1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Relative expression analysis of COL1A1 mRNA in oral tongue squamous cell carcinoma: a study based on gene expression omnibus (GEO) and bioinformatics analysis
Paper ID : 1262-ICB10
Authors:
Naeimeh Parsapour1, Mansoureh Azadeh *2, Mohammad Rezaei3
1Zist Fanavari Novin biotechnology institute
2zist fanavari novin biotechnology institute
3Zist Fanavari Novin Biotechnology institute
Abstract:
Oral Tongue Squamous Cell Carcinomas (OTSCC) is one of the most aggressive and common malignant tumor of the head and neck distinct [1]. Our study aimed to define a competitive endogenous RNA (CeRNA) network that provides valuable biomarkers and boosts the treatment process of OTSCC. Therefore, bioinformatics analysis targets novel biomarkers for diagnosis and curing OTSCC. From the NCBI Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/), we obtained the gene expression data of 10 OTSCC tumor and control samples (GSE160042). GEO2R analyzed the data sets to find out differentially expressed genes in patients (DEGs). A threshold value of |logFC| > 2 and a p-value< 0.05 were chosen, and one of the most significant genes was taken to miRWalk 2.0 [2] to find target miRNA. Target miRNA was searched in LncBase v.3 [2], and appropriate lncRNAs were found. At last, Cytoscape software (3.9.0) was used to show the interaction between the components of the CeRNA network. Pathway enrichment was performed by KEGG [3]. COL1A1 had a significant high expression in the tumor samples (logFC > 2, adj. p. value < 0.05). Moreover, mir-615-3P is a novel suppressor for COL1A1 (score: 1.00). miR-516-3p have RNA interactions with, NORAD, XIST, and MIAT lncRNAs. COL1A1 is an invasion-related gene observed in the ‘extracellular matrix’ (ECM) and cell adhesion signaling pathway. It has been reported to be involved in multiple biological behaviors, including cell proliferation, invasion, metastasis, and angiogenesis. miR-615-3p have a significant suppressor effect on an over-expressed gene (COL1A1) in OTSCC patients. Also, it has the significant RNA interaction with NORAD, XIST, and MIAT lncRNAs. The mentioned lncRNA can regulate the OTSCC development and metastasis by affecting the expression level of COL1A1 by regulating cell proliferation.
Keywords:
Oral Tongue Squamous Cell Carcinomas (OTSCC), mir-615-3P, COL1A1, Biomarker
Status : Paper Accepted (Poster Presentation)