lncRNA-miRNA-mRNA interaction network for colorectal cancer; An in silico analysis

• Published in: Computational biology and chemistry 2020-12, Vol.89, p.107370, Article 107370
• Main Authors: Ghasemi, Tayyebeh, Khalaj-Kondori, Mohammad, Hosseinpour feizi, Mohammad Ali, Asadi, Parviz
• Format: Article
• Language: English
• Subjects: Colorectal cancer; Colorectal Neoplasms - genetics; Computational Biology; Computer Simulation; Databases, Genetic - statistics & numerical data; Gene Regulatory Networks; Genetic Predisposition to Disease; Humans; lncRNA; lncRNA-miRNA-mRNA network; Microarray; MicroRNAs - genetics; RNA, Long Noncoding - genetics; RNA, Messenger - genetics
• ISSN: 1476-9271; 1476-928X
• DOI: 10.1016/j.compbiolchem.2020.107370

[Display omitted] •The microarray data analysis was conducted to identify differentially expressed lncRNAs and mRNAs in CRC.•The lncRNA-miRNA-mRNA interactions network analyses let to identify potential contributors involved in CRC pathobiology.•The lncRNA-miRNA-mRNA interactions network analyses might be considered for further experimental research and biomarker development. Colorectal cancer (CRC) is one of the most frequent and diagnosed diseases. Accumulating evidences showed that mRNAs and noncoding RNAs play important regulatory roles in tumorigenesis. Identification and determining the relationship between them can help diagnosis and treatment of cancer. Here we analyzed three microarray datasets; GSE110715, GSE32323 and GSE21510, to identify differentially expressed lncRNAs and mRNAs in CRC. The adjusted p-value ≤0.05 was considered statistically significant. Gene set enrichment analysis was carried out using DAVID tool. The miRCancer database was searched to obtain differentially expressed miRNAs in colorectal cancer, and the miRDB database was used to attain the targets of the obtained miRNAs. To predict the lncRNA-miRNA interactions we used DIANA-LncBase v2 and RegRNA 2.0. Finally the lncRNA-miRNA-mRNA-signaling pathway network was constructed using Cytoscape v3.1. By analyzing the three datasets, a total of 21 mRNAs (15 up- and 6 down-regulated) and 24 lncRNAs (18 up- and 6 down-regulated) were identified as common differentially expressed genes between CRC tumor and marginal tissues. Nevertheless, the constructed lncRNA-miRNA-mRNA-signaling pathway network revealed a convergence on 6 lncRNAs (3 up- and 3 downregulated), 7 mRNAs (2 up- and 5 downregulated) and 6 miRNAs (3 up- and 3 downregulated). We found that dysregulation of lncRNAs such as PCBP1-AS1, UCA1 and SNHG16 could sequester several miRNAs such as hsa-miR-582-5p and hsa-miR-198 and promote the proliferation, invasion and drug resistance of colorectal cancer cells. We introduced a set of lncRNAs, mRNAs and miRNAs differentially expressed in CRC which might be considered for further experimental research as potential biomarkers of CRC development.