Prognostic Significance of Bile Acid Metabolism in Colorectal Cancer: An Integrative Multi-Omics, Single-Cell, and Spatial Analysis

Metabolic reprogramming is a hallmark of colorectal cancer (CRC), yet the prognostic role of the bile acid metabolism pathway, regulated by host genetics and gut microbiota, remains poorly understood. We utilized an integrative multi-omics framework, combining bulk transcriptomics, single-cell, and spatial transcriptomics with microbiome data, to systematically dissect the prognostic significance of this pathway. The analysis was validated by experimental qRT-PCR on paired patient tumor and normal tissues. The pathway exhibited widespread transcriptional suppression in CRC tumors, a finding confirmed by the development of a robust, 15-gene prognostic signature that reliably predicted overall survival across five independent cohorts. Single-cell analysis demonstrated that bile acid activity is suppressed across epithelial tumor subsets. Crucially, spatial transcriptomics provided cellular context, revealing that the pathway's activity is distinctly enriched in metastatic stromal and CMS3 tumor microenvironment (TME) niches. Furthermore, the pathway's activity was significantly correlated with gut microbiota composition, identifying key associated taxa ( Clostridiales positive, Dorea longicatena negative). Collectively, these integrated results establish the suppression of the bile acid metabolism pathway as a critical prognostic determinant in CRC. This comprehensive analysis, validated at the clinical level (qRT-PCR confirmed the significant downregulation of key components, including ABCA8 and ABCD2 ), provides a novel, multi-source foundation for biomarker discovery and therapeutic targeting aimed at modulating the metabolic TME.