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Comprehensive identification and validation of hub genes targeted by quercetin in hepatocellular carcinoma via
1Department of Oncology, Luzhou Hospital of Traditional Chinese Medicine, Luzhou, China.
Abstract:
Hepatocellular carcinoma (HCC) is a common and highly lethal malignancy worldwide, characterized by complex, multi-step molecular mechanisms. Identifying novel pathogenic genes and potential natural compounds holds great promise for advancing HCC treatment. In this study, we analyzed the GSE65372 dataset from the GEO database using the limma method to identify differentially expressed genes (DEGs). Weighted gene co-expression network analysis (WGCNA) was applied to identify HCC-associated gene modules. The intersection of DEGs, WGCNA-derived genes, and HCC-related genes from the GeneCards database yielded a set of candidate genes. A protein-protein interaction (PPI) network was constructed using the STRING database, and four cytoHubba algorithms (MCC, MNC, degree, EPC) were used to identify hub genes. Functional enrichment analysis (GO and KEGG) was performed, and immune infiltration characteristics were evaluated using the CIBERSORT algorithm. In addition, single-gene GSEA was carried out for hub genes. Potential therapeutic compounds were predicted using the CMap platform and validated by molecular docking using AutoDock Vina. Finally, a quercetin treatment model was established, and CCK-8 assays were used to assess cell viability in LO2 (normal hepatocytes) and HepG2 (HCC cells). The expression of hub genes was further evaluated by RT-qPCR. A total of 1326 DEGs were identified, and 1003 key module genes were selected via WGCNA. Intersection with GeneCards yielded 95 candidate genes, of which 40 showed direct interactions in the PPI network. Functional enrichment revealed that these genes were significantly involved in the cell cycle, p53 signaling pathway, and cellular senescence. Immune infiltration analysis indicated an imbalanced tumor immune microenvironment characterized by macrophage predominance and suppressed T-cell activity. Cross-analysis of cytoHubba algorithms identified six consistent hub genes: CCNB1, CDC20, NCAPG, TPX2, CENPF, and CENPN. GSEA results showed that these genes are associated with cell cycle regulation, apoptosis, and p53 pathway activation. CMap analysis identified quercetin as a potential therapeutic compound, and molecular docking confirmed stable binding to all six hub proteins, with binding energies below - 5 kcal/mol. CCK-8 assays demonstrated that quercetin inhibited HepG2 cell viability in a dose-dependent manner, with minimal effects on LO2 cells. RT-qPCR results showed that quercetin treatment for 24 h significantly downregulated the mRNA expression of all six hub genes. Through multi-omics integration and experimental validation, this study identified six key genes closely associated with HCC and demonstrated the therapeutic potential of the natural compound quercetin via multi-target regulation. These findings provide theoretical and experimental support for targeted therapy and natural drug development in HCC.
Insights
This study identifies six key genes linked to hepatocellular carcinoma (HCC) and shows that quercetin, a natural compound, can potentially treat HCC by targeting these genes. This offers new avenues for HCC therapy.
Area of Science:
- Oncology
- Molecular Biology
- Bioinformatics
Background:
- Hepatocellular carcinoma (HCC) is a lethal cancer with complex molecular underpinnings.
- Identifying novel genes and natural compounds is crucial for advancing HCC treatment.
Purpose of the Study:
- To identify key genes and potential therapeutic compounds for hepatocellular carcinoma (HCC) through multi-omics analysis.
- To validate the therapeutic potential of identified compounds on HCC cells and hub genes.
Main Methods:
- Differential gene expression analysis (limma) and weighted gene co-expression network analysis (WGCNA) on the GSE65372 dataset.
- Protein-protein interaction network construction, hub gene identification (cytoHubba), and functional enrichment analysis (GO, KEGG).
- Immune infiltration analysis (CIBERSORT), compound prediction (CMap), molecular docking, cell viability assays (CCK-8), and gene expression analysis (RT-qPCR).
Main Results:
- Identified 1326 differentially expressed genes and 1003 key module genes, yielding 95 candidate genes and 40 interacting genes.
- Six consistent hub genes (CCNB1, CDC20, NCAPG, TPX2, CENPF, CENPN) were identified, involved in cell cycle and p53 signaling.
- Quercetin was predicted as a therapeutic compound, showing dose-dependent inhibition of HepG2 cell viability and downregulation of hub gene expression.
Conclusions:
- Six hub genes (CCNB1, CDC20, NCAPG, TPX2, CENPF, CENPN) are strongly associated with hepatocellular carcinoma.
- The natural compound quercetin demonstrates therapeutic potential for HCC by targeting these hub genes.
- This research provides a foundation for targeted HCC therapies and natural drug development.
