A systems biology-based study to assess the effects of TNF-α ± apigenin in triple-negative breast cancer cell line

Abstract

Abstract Background: Triple-negative breast cancer (TNBC) refers to the type of breast cancer with no estrogen, progesterone, and HER2 receptors. Various methods can be applied to treating patients with BC, among which the therapeutic-based ones without toxic side effects are extremely important. In this study, we computationally investigated the impact of apigenin on the TNBC cell line as traditional Chinese medicine. Materials and methods: We retrieved the GSE120550 dataset from the NCBI-GEO database. The BRB-array tools employed pre- and post-processing approaches to identify significant differentially expressed genes. Additionally, the DAVID web server was applicable to analyze the three main components, including the "biological process," "cellular component," and "molecular function," as well as the KEGG signaling pathway. Finally, using the Venn diagram, we thoroughly investigated the number of shared genes among fifteen groups constructed from six compared sample sets. Results: The primary analysis of six pairs of samples reveals significant DEGs, which are prone to be ranked in the TOPPGene web server in terms of priority. The identified genes that play vital roles in inhibiting the progression of BC enrich various signaling pathways. Then, protein-protein interaction network analysis revealed the involved biomarkers and the inhibitory effect of apigenin among fifteen possible sets constructed from the six groups in pairs. Conclusion: The outcomes of the current study showed and confirmed the inhibitory effect of apigenin with no toxic side effects on patients with TNBC. This natural product can also target future therapeutics and novel drug designs.