Characteristics of extracellular vesicle-derived lncRNAs during the progression of HBV-related hepatocellular carcinoma

Liver diseases, including hepatitis B virus (HBV) infection, cirrhosis, and hepatocellular carcinoma (HCC), represent significant global health challenges with limited non-invasive biomarkers for early detection. Extracellular vesicles (EVs), enriched with disease-specific RNAs, offer a promising avenue for biomarker discovery. This study characterized EV-derived long non-coding RNAs (lncRNAs) across various stages of liver disease and explored their mechanistic roles. Serum EVs were isolated from 24 participants (5 healthy controls, 5 chronic hepatitis B patients, 5 liver cirrhosis patients, 4 hepatocellular adenoma patients, and 5 HCC patients) using ultracentrifugation and validated by transmission electron microscopy, nanoparticle tracking analysis, and Western blot. High-throughput transcriptome sequencing systematically analyzed RNA expression profiles in EVs across clinical stages, identifying 133 significantly differentially expressed lncRNAs in the HCC group. Multi-step screening and time-series analysis revealed 10 core lncRNAs associated with HCC progression, and a lncRNA-miRNA-mRNA regulatory network (62 nodes, 68 edges) was constructed. Functional enrichment analysis demonstrated involvement in cell proliferation regulation, transmembrane ion transport, cytosol/plasma membrane localization, protein binding, and autophagy/MAPK pathways, while PPI network analysis identified 10 hub genes (e.g., NTRK2, KCNJ10). Validation in an independent plasma cohort confirmed consistent expression patterns of core lncRNAs and downstream genes. The identified HCC-specific lncRNA biomarkers and regulatory network provide theoretical support for developing novel non-invasive liquid biopsy approaches, holding significant promise for early diagnosis and clinical management of HCC.