Abstract
BACKGROUND: Cholangiocarcinoma (CHOL) is a malignancy with poor clinical outcomes and limited treatment options. While extensive research has investigated genetic and signaling pathways in CHOL, the molecular mechanisms underlying disease pathogenesis remain incompletely understood. A key hurdle has been the lack of a systematic, multi-omic approach to illuminate causal relationships between genetic variants and CHOL risk. RESULTS: We integrated gene expression, co-expression network, and Mendelian randomization analyses to elucidate molecular drivers of CHOL. Gene set enrichment of differentially expressed genes from CHOL tumor samples identified enrichment in cancer-related biological processes. Weighted gene co-expression network analysis identified modules highly correlated with CHOL, including genes involved in cell cycle regulation, transcription, and proteolysis. Integrating these data with targets of the herbal formula Juhua, which shows anti-CHOL activity, pinpointed four candidate hub genes (CDK5, CDK7, CTSB, MAP2K2). Molecular docking revealed interactions between Juhua constituents and these hub genes. Mendelian randomization analysis of genetic variants implicated CCL2, CD5, CXCL6, CXCL9, HGF, IL10, IL10RA, IL18, IL24, IL2RB, IL6, IL8, SIRT2 and SLAMF1 as causally associated with CHOL. CONCLUSION: Our multi-omic analysis provides new insight into molecular underpinnings of CHOL and identifies candidate disease drivers, signaling pathways and herbal targets for further validation. This systematic approach established a framework for illuminating causal links between genetics, molecular mechanisms and disease pathogenesis, with potential to accelerate drug and biomarker development for CHOL.