Abstract
BackgroundRadioresistance 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.MethodsThe 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.ResultsBy 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).ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12885-016-2755-6) contains supplementary material, which is available to authorized users.
Highlights
Radioresistance is one of the major factors limiting the therapeutic efficacy and prognosis of patients with nasopharyngeal carcinoma (NPC)
Based on the potential roles proposed for Long noncoding RNA (lncRNA) in cancer-related behaviors, here we investigated the possible lncRNAs mediating NPC radioresistance
Construction of lncRNA profiles that correlated with NPC radioresistance To obtain lncRNA expression profiles associated with radioresistance, we constructed cDNA libraries using our previously established radioresistant CNE-2-Rs and parental CNE-2 cell lines [11]
Summary
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. Here we identified lncRNAs associated with radioresistance in NPC. Radiotherapy is the mainstay treatment for patients with nasopharyngeal carcinoma (NPC). Despite major advances in radiation techniques and radiotherapeutic strategies, the prognosis and survival rates of patients with NPC remain unsatisfactory [1, 2]. One of the major factors contributing to the poor outcomes in NPC is the occurrence of radioresistance, and radioresistance is a hot topic in both basic and clinical research. Previous studies have improved our understanding of radioresistance. The exact molecular mechanisms underlying radioresistance remain unclear
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