1st International and 10th National Iranian Conference on Bioinformatics

Home Accepted Papers

Identification of potential diagnostic microRNAs and lncRNAs in breast carcinoma: Integrated high-throughput bioinformatics investigation

Paper ID : 1271-ICB10

Authors:

Soudabeh Madhkhan Esfahani, Mohammad Rezaei, Ziba Rezvani Sichani, Samaneh Hosseinpour, Mansoureh Azadeh *

Zist Fanavari Novin biotechnology institute

Abstract:

Breast cancer is the second foremost cause of death among women worldwide[1]. MicroRNAs and lncRNAs are involved in regulating the expression of certain genes, as well as some biological processes in breast carcinoma[2]. In the present study, we focused on identifying potential diagnostic microRNAs and lncRNAs in breast cancer using bioinformatics analysis. Breast cancer Microarray dataset GSE29431 was selected from Gene Expression Omnibus (GEO)[3], then differentially expressed genes (DEGs) were screened. DEG analysis was performed using limma[4] and GEOquery[5] packages in R studio (v.4.0.2). The most significant genes (logFC > 3 and adjusted p-value < 0.05) were selected, and taken to miRWalk[6], to find relevant microRNAs. LncBase v.2[7] was employed to find decent lncRNAs (score = 1.000). Finally, we used STRING[8] to find PPI network. After careful analysis of GSE29431 dataset, a total number of 286 up-regulated genes were detected in breast carcinoma. AGR2 (logFC = 3.84, adjusted p-value = 2.48E – 05), Muc1 (logFC = 3.45 and adjusted p-value = 3.76E - 06) and PLPP4 (logFC = 3.41 and adjusted p-value = 1.20E – 07) had remarkable expressions. All of genes were taken to miRWalk. We identified hsa-miR-197-3p, hsa-miR-145-5p as well as hsa-miR-148a-3p relating to AGR2, Muc1 and PLPP4, respectively. According to lncBase v.2, various lncRNAs including KCNQ1OT1, GLIDR and OIP5-AS1 was detected as potential lncRNAs, showing score = 1.000. Except for AGR2-Muc1 interaction network (gene co-expression score = 0.213), there was no gene interaction among other genes. Based on results, three microRNAs including has-miR-197-3p, has-miR-145-5p and has-miR-148a-3p, up-regulated in breast cancer, and have oncogenic role in this kind of carcinoma. Relating to these microRNAs, the expressions of KCNQ1OT1, GLIDR and OIP5-AS1 rise in breast cancer, so, they could be considered as potential diagnosis factors in breast carcinoma.

Keywords:

Breast cancer, microRNAs, lncRNAs, GEO.

Status : Paper Accepted (Poster Presentation)