Integrated transcriptomic analysis reveals a lncRNA-miRNA-TF-mRNA regulatory network underlying quercetin’s anti-hepatocellular carcinoma effects

Background Quercetin (QUR) exhibits multiple pharmacological activities against hepatocellular carcinoma (HCC). Competing endogenous RNA (ceRNA) networks and transcription factors (TFs) play critical roles in oncogenesis and cancer progression, however, the integrated ceRNA- and TF-mediated mechanisms of QUR in HCC treatment remain largely unknown. Methods The anti-proliferative, anti-migratory, and pro-apoptotic effects of QUR on HepG2 cells were evaluated using CCK‑8, colony formation, wound‑healing, and flow cytometry assays. Transcriptome sequencing was performed to identify differentially expressed (DE) long non-coding RNAs (lncRNAs), micro RNAs (miRNAs), and messenger RNAs (mRNAs) after QUR treatment. Functional enrichment, protein–protein interaction (PPI) analysis, and survival analyses were performed to elucidate therapeutic mechanisms and prognostic biomarkers. A lncRNA–miRNA–TF–mRNA regulatory network was constructed by integrating multiple databases, and its clinical relevance was assessed using TCGA and GTEx data. Results QUR dose-dependently inhibited the proliferation, colony formation, migration, and induced apoptosis of HCC cells. Transcriptomic profiling identified 647 DEmRNAs, 304 DElncRNAs, and 17 DEmiRNAs. Down‑regulated DEmRNAs were enriched in nucleosome, chromatin, and telomere metabolism, while up‑regulated DEmRNAs were involved in cytokine activity and immune cell differentiation. Key pathways included metabolic reprogramming, cytokine signaling, PI3K/AKT, and viral carcinogenesis. PPI analysis revealed five functional clusters, and survival analysis identified 12 prognosis‑associated DEmRNAs (e.g., AURKA , CCNB1 , KIF20A , and PLK1 ). The constructed regulatory network comprised three DEmiRNAs, eight TFs, five DEmRNAs, and 20 DElncRNAs, revealing coordinated miRNA-TF cross-talk and lncRNA–meditated ceRNA axes that fine-tuned key mRNAs. Mechanistically, QUR might balance oncogene and tumor suppressor expression, thereby inhibiting metabolism, mitosis, and transcription in HCC cells, while enhancing anti‑cancer immunity and extrinsic apoptosis. Conclusions This study delineated a comprehensive lncRNA–miRNA–TF–mRNA network that elucidated the systematic mechanisms of QUR against HCC, offering potential biomarkers and therapeutic targets for further investigation.