Genome-wide analyses of long noncoding RNA expression profiles correlated with radioresistance in nasopharyngeal carcinoma via next-generation deep sequencing.
Radioresistance is one of the major factors limiting the therapeutic efficacy and prognosis of patients with nasopharyngeal carcinoma (NPC). Accumulating evidence has suggested that aberrant expression of long noncoding RNAs (lncRNAs) contributes to cancer progression. Therefore, here we identified lncRNAs associated with radioresistance in NPC.



The differential expression profiles of lncRNAs associated with NPC radioresistance were constructed by next-generation deep sequencing by comparing radioresistant NPC cells with their parental cells. LncRNA-related mRNAs were predicted and analyzed using bioinformatics algorithms compared with the mRNA profiles related to radioresistance obtained in our previous study. Several lncRNAs and associated mRNAs were validated in established NPC radioresistant cell models and NPC tissues.



By comparison between radioresistant CNE-2-Rs and parental CNE-2 cells by next-generation deep sequencing, a total of 781 known lncRNAs and 2054 novel lncRNAs were annotated. The top five upregulated and downregulated known/novel lncRNAs were detected using quantitative real-time reverse transcription-polymerase chain reaction, and 7/10 known lncRNAs and 3/10 novel lncRNAs were demonstrated to have significant differential expression trends that were the same as those predicted by deep sequencing. From the prediction process, 13 pairs of lncRNAs and their associated genes were acquired, and the prediction trends of three pairs were validated in both radioresistant CNE-2-Rs and 6-10B-Rs cell lines, including lncRNA n373932 and SLITRK5, n409627 and PRSS12, and n386034 and RIMKLB. LncRNA n373932 and its related SLITRK5 showed dramatic expression changes in post-irradiation radioresistant cells and a negative expression correlation in NPC tissues (R = -0.595, p < 0.05).



Our study provides an overview of the expression profiles of radioresistant lncRNAs and potentially related mRNAs, which will facilitate future investigations into the function of lncRNAs in NPC radioresistance.
Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.|Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China.
Guo
G
Li
Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.|Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China.
Yong
Y
Liu
Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.|Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China.
Chao
C
Liu
Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.|Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China.
Zhongwu
Z
Su
Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.|Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China.
Shuling
S
Ren
Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.|Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China.
Yunyun
Y
Wang
Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.|Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China.
Tengbo
T
Deng
Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.|Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China.
Donghai
D
Huang
Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.|Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China.
Yongquan
Y
Tian
Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China. xyqyz@hotmail.com.|Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China. xyqyz@hotmail.com.
Yuanzheng
Y
Qiu
D002277:Carcinoma / Q000235:genetics* / Q000473:pathology / Q000532:radiotherapy; D019295:Computational Biology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D015894:Genome, Human; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D000077274:Nasopharyngeal Carcinoma; D009303:Nasopharyngeal Neoplasms / Q000235:genetics* / Q000473:pathology / Q000532:radiotherapy; D011379:Prognosis; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D011836:Radiation Tolerance / Q000235:genetics*
D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger
Deep sequencing; Long noncoding RNA; Nasopharyngeal carcinoma; Radioresistance