Identification of Novel lncRNAs Related to Colorectal Cancer Through Bioinformatics Analysis.

Abstract

Long noncoding RNA (lncRNA) plays a critical role in cancer cell proliferation, invasion, metastasis, and chemoresistance. The current study introduces novel lncRNAs in colorectal cancer (CRC) through bioinformatics analysis. GSE134834 CRC-related microarray of Gene Expression Omnibus (GEO) was analyzed to identify differentially expressed genes (DEGs) in CRC samples against normal samples. Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA). Novel lncRNAs were identified, and to better understand the biological function of the identified lncRNAs, gene modules were constructed using weighted gene coexpression network analysis (WGCNA), and finally, two modules for lncRNAs were obtained. The coexpression modules with these lncRNAs were subjected to enrichment analysis in FunRich software to predict their functions through their coexpressed genes. Gene ontology results of modules related to novel lncRNA revealed they significantly enriched the cellular pathways regulation in cancer. The protein-protein interaction (PPI) network of novel lncRNAs-related modules was constructed using Search Tool for the Retrieval of Interacting Genes (STRING) and visualized using the Cytoscape software. Hub genes were screened from the PPI network by the CytoHubba plug-in of Cytoscape. The hub genes were MRTO4, CDK1, CDC20, RPF2, NOP58, NIFK, GTPBP4, BUB1, BUB1B, and BOP1 for the lightpink4 module and BYSL, RPS23 (ribosomal protein S23), RSL1D1 (ribosomal L1 domain containing 1), NAT10, NOP14, GNL2, MRPS12, NOL6 (nucleolar protein 6), IMP4, and RRP12 (ribosomal RNA processing 12 homolog) for the pink module. The expression levels of the top DEmRNA and module hub genes in CRC were validated using the Gene Expression Profiling Interactive Analysis (GEPIA) database. Generally, our findings offer crucial insight into the hub genes and novel lncRNAs in the development of CRC by bioinformatics analysis, information that may prove useful in the identification of new biomarkers and treatment targets in CRC; however, more experimental investigation is required to validate the findings of the present study.