Molecular insights into epoxyazadiradione induced death in triple-negative breast cancer cells: A system biology approach.

[Display omitted] • The system biology approach has been used for the first time to elucidate the anticancer potential of epoxyazadiradione (EAD) in TNBC cells. • Able to identify the 1086 upregulated and 752 downregulated genes upon treatment with EAD. • GSEA revealed pathways related to ER stress were upregulated upon EAD treatment and downregulated were pathways related to cell cycle and metabolic. • ToppFun analysis identified two relevant protein clusters in the upregulated gene sets and 4 in the downregulated gene sets. • The identified top 50 hub genes from differentially expressed PPI networks. • These hub genes have an inverse correlation with TNBC clinical trial samples via analysis using the CPTAC/TCGA dataset on the UALCAN web server. Epoxyazadiradione is an important limonoid with immense pharmacological potential. We have reported previously that epoxyazadiradione (EAD) induces apoptosis in triple negative breast cancer cells (MDA-MB 231) by modulating diverse cellular targets. Here, we identify the key genes/pathways responsible for this effect through next-generation sequencing of the transcriptome from EAD treated cells and integrated molecular data analysis using bioinformatics. In silico analysis indicated that EAD displayed favourable drug-like properties and could target multiple macromolecules relevant to TNBC. RNA sequencing revealed that EAD treatment results in the differential expression of 1838 genes in MDA-MB 231 cells, with 752 downregulated and 1086 upregulated. Gene set enrichment analysis of these genes suggested that EAD disrupts protein folding in the endoplasmic reticulum, triggering the unfolded protein response (UPR) and potentially leading to cell death. EAD also induced oxidative stress and DNA damage, downregulated pathways linked to metabolism, cell cycle progression, pro-survival signalling, cell adhesion, motility and inflammatory response. The identification of protein cluster and hub genes were also done. The validation of the identified hub genes gave an inverse correlation between their expression in EAD treated cells and TNBC patient samples. Thus, the identified hub genes could be explored as therapeutic or diagnostic markers for TNBC. Hence, EAD appears to be a promising therapeutic candidate for TNBC by targeting various hallmarks of cancer, including cell death resistance, uncontrolled proliferation and metastasis. To conclude, the identified pathways and validated targets for EAD will provide a roadmap for further in vivo studies and preclinical/clinical validation required for potential drug development. [ABSTRACT FROM AUTHOR]