基于生物信息学的胰腺导管腺癌预后风险长链非编码RNA筛选
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陆晔斌, Email: luyebin6@sina.com

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湖南省自然科学基金资助项目(2017JJ3508)。


Identification of prognostic risk long noncoding RNAs for pancreatic ductal adenocarcinoma by bioinformatics analysis
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    摘要:

    目的:应用生物信息学方法筛选胰腺导管腺癌的预后风险长链非编码RNA(lncRNA)。 方法:从癌症和肿瘤基因图谱(TCGA)数据库下载胰腺导管腺癌患者的RNA-seq Level 2数据及其临床信息。根据NCBI Gene数据库及GENCODE v7数据库的基因注释信息,将下载的mRNA和lncRNA测序数据进行重新注释。然后应用R软件的edgeR包和limma包筛选差异表达的mRNA和lncRNA,并对它们进行相关性分析,进而获得lncRNA-mRNA有统计学意义的共表达关系对,并将其中的mRNA定义为lncRNA的靶基因。通过R软件clusterProfiler包对lncRNA的靶基因进行功能富集分析,以推测lncRNA的生物学功能。最后,绘制差异表达lncRNA的Kaplan-Meier曲线,筛选出与胰腺导管腺癌预后风险相关的lncRNA。 结果:经过基因重新注释,共得到19 791个mRNA和1 623个lncRNA的测序数据,随后共筛选得到260个差异表达的mRNA和15个差异表达的lncRNA。经过相关性分析,共得到包括5个lncRNA和24个mRNA在内的24个有统计学意义的共表达关系对。其中lncRNA LINC00857有6个靶基因,分别为C1orf116、ESRP1、GPRC5A、LIPH、MAL2和PLS1。根据lncRNA靶基因的功能富集分析,推测LINC00857主要富集于磷脂酶活性、细胞骨架结构组成和脂肪酶活性。生存分析发现,CASC8和LINC00857与胰腺导管腺癌的预后风险明显有关(P=0.0052、P=0.027)。 结论:CASC8和LINC00857可能是胰腺导管腺癌的预后风险lncRNA,有望在今后的研究中成为胰腺导管腺癌新的预后监测指标。

    Abstract:

    Objective: To screen the prognostic risk long noncoding RNAs (lncRNAs) for pancreatic ductal adenocarcinoma (PDAC) by bioinformatics approaches. Methods: The RNA-Seq Level 2 data and clinical information of PDAC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The sequencing data of the downloaded mRNAs and lncRNAs were re-annotated according to the gene annotation data from NCBI Gene database and GENCODE v7 database. The differentially expressed mRNAs and lncRNAs were screened by using edgeR and limma packages in R. Then, the significantly co-expressed pairs between mRNAs and lncRNAs were obtained by correlation analysis, in which, the mRNAs were considered as target genes of the lncRNAs. After that, the functional modules of the lncRNAs were predicted by functional enrichment analysis of their target mRNAs with the clusterProfiler package in R. Finally, the significant prognostic risk lncRNAs for PDAC were determined by drawing Kaplan-Meier curves of the differentially expressed lncRNAs. Results: After gene re-annotation, the sequencing data of a total of 19 791 mRNAs and 1 623 lncRNAs were obtained, and then, 260 differentially expressed mRNAs and 15 differentially expressed lncRNAs were picked up. From the correlation analysis, 24 significantly co-expressed pairs comprised of 24 mRNAs and 5 lncRNAs were identified. Of them, LINC00857 had 6 target genes that were C1orf116, ESRP1, GPRC5A, LIPH, MAL2 and PLS1, respectively. According to the functional enrichment analysis, the target genes of lncRNA LINC00857 were mainly enriched in phospholipase activity, structural constituent of cytoskeleton, and lipase activity. The results of survival analysis revealed that lncRNA CASC8 and LINC00857 were significantly associated with prognostic risk of PDAC (P=0.0052, P=0.027). Conclusion: CASC8 and LINC00857 are potential prognostic risk lncRNAs for PDAC, and may probably become the novel indictors for prognosis of PDAC in the future.

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张志鹏, 孙维佳, 陈泓西, 夏华, 陆晔斌.基于生物信息学的胰腺导管腺癌预后风险长链非编码RNA筛选[J].中国普通外科杂志,2018,27(9):1126-1134.
DOI:10.7659/j. issn.1005-6947.2018.09.007

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  • 收稿日期:2018-07-03
  • 最后修改日期:2018-08-17
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  • 在线发布日期: 2018-09-15