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

Dini, Salome; Ghorbani, Abozar; Eskandarzade, Neda; Alibeiki, Maryam

doi:10.22034/jmpb.2026.371148.2081

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

Articles in Press

Document Type : Research Paper

Authors

¹ Young and Elite Researchers Club, Karaj Branch, Islamic Azad University, Karaj, Iran

² Department of Plant Protection, Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran

³ Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran

⁴ Department of Microbiology, Faculty of Basic Sciences, Shahrood Branch, Islamic Azad University, Shahrood, Iran

10.22034/jmpb.2026.371148.2081

Abstract

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 88 differentially expressed lncRNAs in the shikonin-treated groups. After identifying the 10 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 NEAT1, ALDH1A3-AS1-201, MIR3142HG, AC079305.1, and DDR1-AS1. 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.

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