Enterococcus-driven metabolite-host gene networks in IBD-associated colorectal carcinogenesis: integrative multi-omics and experimental validation

Background This study aims to elucidate the role of Enterococcusin the progression from inflammatory bowel disease to colorectal cancer (CRC), with a focus on identifying key metabolites and host genes regulated by Enterococcusand their influence on CRC development. Methods Using the database gutMGene, gutMDisorder and MACdb, we mined the key metabolites and human genes. We acquired the activated genes (panel 1) and inhibited genes (panel 2), and metabolite associated genes (MAGs, panel 3). Subsequent analyses included protein-protein interaction (PPI) network construction, functional enrichment, differential expression and survival analysis in CRC, and immune infiltration assessment. In vitro experiments validated the regulatory effects of E. faecalisand its key metabolites on candidate genes. Single-cell RNA sequencing (scRNA-seq) was used to dissect cell-type-specific expression patterns within the tumor microenvironment. Results We screened 12 activated genes (Panel1: IL11, IL24, IFNG, IL10, IL12B, IL1B, IL6, TNF, ANGPTL4, CXCL10, PLIN2, and PPARG ) and four inhibited genes (Panel 2: CXCL8, IL6, TNF, and PDCD6IP ). Three metabolites were found important in CRC development: agmatine, formate, and levodopa, linking with 28 MAGs. In particular, IL10, IL11, CXCL10, IL1B, and IFNG are protective genes in CRC; and there are four MAGs associated with CRC PFS, and they are all survival-risk genes: COMT, PRL, EDNRA, and MAPK3 . Experimental validation showed that E. faecalis significantly upregulated the level of IL-10 and IL-1B in CRC, while its metabolites agmatine and levodopa markedly induced the expression of the survival-risk gene MAPK3 . scRNA-seq revealed cell-type-specific expression patterns, where IL1B was significantly upregulated in both tumor epithelial and myeloid cells, and IL10 was specifically elevated in tumor epithelial cells. In contrast, MAPK3 exhibited divergent trends, showing downregulation in tumor epithelial cells but significant upregulation in myeloid cells. Conclusion Enterococcus exhibits a dual role in colitis-associated CRC, correlating with both tumor-suppressing and tumor-promoting effects. It may activate protective immune genes while its metabolites, agmatine and levodopa, alter the expression of oncogenic MAGs. The findings highlight the complex metabolite-host gene networks driven by Enterococcusand suggest estradiol and sodium arsenite as potential adjuvant therapies, offering new insights into precision intervention for CRC.