胶质母细胞瘤中全转录组测序及ceRNA调控网络的构建与验证

Whole-transcriptome sequencing with ceRNA regulation network construction and verification in glioblastoma.

作者信息

Zeng Zhao-Mu, Chen Yue-Yue, Wen Xi-Chao, Geng Xiu-Chao, Zhu Yi-Xi, Hao Liang-Chao, Dong Zi-Shu, Yang Ji-Feng, Wang Ting-Ting, Zhang Ruo-Bing, Sun Zhi-Wei, Zhang Yu-Hao, Zheng Ke-Bin

机构信息

Department of Neurosurgery, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College Nanchang 330000, Jiangxi, PR China.

Department of Neurosurgery, Affiliated Hospital of Hebei University Baoding 071000, Hebei, PR China.

出版信息

Am J Transl Res. 2023 Jun 15;15(6):4291-4313. eCollection 2023.

PMID:37434823

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10331694/

Abstract

OBJECTIVES

To explore the key genes involved in the occurrence and development of glioblastoma (GBM) by analyzing whole-transcriptome sequencing and biologic data from GBM and normal cerebral cortex tissues and to search for important noncoding RNA (ncRNA) molecular markers based on the competitive endogenous RNA (ceRNA) network.

METHODS

Ten GBM and normal cerebral cortex tissues were collected for full transcriptome sequencing, screened for differentially expressed (DE) mRNAs, miRNAs, lncRNAs, and circRNAs, and subjected to bioinformatic analysis. We constructed a Protein-Protein Interaction (PPI) network and a circRNA/lncRNA-miRNA-mRNA regulatory network and identified them using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Finally, The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases were used to validate and conduct a survival analysis of the target genes.

RESULTS

A total of 5341 DEmRNAs, 259 DEmiRNAs, 3122 DElncRNAs, and 2135 DEcircRNAs were identified. Enrichment analysis showed that target genes regulated by DEmiRNA, DElncRNA, and DEcircRNA were closely related to chemical synaptic transmission and ion transmembrane transport. A PPI network analysis screened 10 hub genes that directly participate in tumor cell mitosis regulation. In addition, the ceRNA composite network showed that hsa-miR-296-5p and hsa-miR-874-5p were the central nodes of the network, and the reliability of relevant key molecules was successfully verified through RT-qPCR identification and the TCGA database. The CGGA database survival analysis produced 8 DEmRNAs closely related to GBM patient survival prognosis.

CONCLUSIONS

This study revealed the important regulatory functions and molecular mechanisms of ncRNA molecules and identified hsa-miR-296-5p and hsa-miR-874-5p as key molecules in the ceRNA network. They may play an important role in GBM pathogenesis, treatment, and prognosis.

摘要

目的

通过分析胶质母细胞瘤（GBM）和正常大脑皮质组织的全转录组测序及生物学数据，探索参与GBM发生发展的关键基因，并基于竞争性内源RNA（ceRNA）网络寻找重要的非编码RNA（ncRNA）分子标志物。

方法

收集10例GBM组织和正常大脑皮质组织进行全转录组测序，筛选差异表达（DE）的mRNA、miRNA、lncRNA和circRNA，并进行生物信息学分析。构建蛋白质-蛋白质相互作用（PPI）网络和circRNA/lncRNA-miRNA-mRNA调控网络，并用逆转录定量聚合酶链反应（RT-qPCR）进行鉴定。最后，利用癌症基因组图谱（TCGA）和中国胶质瘤基因组图谱（CGGA）数据库对靶基因进行验证和生存分析。

结果

共鉴定出5341个DEmRNA、259个DEmiRNA、3122个DElncRNA和2135个DEcircRNA。富集分析表明，受DEmiRNA、DElncRNA和DEcircRNA调控的靶基因与化学突触传递和离子跨膜转运密切相关。PPI网络分析筛选出10个直接参与肿瘤细胞有丝分裂调控的枢纽基因。此外，ceRNA复合网络显示hsa-miR-296-5p和hsa-miR-874-5p是该网络的中心节点，通过RT-qPCR鉴定和TCGA数据库成功验证了相关关键分子的可靠性。CGGA数据库生存分析得出8个与GBM患者生存预后密切相关的DEmRNA。