Genome-wide analysis of long non-coding RNA in primary nasopharyngeal carcinoma by microarray

Alterations in the expression of several long non-coding RNAs (lncRNAs) have been found in primary nasopharyngeal carcinoma (NPC). However, the effect of lncRNA expression on primary NPC as well as the molecular mechanism of lncRNA remains vague. This study was to identify differentially expressed lncRNAs involved in NPC on a genome-wide scale and predict their potential functions.

Using high-throughput microarray with 30,586 lncRNA and 26,109 mRNA probes, 856 lncRNAs and 767 mRNAs were expressed differentially between NPC and chronic nasopharyngitis tissues. Bioinformatic analysis (clustering analysis, gene ontology analysis and pathway analysis) was used for further research. Differentially expressed lncRNAs were subgrouped into three types and differentially expressed mRNAs were clustered into 28 pathways. The first coexpression network analysis revealed that 46 lncRNAs interacting with three mRNAs involved the Janus kinase-signal transducer and activator of transcription (JAK-STAT) signalling pathway. Quantitative real-time polymerase chain reaction (PCR) verified 11 up- and down-regulated lncRNAs and eight mRNAs in NPC. The second coexpression network analysis showed that 23 significantly aberrantly expressed mRNAs interacted with three validated lncRNAs.

This study could provide new insight into the molecular mechanisms of lncRNAs and their potential role in NPC for further study. These differentially expressed lncRNAs may act as novel biomarkers and therapeutic targets for NPC.