J Cancer 2018; 9(11):1943-1950. doi:10.7150/jca.23481 This issue

Research Paper

Analysis of Differential Expressions of Long Non-coding RNAs in Nasopharyngeal Carcinoma Using Next-generation Deep Sequencing

Xiao-xiao Li1, Xu-jun liang1, Liu-ying Zhou1, Rui-jie Liu1, Wu Bi1, Sai Zhang1, Shi-sheng Li2, Wen-hui Yang3, Zhu-chu Chen1, Xin-ming Yang2✉, Peng-fei Zhang1✉

1. Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P.R. China
2. Department of Otolaryngology Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan,410011, P.R. China
3. International College, Guangdong University of Foreign Studies, Guangzhou, Guangdong, 510420, P.R. China

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Li Xx, liang Xj, Zhou Ly, Liu Rj, Bi W, Zhang S, Li Ss, Yang Wh, Chen Zc, Yang Xm, Zhang Pf. Analysis of Differential Expressions of Long Non-coding RNAs in Nasopharyngeal Carcinoma Using Next-generation Deep Sequencing. J Cancer 2018; 9(11):1943-1950. doi:10.7150/jca.23481. Available from https://www.jcancer.org/v09p1943.htm

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Background: Little knowledge about long non-coding RNAs(lncRNAs) in nasopharyngeal carcinoma (NPC) has been acquired.

Methods: Next-generation sequencing was applied in 7 cases of NPC tissues and 7 cases of normal tissues in nasopharynx. PLEX, CNCI and CPAT soft-wares were used to predict novel lncRNAs. Real-time Quantitative PCR (qPCR) further validated the data in 20 cases of NPC tissues and 14 cases of normal tissues. Then the cis-regulators and trans-regulators and potential biological functions together with pathways were predicted by Bioinformatics.

Results: Totally, 4248 novel lncRNAs were found to be expressed in our samples. And 2192 lncRNAs and 23342 mRNAs were considered to be differentially expressed in NPC. Among the results, 306 lncRNAs and 4599 mRNAs were significantly up-regulated, whereas 204 lncRNAs and 2059 mRNAs were significantly down-regulated, respectively. Moreover, 62 lncRNAs trans-regulated genes were involved in Epstein-Barr virus (EBV) infection pathway in our study. Jun proto-oncogene (JUN), which was related to a cis-regulator lncRNA RP4-794H19.1, was enriched in cancers and involved in Tumor Necrosis Factor (TNF) signaling pathway, might play a key role in NPC.

Conclusion: These findings broadened the lncRNAs landscape of NPC tissues and shed light on the roles of these lncRNAs, which might be conducive to the comprehensive management of NPC.

Keywords: Nasopharyngeal carcinoma, RNA sequencing, Long non-coding RNAs, Bioinformatics analysis, QPCR