in CRC pathogenesis. MR analysis revealed that IRF4, monocyte-associated TF, was causally linked to increased CRC risk. IRF4 expression was significantly downregulated in CRC tissues at both mRNA and protein levels, with elevated methylation and association with poor prognosis. Multi-omics immune profiling demonstrated that IRF4 correlated with immune cell infiltration, cancer immunity cycle scores, and immunotherapy response. Spatially, IRF4 was enriched in normal or low-malignant regions. Experimentally, IRF4 overexpression in HCT116 CRC cell enhanced CXCL8 and CCL5 secretion, increased the number of CD14⁺IRF4⁺ monocytes and CD3⁺CD8⁺IRF4⁺ T cells in co-culture systems, and suppressed epithelial-mesenchymal transition (EMT), whereas IRF4 knockdown reversed these effects.<h4>Conclusions</h4>IRF4, monocyte-associated TF, is a causal factor in CRC development. Its downregulation correlates with adverse prognosis and impaired antitumor immunity. IRF4 modulates the tumor microenvironment by regulating chemokine secretion, immune cell recruitment, and EMT, positioning it as a potential therapeutic target for CRC immunotherapy.