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Objective: To investigate the regulation mechanism of baicalin on triple negative breast cancer (TNBC)’s biological network by a systematic biological strategy and cytology experiment. Methods: A systematic biological methodology is utilized to predict the potential targets of baicalin, collect the genes of TNBC, and analyze the TNBC and baicalin’s network. After the systematic biological analysis is performed, the cytology experiment, real-time quantitative PCR (qPCR) is used to validate the key biological processes and signaling pathways. Results: After systematic biological analysis, two networks were constructed and analyzed: (1) TNBC network; (2) Baicalin-TNBC protein-protein interaction (PPI) network. Several TNBC-related, treatment-related targets, clusters, signaling pathways and biological processes were found. Cytology experiment shows that baicalin can inhibit the proliferation, migration and invasion of breast cancer MDA-MB-231 cells in vitro (P < 0.05). The results of qPCR showed that baicalin increase the expression of E-cadherin mRNA, and decrease the expression of vimentin, β-catenin, c-Myc and MMP-7 mRNA in LPS-induced breast cancer MDA-MB-231 cells (P < 0.05). Conclusion: Baicalin may achieve anti-tumor effects through regulating the targets, biological processes and pathways found in this research.