Ion Torrent RNA-Seq detection and analysis of the long non-coding RNA in tongue squamous cell carcinoma

doi:10.12016/j.issn.2096-1456.2016.01.003

Abstract

Abstract: Objective To study the difference of LncRNA expression profiles between tongue squamous cell carcinoma (TSCC) and the corresponding adjacent normal tissue. To explore the role of long non-coding RNA in gene regulation. Methods One fresh sample of TSCC tissue and the adjacent normal tongue tissue were selected. After extracting the total RNA, the LncRNA from different tissues was screened and compared by Ion Torrent RNA-Seq. Pick LncRNA read sequence by the method used Bowtie2, then calculate the reads per kilo bases per million reads, RPKM of LncRNA by the method then Cufflinks. Choose the RPKM ratio of LncRNA from Cancer and adjacent tissue as a candidate target. Results According to RNA-Seq, 52 LncRNA whose value of RPKM with a fold＞10 or ＜0.1 compared to the adjacent normal tongue tissue was enrolled in this study, of which 28 was up-regulated expression, 24 was down-regulated expression. Conclusion LncRNA expression profiles may be an important potential targets in TSCC.

Key words: Long non-coding RNA, Tongue squamous cell carcinoma, High-throughput sequencing

摘要： 目的研究舌鳞癌组织及其癌旁组织之间长链非编码RNA(long non-coding RNA,LncRNA)表达谱的差异,探讨LncRNA在基因调控中的作用。方法应用Ion Torrent高通量测序技术对1例新鲜舌鳞癌组织及其癌旁组织的LncRNA表达谱进行检测比较。将测出的LncRNA序列和Ensemble 6.8数据库中LncRNA的数据进行比对,用Bowtie2的方法挑出LncRNA的读序,然后用Cufflinks方法计算LncRNA每百万读序中来自某基因每千碱基长度的读序数（reads per kilo bases per million reads，RPKM）。截取癌症组织比癌旁组织RPKM值大于10和小于0.1的LncRNA作为候选目标。结果纳入候选目标LncRNA的有52个，其中表达上调的有28个，表达下调的有24个。结论舌鳞癌组织和癌旁组织中存在差异表达的LncRNA分子，提示其靶基因有可能成为舌鳞癌基因治疗的潜在靶点。

关键词: 长链非编码RNA, 舌鳞癌, 高通量测序

CLC Number:

R739.86

OUYANG Ke-xiong1, LIANG Jun, ZOU Rui, LI Zhi-qiang, BAI Zhi-bao, PIAO Zheng-guo, ZHAO Jian-Jiang.. Ion Torrent RNA-Seq detection and analysis of the long non-coding RNA in tongue squamous cell carcinoma[J]. journal1, 2016, 24(1): 15-19.

欧阳可雄, 梁军, 邹瑞, 李志强, 白植宝, 朴正国, 赵建江. 舌鳞癌组织长链非编码RNA的Ion Torrent高通量检测和分析[J]. 口腔疾病防治, 2016, 24(1): 15-19.

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