Transcriptomic Effects of Soy-Derived Isoflavone Exposure in Breast Cancer: An Integrative Bioinformatics Analysis

Background: Breast cancer is the leading cause of cancer mortality in women. Studies indicate that soybeans contain powerful compounds that may influence molecular pathways relevant to breast cancer biology. This study aims to identify differentially expressed genes (DEGs) and pathways associated with soy-derived isoflavone exposure using publicly available breast cancer transcriptomic datasets. Methods: Four microarray datasets were analyzed using GEO2R to identify DEGs (|logFC| > 1, P < 0.05). Venn diagrams identified common genes across the studies. Breast cancer-specific genes were further isolated from the DEGs using the Gene Expression Profiling Interactive Analysis (GEPIA) database, with a focus on candidate genes and signaling pathways potentially modulated by soy-derived isoflavone exposure under experimental conditions. Results: The analysis revealed that isoflavone exposure was associated with upregulation of pathways like cell senescence, actin cytoskeleton regulation, and apoptosis processes often elevated in breast cancer. Conversely, pathways, such as the cell cycle and p53 signaling were downregulated. Notably, the cell cycle pathway, pivotal in breast cancer, exhibited downregulation of key genes (CDC20, CCNB1, CDC6, MAD2L1, CCNA2, TTK, MCM4, CDC25C, MCM2, and ESPL1), which are critical for cell cycle progression and checkpoint regulation. Dysregulation of these genes is associated with cancer development. Additionally, enrichment of components related to PI3K/Akt signaling and epithelial-mesenchymal transition was observed, without implying pathway activation or functional benefit. Conclusion: These findings offer exploratory insights into molecular pathways that may be modulated by isoflavone exposure and warrant further experimental validation.