基于TCGA数据的女性不吸烟肺癌患者相关lncRNAs的筛选
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摘要
目的通过对TCGA数据库中女性不吸烟肺癌患者相关基因测序数据进行分析,筛选差异表达的长链非编码RNA(lncRNAs)。方法下载TCGA中女性不吸烟肺癌患者的基因表达数据及相应的临床信息,利用R软件包对数据进行处理、整合和分析,筛选差异表达基因,并通过Survival包进行预后分析。结果筛选获得354个与女性不吸烟肺癌相关的差异表达lncRNAs,其中在肿瘤组织中降低表达的lncRNAs 45个,高表达的lncRNAs 309个,预后分析表明LINC01863的表达水平与女性不吸烟肺癌患者的预后呈正相关(P<0.05),LINC02487、LINC01419和DSCAM-AS1的表达水平与患者的预后呈负相关(P<0.05)。结论对TCGA中的高通量测序数据进行再分析筛选获得多个与女性不吸烟肺癌患者致病相关的lncRNAs,为女性不吸烟肺癌患者的诊断和预后评估提供了潜在的新靶标。
Objective To screen the differentially expressed long non-coding RNAs(lncRNAs) by analyzing the related gene sequencing data of female non-smoking lung cancer patients in the database of The Cancer Genome Atlas(TCGA).Methods The gene expression data and the corresponding clinical information of female non-smoking lung cancer patients were downloaded from the TCGA database.Then,the data were processed,integrated and analyzed with the R software package,and the differentially expressed genes were screened out.The prognosis was analyzed by the Survival package.Results A total of 354 differentially expressed lncRNAs associated with female non-smoking lung cancer were obtained,of which 45 were down-regulated and 309 were up-regulated in tumor tissues.The prognosis analysis showed that the expression level of LINC01863 was positively correlated with the prognosis of female nonsmoking lung cancer patients(P<0.05),and that the expression levels of LINC02487,LINC01419 and DSCAM-AS1 were negatively correlated with the prognosis of female non-smoking lung cancer patients(P<0.05).Conclusion The re-analysis on the high-throughput sequencing data in TCGA database obtains a large number of lncRNAs related to the development of female non-smoking lung cancer,which provides the potential new targets for the diagnosis and prognosis assessment of female non-smoking lung cancer.
Objective To screen the differentially expressed long non-coding RNAs(lncRNAs) by analyzing the related gene sequencing data of female non-smoking lung cancer patients in the database of The Cancer Genome Atlas(TCGA).Methods The gene expression data and the corresponding clinical information of female non-smoking lung cancer patients were downloaded from the TCGA database.Then,the data were processed,integrated and analyzed with the R software package,and the differentially expressed genes were screened out.The prognosis was analyzed by the Survival package.Results A total of 354 differentially expressed lncRNAs associated with female non-smoking lung cancer were obtained,of which 45 were down-regulated and 309 were up-regulated in tumor tissues.The prognosis analysis showed that the expression level of LINC01863 was positively correlated with the prognosis of female nonsmoking lung cancer patients(P<0.05),and that the expression levels of LINC02487,LINC01419 and DSCAM-AS1 were negatively correlated with the prognosis of female non-smoking lung cancer patients(P<0.05).Conclusion The re-analysis on the high-throughput sequencing data in TCGA database obtains a large number of lncRNAs related to the development of female non-smoking lung cancer,which provides the potential new targets for the diagnosis and prognosis assessment of female non-smoking lung cancer.
引文
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[13]Qiao F,Li N,Li W.Integrative bioinformatics analysis reveals potential long non-coding RNA biomarkers and analysis of function in non-smoking females with lung cancer[J].Med Sci Monit,2018,24:5771-5778.
[2]Chen W,Zheng R,Baade PD,et al.Cancer statistics in China,2015[J].CA Cancer J Clin,2016,66(2):115-32.
[3]Li W,Li N,Kang X,et al.Circulating long non-coding RNA AFAP1-AS1 is a potential diagnostic biomarker for non-small cell lung cancer[J].Clin Chim Acta,2017,475:152-156.
[4]Huang Y,Xiang B,Liu Y,et al.LncRNA CDKN2B-AS1 promotes tumor growth and metastasis of human hepatocellular carcinoma by targeting let-7c-5p/NAP1L1 axis[J].Cancer Lett,2018,437:56-66.
[5]Lekka E,Hall J.Noncoding RNAs in disease[J].FEBS Lett,2018,592(17):2884-2900.
[6]Zhang HY,Yang W,Zheng FS,et al.Long non-coding RNASNHG1 regulates zinc finger E-box binding homeobox 1 expression by interacting with TAp63 and promotes cell metastasis and invasion in Lung squamous cell carcinoma[J].Biomed Pharmacother,2017,90:650-658.
[7]Dai M,Chen S,Wei X,et al.Diagnosis,prognosis and bioinformatics analysis of lncRNAs in hepatocellular carcinoma[J].Oncotarget,2017,8(56):95799-95809.
[8]Zhang H,Zhu C,Zhao Y,et al.Long non-coding RNA expression profiles of hepatitis C virus-related dysplasia and hepatocellular carcinoma[J].Oncotarget,2015,6(41):43770-43778.
[9]Niknafs YS,Han S,Ma T,et al.The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression[J].Nat Commun,2016,7:12791.
[10]Xu S,Kong D,Chen Q,et al.Oncogenic long noncoding RNAlandscape in breast cancer[J].Mol Cancer,2017,16(1):129.
[11]Miano V,Ferrero G,Rosti V,et al.Luminal lncRNAs regulation by ERα-Controlled enhancers in a ligand-independent manner in breast cancer cells[J].Int J Mol Sci,2018,19(2):593.
[12]李伟,石柯.女性非吸烟肺癌相关lncRNAs的生物信息学筛选及判断预后价值[J].临床检验杂志,2016,34(10):791-794.
[13]Qiao F,Li N,Li W.Integrative bioinformatics analysis reveals potential long non-coding RNA biomarkers and analysis of function in non-smoking females with lung cancer[J].Med Sci Monit,2018,24:5771-5778.