A Bioinformatics Approach to Predict Long non-coding RNA Targets of Shikonin in Apoptosis Induction of Breast Cancer Cells

Phytochemicals such as shikonin accomplish their pleiotropic anti-tumor activities by modulating the expression of non-coding RNAs. The role of shikonin in modulating long non-coding RNAs (lncRNAs) to induce apoptosis in vitro in breast cancer cells was investigated. An RNA-Seq dataset available in NCBI, in which shikonin induced apoptosis in different breast cancer cell lines, was analysed to examine lncRNA expression. We identified ۸۸ differentially expressed lncRNAs in the shikonin-treated groups. After identifying the ۱۰ up- and down-regulated lncRNAs, we found that dysregulation of putative lncRNAs is associated with cancer pathophysiology, particularly breast cancer. The significantly up- and down-regulated lncRNAs in shikonin-treated cell lines were NEAT۱, ALDH۱A۳-AS۱-۲۰۱, MIR۳۱۴۲HG, AC۰۷۹۳۰۵.۱, and DDR۱-AS۱. Furthermore, a network of interactions between key lncRNAs and miRNAs was constructed. Our comparative analysis of the lncRNA transcriptional landscape identified several novel lncRNA candidates that may regulate breast cancer cells' response to shikonin treatment. This may pave the way for the development of new molecular biomarkers with diagnostic, prognostic, and potentially therapeutic applications.

کلیدواژه ها:

Apoptosis ، LncRNAs-miRNAs network ، Shikonin ، Breast cancer ، Phytochemicals