Identification of Differentially Expressed Genes and Molecular Pathways Involved in Primary Biliary Cholangitis Using RNA-Seq

<b>Objective</b>: This study aims to investigate the functional role of lncRNA STX17-DT, which was previously found to be upregulated in peripheral blood mononuclear cells (PBMCs) of PBC patients, by examining its impact on gene expression and cellular behavior in a human monocyte model. <b>Methods</b>: STX17-DT was overexpressed in THP-1 cells, which was assessed via plasmid transfection. Transcriptomic changes were analyzed by RNA sequencing, followed by comprehensive bioinformatics analyses including differential expression, functional enrichment, transcription factor network, and protein-protein interaction (PPI) analysis. Functional validation was performed using CCK-8 and TUNEL assays to assess proliferation and apoptosis, respectively. <b>Results</b>: Overexpression of STX17-DT led to 1973 differentially expressed genes (DEGs), with 1201 upregulated and 772 downregulated. Key upregulated genes included interferon-stimulated genes (e.g., <i>interferon induced protein 44 like</i> (<i>IFI44L</i>), <i>interferon induced protein 44</i> (<i>IFI44</i>), <i>guanylate binding protein 1</i>(<i>GBP1</i>)) and chemokines (<i>CCL4</i>, <i>CCL8</i>). Upregulated DEGs were significantly enriched in immune-related pathways such as NF-κB signaling, Toll-like receptor signaling, TNF signaling, and cytokine-cytokine receptor interaction. Downregulated genes were involved in metabolic and signaling pathways such as PI3K-Akt, cAMP, and butanoate metabolism. Transcription factor analysis revealed significant alterations in regulators like <i>Yes1 associated transcriptional regulator</i>(<i>YAP1</i>), <i>nuclear receptor subfamily 4 group A member 1</i>(<i>NR4A1</i>), and <i>MAF bZIP transcription factor B</i>(<i>MAFB</i>). PPI network analysis suggested <i>TNF</i>, <i>TLR4</i>, <i>TLR6</i>, and <i>STAT2</i> as central hubs. Functionally, STX17-DT overexpression enhanced THP-1 cell proliferation and significantly reduced apoptosis. <b>Conclusions</b>: STX17-DT promoted a pro-inflammatory transcriptomic profile and enhanced monocyte survival in our study, suggesting a potential role in PBC immunopathology. It may represent a potential biomarker and therapeutic target, particularly for patients with advanced disease or suboptimal response to ursodeoxycholic acid. Further studies in primary cells, animal models, and histological samples are warranted to validate its role in PBC pathogenesis.