Xie Xinsheng, Hong Xiang, Hong Shichai, Huang Yulong, Chen Gang, Chen Yihui, Lin Yue, Lu Weifeng, Fu Weiguo, Wang Lixin
Department of Vascular Surgery, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen 361015, China.
Department of Vascular Surgery, Vascular Surgery Institute of Fudan University, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
Biomedicines. 2023 Feb 15;11(2):571. doi: 10.3390/biomedicines11020571.
The molecular mechanisms associated with thoracic aortic dissection (TAD) remain poorly understood. A comprehensive high-throughput sequencing-based analysis of the circRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) regulatory network in TAD has not been conducted. The purpose of this study is to identify and verify the key ceRNA networks which may have crucial biological functions in the pathogenesis of TAD.
Gene expression profiles of the GSE97745, GSE98770, and GSE52093 datasets were acquired from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified using the GEO2R tools. Protein-protein interaction (PPI) networks of the hub genes were constructed using STRING; the hub genes and modules were identified by MCODE and CytoHubba plugins of the Cytoscape. We analyzed the hub genes using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. The functions of these hub genes were assessed using Cytoscape software. Our data-along with data from GSE97745, GSE98770, and GSE52093-were used to verify the findings.
Upon combined biological prediction, a total of 11 ce-circRNAs, 11 ce-miRNAs, and 26 ce-mRNAs were screened to construct a circRNA-miRNA-mRNA ceRNA network. PPI network and module analysis identified four hub nodes, including IGF1R, JAK2, CSF1, and GAB1. Genes associated with the Ras and PI3K-Akt signaling pathways were clustered in the four hub node modules in TAD. The node degrees were most significant for IGF1R, which were also the most significant in the two modules (up module and hub module). IGF1R was selected as a key gene, and the hsa_circ_0007386/miR-1271-5P/IGF1R/AKT regulatory axis was established. The relative expression levels of the regulatory axis members were confirmed by RT-PCR in 12 samples, including TAD tissues and normal tissues. Downregulation of IGF1R expression in smooth muscle cells (SMCs) was found to induce apoptosis by regulating the AKT levels. In addition, IGF1R showed high diagnostic efficacy in both AD tissue and blood samples.
The hsa_circ_0007386/miR-1271-5P/IGF1R/AKT axis may aggravate the progression of TAD by inducing VSMCs apoptosis. CeRNA networks could provide new insights into the underlying molecular mechanisms of TAD. In addition, IGF1R showed high diagnostic efficacy in both tissue and plasma samples in TAD, which can be considered as a diagnostic marker for TAD.
与胸主动脉夹层(TAD)相关的分子机制仍知之甚少。尚未对TAD中基于circRNA-miRNA-mRNA竞争性内源RNA(ceRNA)调控网络进行全面的高通量测序分析。本研究的目的是识别和验证可能在TAD发病机制中具有关键生物学功能的关键ceRNA网络。
从基因表达综合数据库(GEO)获取GSE97745、GSE98770和GSE52093数据集的基因表达谱。使用GEO2R工具鉴定差异表达基因(DEG)。使用STRING构建枢纽基因的蛋白质-蛋白质相互作用(PPI)网络;通过Cytoscape的MCODE和CytoHubba插件识别枢纽基因和模块。我们使用基因本体论和京都基因与基因组百科全书通路富集分析对枢纽基因进行分析。使用Cytoscape软件评估这些枢纽基因的功能。我们的数据以及来自GSE97745、GSE98770和GSE52093的数据用于验证研究结果。
经过综合生物学预测,共筛选出11个ce-circRNA、11个ce-miRNA和26个ce-mRNA,构建了circRNA-miRNA-mRNA ceRNA网络。PPI网络和模块分析确定了四个枢纽节点,包括IGF1R、JAK2、CSF1和GAB1。与Ras和PI3K-Akt信号通路相关的基因在TAD的四个枢纽节点模块中聚集。IGF1R的节点度最为显著,在两个模块(上调模块和枢纽模块)中也最为显著。选择IGF1R作为关键基因,建立了hsa_circ_0007386/miR-1271-5P/IGF1R/AKT调控轴。通过RT-PCR在包括TAD组织和正常组织在内的12个样本中确认了调控轴成员的相对表达水平。发现平滑肌细胞(SMC)中IGF1R表达下调通过调节AKT水平诱导细胞凋亡。此外,IGF1R在AD组织和血液样本中均显示出高诊断效能。
hsa_circ_0007386/miR-1271-5P/IGF1R/AKT轴可能通过诱导血管平滑肌细胞凋亡加重TAD的进展。CeRNA网络可为TAD潜在的分子机制提供新的见解。此外,IGF1R在TAD的组织和血浆样本中均显示出高诊断效能,可被视为TAD的诊断标志物。