Berberine Modulates Mitophagy-Related Gene Expression and Suppresses Breast Cancer Cells: A Multi-Omics and Experimental Study.

Breast cancer became the most commonly diagnosed cancer worldwide in 2020. Mitophagy, as a key mechanism for selectively clearing damaged mitochondria, plays an important role in breast cancer-related processes. Berberine has shown its anti-tumor ability in multiple types of tumors, but whether berberine exerts its anti-breast cancer effects through modulating mitophagy-related genes remains to be elucidated. This study integrated the Gene Expression Omnibus (GEO) database and single-cell sequencing, explored the key genes that interfere with breast cancer, evaluated and verified the efficacy of berberine against breast cancer by molecular docking and in vitro experiments, and provided a novel direction to breast cancer prevention and therapy and drug development. Screening autophagy-related targets through the GEO database combined with the autophagy gene library and revealing the relationship within cancerous cells with immunological cells through single-cell sequencing. Using molecular docking and in vitro tests to evaluate and confirm the efficacy of berberine against breast cancer. In this study, 20 pivotal genes were screened and identified. These genes are mainly involved in autophagy-related pathways that are significantly activated in breast cancer. Enrichment analysis showed that autophagy and mitophagy pathways were obvious in breast cancer. The immune microenvironment of single-cell shows that pathological changes of fibroblasts and NK cells mediated by macrophage invasion in tumor tissue may be an important molecular mechanism of breast cancer. Molecular docking and in vitro experiments suggest that berberine can effectively inhibit breast cancer by targeting BECN1, BCL2, HIF1A, MYC, PINK1, and FOXO3 to regulate autophagy initiation and mitochondrial quality control, while CASP3 was assessed only at the mRNA level due to the intrinsic CASP3 deficiency in MCF-7 cells. Through GEO data combined with single-cell sequencing and in vitro experimental verification, this study revealed the pivotal gene of mitophagy in breast cancer and provides evidence that berberine modulates mitophagy-related genes and induces mitochondrial damage. These findings offer a theoretical basis for further investigation into berberine in breast cancer therapy.