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

Aims Alterations in the expression of several long non‐coding RNA s (lnc RNA s) have been found in primary nasopharyngeal carcinoma ( NPC ). However, the effect of lnc RNA expression on primary NPC as well as the molecular mechanism of lnc RNA remains vague. This study was to identify differentially expressed lnc RNA s involved in NPC on a genome‐wide scale and predict their potential functions. Methods and results Using high‐throughput microarray with 30 586 lnc RNA and 26 109 mRNA probes, 856 lnc RNA s and 767 mRNA s 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 lnc RNA s were subgrouped into three types and differentially expressed mRNA s were clustered into 28 pathways. The first coexpression network analysis revealed that 46 lnc RNA s interacting with three mRNA s 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 lnc RNA s and eight mRNA s in NPC . The second coexpression network analysis showed that 23 significantly aberrantly expressed mRNA s interacted with three validated lncRNAs. Conclusions This study could provide new insight into the molecular mechanisms of lnc RNA s and their potential role in NPC for further study. These differentially expressed lnc RNA s may act as novel biomarkers and therapeutic targets for NPC .