Characterization of long non-coding RNA-associated ceRNA network in nasopharyngeal carcinoma
Abstract: Nasopharyngeal carcinoma (NPC) is a common malignant tumor of the head and neck. The aim of this study was to construct long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) regulation networks for NPC using bioinformatics methods. LncRNAs related to NPC was retrieved by searching Pubmed, MNDR v2.0, and LncRnaDisease database. The location of these lncRNAs was found in RNALocate and lncATLAS. For screened cytoplasmic lncRNAs, RAID v2 and miRTarBase were used to predict the possible ceRNA relationship between lncRNA-miRNA-mRNA. STRING and Cytoscape resources were used for systematical analysis of the molecular function, biological processes, and signal pathways of differentially expressed genes. So far 39 lncRNAs have been reported to be differentially expressed in NPC. Among them, 5 lncRNAs, namely AFAP1-AS1, DANCR, CCAT1, UCA1, and H19, were identified to be mainly cytoplasmic and had the potential to be ceRNAs. There have been strong evidences that 3 of the lncRNAs, namely CCAT1, UCA1, and H19, could bind to 11 miRNAs (miR-490-3p, miR-485-5p, miR-145-5p, miR-143-3p, miR-16-5p, miR-141-3p, miR-429, miR-200, miR-148a-3p, miR-22-3p, and miR-765-5p) and further regulate their corresponding downstream target mRNAs. A protein-protein interaction network of 356 nodes and 4676 edges was constructed, with proteins enriched in kinases and positive regulator of cellular metabolism. After MCODE analysis, the proteins were further enriched to 6 nodes, namely DEAD-box helicase 53, high mobility group box-1 protein, CD40, CD28, interferon beta, and transferrin receptor. This study will provide novel insight for better understanding of lncRNA-associated ceRNA network and facilitate the exploration of new diagnostic and therapeutic markers for NPC.
Keywords: competing endogenous RNA, long non-coding RNA, nasopharyngeal carcinoma, bioinformatics analysis