• level of GSK3B expression level is regulated by TSIX as a significant low-expressed gene and potential biomarker in breast cancer patients: integrated systems biology and bioinformatics investigation
  • Mahla Bagheri,1 Mahdi Hajisadeghian,2 Mansoureh Azadeh,3,* Mohammad Rezaei,4
    1. Zist Fanavari Novin Biotechnology Institute
    2. Zist Fanavari Novin
    3. Zist Fanavari Novin
    4. Zist Fanavari Novin


  • Introduction: Recently, breast cancer is recognized as a second death factor for women among other cancer-related diseases, and prevention treatments for this cancer are extremely challenging (1). Besides, uncontrolled growth and division of breast cells lead to making a huge number of tissues which are called tumors (2). Accordingly, this cancer can be categorized based on its presence or absence of molecular markers for estrogen or progesterone receptors and human epidermal growth factor 2 (ERBB2; formerly HER2) (3). Due to the existence of a wide range of information in the field of biomedical technologies, this research is performed in a virtual lab instead of real-life-based experiments (4). In this experiment, RNA isolated from human MDA-MB-436 cells and HCC1954 cells from human mammary epithelial cells were studied.
  • Methods: Expression analysis of GSE1299 was achieved from GEO2R online software and validation of expression analyses was performed by GEPIA2 (5). For supporting the possibility of a correlation between GSK3B and breast cancer, GEPIA2 and ENCORI databases were used and they evaluated the correlation between the gene and patients’ survival. Gene ontology information and biological pathway and molecular function were processed by ENRICHR, KEGG, and REACTOME databases. Initially, for exploring the effects of single nucleotide polymorphisms (SNPs) of GSK3B on the 3`UTR miRNA SNP database was used, and for finding out the coding SNPs dbSNP database was used. Also, SIFT was used to find out the deleterious SNPs. HOPE database also was used for recognizing the changing of amino acid chains that are made by SNPs, and for extracting the accession code of the gene UNIPROT database was used. In addition, STRING database was used to demonstrate the protein-protein interactions, and the importance of each protein can be achieved depending on their node degrees. For exploring the microRNA interactions, miRWALK database was used, then for more finding out the co-expression and survival of each microRNA with the target gene (GSK3B), ENCORI was explored. Furthermore, the LncRRIsearch database for the interaction of each microRNA with LncRNA was searched, but GeneCard had to be used to make sure that those RNAs are the exact LnsRNAs. Finally, lncRNA with microRNA interactions were examined by LncBase database.
  • Results: According to the analysis of the GEO dataset, a gene named GSK3B was found to be considerably downregulated (|logFC|= 1.505, adj. P value = 0.00300252, P Value = 2.78e-05). This gene plays an important role as a serine-threonine protein kinase that was originally identified as the kinase that phosphorylates and inhibits glycogen synthase. GSK3B plays a role as a tumor suppressor for mammary tumors, and it is able to make breast cancer cells sensitive to chemotherapy drugs (6). Also, relating to the information of ENCORI, Gepia2, and Reactome datasets, GSK3B gene plays a function in some pathways such as Hedgehog signaling, Prolactin signaling, B cell receptor signaling, and IL-17 signaling. Moreover, this gene is a part of some diseases such as Endometrial cancer, Colorectal cancer, and Prostate cancer. To the data from the STRING, the interaction of GSK3B has been shown with other proteins such as MAPT, AKT1, CTNNB1, MYC, APC, AXIN2, LRP6, TP53, CSNK141, and AXIN1. Studying on the miRWALK has revealed has-mir-7160-5p (energy = -28.5), and has-mir-6775-5p (energy = -34.6) has illustrated significant interactor to GSK3B. Then, both those microRNAs were examined in LncRRIsearch and LncBase to show lnsRNAs that have interactions with those microRNAs, so GSK3B had interactions with three important lncRNAs : TSIX (energy = -41.98), HELLPAR(energy = -31.85), and KCNQ1OT1 (energy = -34.96).
  • Conclusion: To conclude, the expression of GSK3B was decreased in the breast cancer samples, and has-mir-7160-5p and has-mir-6775-5p worked as an inhibitor of microRNA factors on GSK3B. Also, rs201010589, rs201010589, etc. were recognized as deleterious SNPs.
  • Keywords: bioinformatics, Microarray, breast cancer, Biomarker analysis, GSK3B