Integrating Machine Learning and Multi-Omics Analyses to Identify Immune-Related Biomarkers and Mechanisms in Primary Biliary Cholangitis

Background: Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease that gradually progresses, making early diagnosis and treatment challenging. Reliable biomarkers could enhance diagnostic accuracy and therapeutic development. Methods: This study analyzed three publicly available gene expression datasets from the GEO database: GSE119600 (90 PBC patients and 47 healthy controls), GSE159676 (12 PBC patients and 6 controls), and GSE61260 (11 PBC patients and 38 controls). To identify genes closely linked to PBC, we applied machine learning techniques, including LASSO, SVM-RFE, and random forest. We subsequently conducted gene set enrichment (GSEA) and immune cell infiltration analyses to investigate their biological significance. Additionally, potential drug interactions were explored via the DGIdb database, and a ceRNA regulatory network was developed to examine gene regulation. Finally, the expression of selected genes was validated through multiplex immunofluorescence staining of liver tissue samples from PBC patients. Results: We identified PSMB7, TBK1, SLC29A1, and CD244 as key genes associated with PBC; these genes were significantly enriched in immune-related pathways and strongly correlated with immune regulation. Drug target prediction indicated that some genes could interact with existing immunomodulators or anticancer drugs. ceRNA network analysis revealed that TBK1, SLC29A1, and CD244 interact with multiple miRNAs and lncRNAs, potentially regulating the immune microenvironment of PBC through noncoding RNA mechanisms. Immunofluorescence staining confirmed that these genes were highly expressed in liver tissues from PBC patients. Conclusion: By integrating machine learning and functional analyses, this study identified four genes that may serve as potential biomarkers for PBC. Their involvement in immune regulation suggests possible applications in both diagnosis and therapy. Further studies are necessary to explore their clinical relevance and therapeutic potential.