2型糖尿病(T2DM)影响颈动脉粥样硬化斑块(CAPs)的形成,患者易出现斑块不稳定性。阐明转录组学谱和确定与T2DM并发CAPs进展相关的生物标志物至关重要。获得了十个人CAP样本,进行全转录组测序(RNA-seq)。将样品分为两组:糖尿病(DM)相对于非DM组以及不稳定相对于稳定组。R中的Limma包用于鉴定lncRNAs,circRNAs,和mRNA。基因本体论(GO)注释和京都基因和基因组百科全书(KEGG)途径分析,蛋白质-蛋白质相互作用(PPI)网络创建,并对差异表达的mRNA进行模块生成。Cytoscape用于创建转录因子(TF)-mRNA调控网络,lncRNA/circRNA-mRNA共表达网络,和竞争性内源性RNA(ceRNA)网络。GSE118481数据集和RT-qPCR用于验证潜在的mRNA。基于已验证的核心基因构建调控网络,并从上述网络中提取关系。总的来说,180个差异表达的lncRNAs,343个circRNAs,在DM与非DM组中鉴定出1092个mRNA;240个差异表达的lncRNAs,390个circRNAs,在不稳定与稳定组中鉴定出677个mRNA。五个circRNAs,14个lncRNAs,在所有四个组中共有的171个mRNAs向同一方向变化。GO/KEGG功能富集分析表明,171个mRNA主要与生物过程有关,比如免疫反应,炎症反应,和细胞粘附。五个circRNAs,14个lncRNAs,46个miRNAs,CERNA网络中的54个mRNA形成了调控关系。C22orf34-hsa-miR-6785-5p-RAB37、hsacirc_013887-hsa-miR-6785-5p/hsa-miR-4763-5p/hsa-miR-30b-3p-RAB37、MIR4435-1HG-hsa-miR-30b-3p-RAB37和GAS5-hsa-3b使用GSE118481数据集和RT-qPCR验证了七个上调的mRNA。调控网络包括七个mRNA,五个circRNAs,六个lncRNAs,和14个TFs。我们提出了五个circRNAs(hsacirc_028744,hsacirc_037219,hsacirc_006308,hsacirc_013887和hsacirc_045622),六个lncRNAs(EPB41L4A-AS1,LINC00969,GAS5,MIR4435-1HG,MIR503HG,和SNHG16),和七个mRNA(RAB37,CCR7,CD3D,TRAT1,VWF,ICAM2和TMEM244)作为与T2DM并发CAP进展相关的潜在生物标志物。构建的ceRNA网络对潜在的RNA调控途径具有重要意义。
Type 2 diabetes mellitus (T2DM) affects the formation of carotid atherosclerotic plaques (CAPs) and patients are prone to plaque instability. It is crucial to clarify transcriptomics profiles and identify biomarkers related to the progression of T2DM complicated by CAPs. Ten human CAP samples were obtained, and whole transcriptome sequencing (RNA-seq) was performed. Samples were divided into two groups: diabetes mellitus (DM) versus non-DM groups and unstable versus stable groups. The Limma package in R was used to identify lncRNAs, circRNAs, and mRNAs. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, protein-protein interaction (PPI) network creation, and module generation were performed for differentially expressed mRNAs. Cytoscape was used to create a transcription factor (TF)-mRNA regulatory network, lncRNA/circRNA-mRNA co-expression network, and a competitive endogenous RNA (ceRNA) network. The GSE118481 dataset and RT-qPCR were used to verify potential mRNAs.The regulatory network was constructed based on the verified core genes and the relationships were extracted from the above network. In total, 180 differentially expressed lncRNAs, 343 circRNAs, and 1092 mRNAs were identified in the DM versus non-DM group; 240 differentially expressed lncRNAs, 390 circRNAs, and 677 mRNAs were identified in the unstable versus stable group. Five circRNAs, 14 lncRNAs, and 171 mRNAs that were common among all four groups changed in the same direction. GO/KEGG functional enrichment analysis showed that 171 mRNAs were mainly related to biological processes, such as immune responses, inflammatory responses, and cell adhesion. Five circRNAs, 14 lncRNAs, 46 miRNAs, and 54 mRNAs in the ceRNA network formed a regulatory relationship. C22orf34-hsa-miR-6785-5p-RAB37, hsacirc_013887-hsa-miR-6785-5p/hsa-miR-4763-5p/hsa-miR-30b-3p-RAB37, MIR4435-1HG-hsa-miR-30b-3p-RAB37, and GAS5-hsa-miR-30b-3p-RAB37 may be potential RNA regulatory pathways. Seven upregulated mRNAs were verified using the GSE118481 dataset and RT-qPCR. The regulatory network included seven mRNAs, five circRNAs, six lncRNAs, and 14 TFs. We propose five circRNAs (hsacirc_028744, hsacirc_037219, hsacirc_006308, hsacirc_013887, and hsacirc_045622), six lncRNAs (EPB41L4A-AS1, LINC00969, GAS5, MIR4435-1HG, MIR503HG, and SNHG16), and seven mRNAs (RAB37, CCR7, CD3D, TRAT1, VWF, ICAM2, and TMEM244) as potential biomarkers related to the progression of T2DM complicated with CAP. The constructed ceRNA network has important implications for potential RNA regulatory pathways.