Bioinformatic analysis and experimental validation identify prognostic hub genes associated with apigenin response in breast cancer

Background Breast cancer (BC) has emerged as the second most common cancer globally, making the exploration of its molecular mechanisms and novel therapeutic targets an urgent priority. Objectives This study aimed to identify key genes mediating the anti-BC effects of apigenin through bioinformatics analysis. Methods Weighted gene co-expression network analysis (WGCNA) was used to identify BC-associated gene modules (turquoise, yellow, and brown). Genes from these modules were intersected with differentially expressed genes (DEGs) from apigenin-treated BC cells, and then protein-protein interaction (PPI) analysis was performed to identify hub genes. The TCGA‑BRCA dataset, the Gene Expression Profiling Interactive Analysis (GEPIA), and the Human Protein Atlas were employed for expression validation, as well as for prognostic and immune-infiltration analyses. KEGG enrichment analysis, molecular docking, and Western blotting were carried out to elucidate pathways, ligand-binding affinities, and the changes of protein-level expression. Results The intersection analysis and PPI screening jointly identified 10 hub genes. Validation using TCGA-BRCA, GEPIA, and the Human Protein Atlas confirmed that these genes exhibited distinct expression patterns between tumor and normal tissues, along with significant associations with survival outcomes and immune-cell infiltration. KEGG enrichment analysis suggested that these hub genes are involved in arginine and proline metabolism, as well as in cancer-related pathways. Molecular docking and Western blotting demonstrated that apigenin exhibits high binding affinity for IPO4, RRP9, and METTL1, and that the downregulation of their protein expression accompanies this. Conclusion The 10 hub genes could serve as potential prognostic biomarkers and candidate therapeutic targets for apigenin-based BC therapy, thereby providing mechanistic insights into the antitumor effects mediated by this traditional Chinese medicine (TCM) monomer.