Introduction of hub genes and herbal treatment of breast cancer through bioinformatics

Breast cancer is a prevalent form of endocrine cancer that affects women globally, and its incidence and mortality rates are predicted to rise significantly in the coming years. As a result, breast cancer continues to pose a significant health issue and is a top priority for biomedical research.

We used bioinformatics and reverse pharmacology techniques to identify herbal medicines that could be effective in treating breast cancer. To do this, we analyzed 121 genes from a dataset (GSE 42568) containing both cancer and normal samples. Through this analysis, we identified differentially expressed genes (DEGs) and then used the protein-protein interaction (PPI) network to identify 19 hub genes. To pinpoint hub genes, the widely-used bioinformatics tool, Search Tool for Retrieving Reciprocal Genes (STRING), was utilized. To conduct a more detailed analysis, subnetworks were identified using the MCODE algorithm.

The hub genes identified in our reaserch are involved in various functions, including positive regulation of cold-induced thermogenesis, patched binding, and the PPAR signaling pathway, as revealed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. We understood that the herbs Ginkgo biloba seeds, Polygoni Cuspidati Rhizoma Et Radix, Smilacis Glabrae Rhixoma, Capsici Fructus, Cyathulae Radix, Puerariae Flos, and Ardisiae Japonicae Herba can target hub genes such as PPARG, CCNB1, CAV1, CDH1, ADIPOQ, LEP, IGF1, LPL, DGAT2, ACSL1, and PCK1. Using nine identified ingredients, these herbs were identified as key in targeting hub genes.