利用高通量转录组测序数据预测喉鳞状细胞癌转录组新长链非编码RNA的初步研究  

Prediction of new long non-coding RNA of laryngeal carcinoma by high-throughput RNA-Seq data

作　　者：张洋[1] 刘贵明[2] 王国良[2] 钟琦[1] 陈晓红[1] 房居高[1] 黄志刚[1] 

机构地区：[1]首都医科大学附属北京同仁医院耳鼻咽喉头颈外科,耳鼻咽喉头颈科学教育部重点实验室(首都医科大学),100730 [2]中国科学院北京基因组研究所基因组科学及信息重点实验室基础组与精准医学检测技术北京市重点实验室

出　　处：《中华耳鼻咽喉头颈外科杂志》2014年第8期637-642,共6页Chinese Journal of Otorhinolaryngology Head and Neck Surgery

基　　金：国家自然科学基金（81302374,81241084）;北京市自然科学基金（7121005,5122016）;北京市科技新星计划（xx2013043）;北京市教育委员会科技计划重点项目（KZ201310025025）;北京市优秀博士学位论文指导教师科技项目（PXM_2013_014226_07_000060,20121002502）;首都卫生发展科研专项（首发-2011-2005-06）

摘　　要：目的 利用链特异性转录组测序（RNA-Seq）技术,通过生物信息学手段,筛选并鉴定喉鳞状细胞癌（鳞癌）患者转录组中新的长链非编码RNA并对其进行差异表达分析,为进一步阐明喉鳞癌发病的分子机制提供基础.方法 选取10例喉鳞癌患者的肿瘤组织并提取RNA,构建链特异性转录组文库,利用高通量测序平台进行测序.滤除低质量数据后进行比对组装,对得到的转录本进行分类和注释,采用优化的长链非编码RNA（long non-coding RNA,LncRNA）识别流程鉴定喉鳞癌转录中新的LncRNA,并对其特征进行分析.结果 建立了一个优化的流程,从10个喉鳞癌转录组中,共发现了134条目前LncRNA数据库中未收录的新的LncRNA,并分析其长度分布、开放阅读框（open reading frame,ORF）长度、表达差异特征.结论 通过高通量测序手段从喉鳞癌转录组中预测得到新的及其差异表达的LncRNA,可能为喉鳞癌LncRNA的生物信息学分析建立一个较好的流程.Objective To screen and identify the new long non-coding RNAs from transcriptome of laryngeal squamous cell cancer using strand-specific RNA-Seq technology and bioinformatics tools,and to analyze the difference expression of these LncRNAs.Methods RNA was extracted from laryngeal squamous cell cancer tissues of 10 patients and the strand-specific libraries were constructed for high-throughput sequencing.The low-quality data were filtered and the high quality sequencing reads were mapped to the reference genome and assembled.The obtained transcripts were classified and annotated,the optimized LncRNA identification pipeline was used to discover novel LncRNA in these transcriptome,and the characteristics of LncRNA were analyzed.Results A more optimized pipeline were established and 134 new LncRNA transcripts were found,which was not included in the public database.The new LncRNA transcripts had some characteristics in length distribution,ORF length,and expression.Conclusion Some new LncRNA from the transcriptome of laryngeal carcinoma were identified,with different expression,and they may play an important role in laryngeal squamous cell cancer.

关 键 词：喉肿瘤 癌 鳞状细胞 转录组 RNA 长链非编码 基因表达谱 计算生物学 

分 类 号：R739.65[医药卫生—肿瘤]