Integrative subtyping by bile acid metabolism identifies CLCA1/UGT2A3/ZG16 as markers of immune dysfunction and poor prognosis in colorectal cancer

Background Colorectal cancer (CRC) is the primary driver of cancer-related death and illness across the world. Despite the full-scale shift of the treatment approach for some colorectal cancer patients due to the use of immune checkpoint inhibitors (ICIs), primary resistance still poses a huge challenge to clinicians. Bile acid metabolism is involved in the pathogenesis of CRC. However, its particular function in shaping the tumor immune microenvironment (TIME) and its effect on prognosis and immune treatment response remain unclear. Methods Based on the transcriptome and clinical data from The Cancer Genome Atlas-Colon Adenocarcinoma (TCGA-COAD) cohort, we performed unsupervised consensus clustering and classified patients into different molecular subtypes according to bile acid metabolism. We subsequently compared overall survival (OS), immune cell infiltration levels, and differentially expressed genes among the subtypes. In addition, protein–protein interaction (PPI) network and Cox proportional hazards regression were used to identify key hub genes. Finally, the expression of these crucial hub genes was validated in the Gene Expression Omnibus (GEO) cohort and independent clinical patients. Results The bile-low group showed a significant reduction in OS time ( p = 0.0049). The infiltration levels of CD8 + T cells ( p < 0.05) and M1 macrophages ( p < 0.01) were significantly higher in the bile-low group than in the bile-high group. We identified three key genes— CLCA1 , UGT2A3 , and ZG16 —and found that they all were downregulated in tumor tissues across the TCGA-COAD and GEO datasets, as well as in independent clinical samples. Survival analysis showed that high CLCA1 expression was significantly associated with favorable overall survival ( p < 0.001), whereas UGT2A3 ( p = 0.23) and ZG16 ( p = 0.17) did not reach statistical significance. The three hub genes were negatively correlated with the (TIDE) score ( CLCA1 : R = − 0.24, p < 0.001; UGT2A3 : R = − 0.15, p = 0.0022; ZG16 : R = − 0.14, p = 0.0039). Conclusion Our findings suggest that bile acid metabolism could shape the TIME via key genes CLCA1 , UGT2A3 , and ZG16 , and subsequently modify CRC prognosis and immunotherapy responses. These genes may serve as potential prognostic indicators and mechanistic mediators linking bile acid metabolism to T-cell dysfunction, offering insights for future combination strategies targeting the metabolism–barrier–immunity axis.