基于lncRNA-miRNA-mRNA的ceRNA网络构建筛选老年胶质母细胞瘤相关lncRNAs
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摘要
目的:识别老年胶质母细胞瘤患者相关lncRNA(Long non-coding RNA,长链非编码RNA)。方法:从TCGA数据库下载TCGA-GBM RNA-seq、miRNA-seq、clinical数据。将样本按照年龄大于70岁和小于70岁进行分组。利用edgeR软件进行lncRNA、miRNA、mRNA的差异表达分析。利用miRanda软件分别预测miRNA的mRNA靶基因以及miRNA的lncRNA靶基因。针对筛选出的差异lncRNA和差异mRNA,进行表达相关性分析。根据lncRNA-mRNA相关性分析以及miRNA靶基因分析结果,构建ceRNA网络。结果:根据本文的筛选条件共筛选得到48个lncRNA-miRNA-mRNA调控网络。结论:筛选得到7个lncRNA及48个ceRNA网络可作为老年胶质母细胞瘤患者的生物学标志物进行研究。
Objective:To identify the lncRNAs related to the diagnose and prognosis of glioma in the elderly.Methods:Firstly,data from TCGA was downloaded which involved RNA-seq,miRNA-seq,clinical data of TCGAGBM. Then,the samples from the data were divided into two groups based on the age with the critical value 70 years old and the R package edgeR was applied to analyze the differential expression of lncRNA,miRNA and mRNA. Next,the technical software MiRanda was used to predict the target site between the pairs of miRNA-mRNA as well as miRNA-lncRNA in differential expression,whose result was put into the ceRNA network. Results:we screened out 48 lncRNAs,miRNAs and mRNAs which formed the complicated ceRNA network which might be associated with the classification of glioma. Conclusion:Some specific biomarkers within the ceRNA network in this research might play an important role in the diagnosis and prognosis of glioma in the elderly.
Objective:To identify the lncRNAs related to the diagnose and prognosis of glioma in the elderly.Methods:Firstly,data from TCGA was downloaded which involved RNA-seq,miRNA-seq,clinical data of TCGAGBM. Then,the samples from the data were divided into two groups based on the age with the critical value 70 years old and the R package edgeR was applied to analyze the differential expression of lncRNA,miRNA and mRNA. Next,the technical software MiRanda was used to predict the target site between the pairs of miRNA-mRNA as well as miRNA-lncRNA in differential expression,whose result was put into the ceRNA network. Results:we screened out 48 lncRNAs,miRNAs and mRNAs which formed the complicated ceRNA network which might be associated with the classification of glioma. Conclusion:Some specific biomarkers within the ceRNA network in this research might play an important role in the diagnosis and prognosis of glioma in the elderly.
引文
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[12]Cohen AL,Colman H. Glioma biology and molecular markers. Cancer Treat Res[J],2015,163:E15.
[13]Kraus TF,Greine A,Guibourt V,et al. Identification of stably expressed lncRNAs as valid endogenous controls for profiling of human glioma[J]. J Cancer,2015,6(2):E111.
[2] Wirsching HG,Happold C,Roth P,et al. Management of diffusely infiltrating glioma in the elderly[J]. Curr Opin Oncol,2015,27(6):E502.
[3] Almenawer SA,Badhiwala JH,Alhazzani W,et al. Biopsy versus partial versus gross total resection in older patients with high-grade glioma:a systematic review and meta-analysis[J]. Neuro Oncol,2015,17(6):E868.
[4] Ferguson M,Rodrigues G,Cao J,et al. Management of high-grade gliomas in the elderly[J]. Semin Radiat Oncol,2014,24(4):E279.
[5] Ludwig K,Kornblum HI. Molecular markers in glioma[J]. J Neurooncol,2017,134(3):E505.
[6] Masui K,Mischel PS,Reifenberger G. Molecular classification of gliomas[J]. Handb Clin Neurol,2016,134:E97.
[7] Fosmark S,Hellwege S,Dahlrot RH,et al. APNG as a prognostic marker in patients with glioblastoma[J].PLoS One,2017,12(6):E0178693.
[8] Wick W,Weller M,van den BentM,et al. MGMT testing--the challenges for biomarker-based glioma treatment[J]. Nat Rev Neurol,2014,10(7):E372.
[9] Li Y,Shan X,Wu Z,et al. IDH1 mutation is associated with a higher preoperative seizure incidence in lowgrade glioma:A systematic review and meta-analysis[J]. Seizure,2018,55:E76.
[10]Veganzones S,de la Orden V,Requejo L,et al. Genetic alterationsof IDH1 and Vegf in brain tumors. Brain Behav[J]. 2017,7(9):e00718.
[11]Siegal T. Clinical Relevance of Prognostic and Predictive Molecular Markers in Gliomas. Adv Tech Stand Neurosurg[J],2016,18(43):E91.
[12]Cohen AL,Colman H. Glioma biology and molecular markers. Cancer Treat Res[J],2015,163:E15.
[13]Kraus TF,Greine A,Guibourt V,et al. Identification of stably expressed lncRNAs as valid endogenous controls for profiling of human glioma[J]. J Cancer,2015,6(2):E111.