Dysregulated miRNAs profile in triple negative breast cancer: in silico analysis

Dysregulated miRNAs profile in triple negative breast cancer: in silico analysis

Code: G-1054

Authors: Melika Soltani Sarvestani ℗, Zahra Sadat Tabatabaei Jafari, Somayeh Reiisi ©

Schedule: Wednesday 2023-12-06 16:45 on Unit Panel A

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Abstract:

Abstract

Introduction and Objectives: Breast cancer is the most common malignancy in ladies worldwide(1) and the second leading reason of cancer-associated demise amongst ladies(2), that is curable in about 70-80% of patients with non-metastatic disease in the early stages (2).Triple-negative breast cancer is described as tumors that lack expression of estrogen receptor (ER), progesterone receptor (PR), and HER2(3). future therapeutic concepts in breast cancer aim at individualization of therapy as well as at treatment de-escalation and escalation based on tumour biology and early therapy response (1). Therefore, the aim of this study is to identify and introduce important miRNAs and genes that are dysregulated and involved in triple-negative breast cancer. Materials and Methods: The raw data set GSE38167 was downloaded from the Gene Expression Omnibus, then differentially expressed miRNAs were recognized between control samples and Cancer samples from patients in different stages of triple-negative breast cancer by using the R packages including GEOquery, limma, BiocGenerics, affy, and oligo. Then multiMiR package in R was used to predict DEmiRNAs target genes. A protein-protein interaction (PPI) network was composed to show key target genes. Next Gene ontology and KEGG pathway analysis were achieved to identify the potential function of these target genes. Results: The differential expression was calculated between the Cancer samples and the control samples. Then DEmiRNAs were obtained with│log2FC│ 2 and adjusted p value 0.05; Accordingly, miRNAs that were upregulated include: hsa-miR-135b, hsa-miR-183, hsa-miR-18b, hsa-miR-96 and hsa-miR-7; and those were downregulated include: hsa-miR-377, hsa-miR-376a, hsa-miR-145, hsa-miR-451 and hsa-miR-376c. In the next step, target genes for these DEmiRNAs were obtained by the multiMiR package in R. the ten hub genes were detected from the PPI network in the following order (MYC, HIF1A, JUN, FN1, CD44, ERBB2, MMP2, CCN2, THBS1, AXL). GO analysis showed that target genes were mainly enriched in positive regulation of DNA-templated transcription, nucleus and RNA binding. KEGG pathway analysis suggested that target genes were enriched in focal adhesion. Conclusion: The results of our study can be helpful for furthermore researches attempted at finding the basic mechanisms of regulation of miRNAs and their target genes in triple negative breast cancer.

Keywords

Triple negative breast cancer, Gene Expression Omnibus dataset, DmiRNAs, Target genes

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