journal1 ›› 2016, Vol. 24 ›› Issue (1): 15-19.doi: 10.12016/j.issn.2096-1456.2016.01.003

Special Issue: 11

• Basic Study • Previous Articles     Next Articles

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

OUYANG Ke-xiong1, LIANG Jun, ZOU Rui, LI Zhi-qiang, BAI Zhi-bao, PIAO Zheng-guo, ZHAO Jian-Jiang.   

  1. Key Laboratory of Oral Medicine, School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou 510140, China
  • Received:2015-09-02 Online:2016-01-20 Published:2016-01-20
  • Contact: ZHAO Jian-Jiang, Email: zhaojianjiang1965@hotmail.com, Tel: 0086-20-84436981

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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

CLC Number: 

  • R739.86
[1] Wilusz JE, Sunwoo H, Spector DL.Long noncoding RNAs: functional surprises from the RNA world[J].Genes Dev, 2009,23(13):1494-1504.
[2] Ponting CP, Oliver PL, Reik W.Evolution and functions of long nodcoding RNAs[J].Cell, 2009,136(4),629-641.
[3] Struhl K. Transcriptional noise and the fidelity of initiation by RNA polymerase Ⅱ[J]. Nat Struct Mol Biol, 2007,14(2):103-105.
[4] 杨静,曾曙光,刘启才,等.小干扰RNA沉默Dicer酶对人舌鳞癌细胞Tca-8113的增殖和细胞周期的影响[J].广东牙病防治,2013,21(2),61-67.
[5] Tripathi V, Ellis JD, Shen Z, et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation[J]. Mol Cell, 2010,39(6):925-938.
[6] Wang J, Liu X, Wu H, et al. CREB up-regulates long non-coding RNA,HULC expression through interaction with microRNA-372 in liver cancer[J]. Nucleic Acids Res, 2010,38(16):5366-5383.
[7] Gupta RA, Shah N, Wang KC, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis[J]. Nature, 2010,464(7291):1071-1076.
[8] 徐丹丹,赵建江,褚红星,等.应用蛋白质芯片技术筛选人舌鳞癌细胞株差异性炎症因子的初步研究[J].广东牙病防治,2013,21(5):234-239.
[9] Fang Z, Wu L, Wang L, et al. Increased expression of the long non-coding RNA UCA1 in tongue squamous cell carcinomas: a possible correlation with cancer metastasis[J]. Oral Surg Oral Med Oral Pathol Oral Radiol, 2014,117(1):89-95.
[10] Panzitt K, Tschernatsch MM, Guelly C, et al.Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma,as noncoding RNA[J].Gastroenterology, 2007,132(1):330-342.
[11] 朱艳慧,贺树香,王晓春,等.通往个性化医疗的新一代测序技术:Ion Torrent[J].生物技术通讯,2013,24(4):587-591.
[12] Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing[J]. Nature, 2011,475(7356):348-352.
[13] Flusberg BA, Webster DR, Lee JH, et al. Direct detection of DNA methylation during single-molecule real-time sequencing[J]. Nat Methods, 2010,7(6):461-465.
[14] 张濛,张青云,徐国宾.新一代测序技术在肿瘤临床中的应用[J].临床检验杂志,2014,32(9):641-646.
[15] Loman NJ, Misra RV, Dallman TJ, et al. Performance comparison of benchtop high-throughput sequencing platforms[J]. Nat Biotechnol, 2012,30(5):434-439.
[16] Quail MA, Smith M, Coupland P, et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers[J/OL]. BMC Genomics, 2012[2015-08-01]. http://www.biomedcentral.com/1471-2164/13/341.
[17] Lujambio A, Portela A, Liz J, et al. CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer[J]. Oncogene, 2010,29(48):6390-6401.
[18] Braconi C, Valeri N, Kogure T, et al. Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma[J]. Proc Natl Acad Sci USA, 2011,108(2):786-791.
[19] Huang MD, Chen WM, Qi FZ, et al. Long non-coding RNA TUG1 is up-regulated in hepatocellular carcinoma and promotes cell growth and apoptosis by epigenetically silencing of KLF2[J/OL]. Mol Cancer, 2015[2015-07-15]. http://molecular-cancer.biomedcentral.com/ 14:165.
[20] Fernandez-Zapico ME, Lomberk GA, Tsuji S, et al. A functional family-wide screening of SP/KLF proteins identifies a subset of suppressors of KRAS-mediated cell growth[J]. Biochem J, 2011,435(2):529-537.
[21] Yan J, Guo X, Xia J, et al. MiR-148a regulates MEG3 in gastric cancer by targeting DNA methyltransferase 1[J]. Med Oncol, 2014,31(3):879-881.
[22] Yin DD, Liu ZJ, Zhang E, et al. Decreased expression of long noncoding RNA MEG3 affects cell proliferation and predicts a poor prognosis in patients with colorectal cancer[J/OL]. Tumour Biol,2015[2015-08-03]. http://link.springer.com/article/10.1007%2Fs13277-015-3139-2.
[23] Jia LF, Wei SB, Gan YH, et al. Expression, regulation and roles of miR-26a and MEG3 in tongue squamous cell carcinoma[J].Int J Cancer, 2014,135(10):2282-2293.
[24] Li M, Qiu M, Xu Y, et al. Differentially expressed protein-coding genes and long noncoding RNA in early-stage lung cancer[J/OL]. Tumour Biol,2015[2015-08-05]. http://link.springer.com/article/10.1007%2Fs13277-015-3714-6.
[25] Pinto EM, Chen X, Easton J, et al. Genomic landscape of pediatric adrenocortical tumors[J/OL].Nat Commun, 2015[2015-08-15]. http://www.ncbi.nlm.nih.gov/pubmed/?term=Genomic+landscape+of+pediatric+adrenocortical+tumors.
[26] 邹瑞,林颖,欧阳可雄,等.H19基因在肿瘤发生发展中作用的研究新进展.实用医学杂志[J].2015,31(19):151-153.
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