2型糖尿病外周血长链非编码RNA-微小RNA-mRNA网络构建及功能富集分析

目的本研究通过构建长链非编码RNA(lncRNA)-微小RNA(miRNA)-mRNA网络和功能富集分析,预测参与T2DM外周血竞争性内源RNA(ceRNA)机制的关键lncRNA,以发现DM新的标志物或治疗靶点。方法采用基因芯片技术检测T2DM外周血差异lncRNA的表达谱,采用R语言及相关生物信息学工具处理芯片数据,预测靶基因,构建lncRNA-miRNA-mRNA网络,对差异lncRNA进行KEGG通路及GO功能富集分析,并预测关键lncRNA。结果相关性分析得到关系对2016对,包括125个lncRNA和163个mRNA。KEGG及GO分析显示有多个通路与T2DM的发生发展有联系。根据相关性分析以及软件预测数据,成功构建了lncRNA-miRNA-mRNA网络,包括21个miRNA、12个mRNA、82个lncRNA和187个相互作用关系对。预测工具筛选出6个关键lncRNA。结论 lncRNA可能通过ceRNA机制介导了DM的发生发展,其关键lncRNA可能成为未来新的DM筛查标志物或治疗靶点。     

冠心病外周血中环状RNA表达谱及分子网络分析

采用circRNA微阵列芯片筛选冠心病人和健康对照外周血中差异表达的circRNA,分析表达谱特征,为冠心病发生机制提供新思路并寻找血液标志物。方法 选取6个冠心病人和6个与之年龄性别配对的健康对照,检测circRNA并进行比较分析,火山图显示差异circRNAs的情况。运用miRanda软件预测对应结合的miRNA;根据文献报道的参与冠心病发病机制的miRNA对结果进一步筛选,再利用两组之间FC>2,p <0.05,找出显著差异表达的circRNA;对差异表达基因进行GO功能注释及KEGG pathway分析,利用cytoscape软件对结合冠心病相关miRNA最多的10个circRNA进行分析,建立circRNA-miRNA-mRNA分子调控网络。结果 与对照相比,病例组外周血中表达显著差异的circRNA有793个;其中上调599个,下调194个。GO分析结果显示主要涉及细胞外基质,内皮细胞分化等方面,KEGG涉及Wnt,PI3K-Akt信号通路。网络图共纳入10个circRNAs,17个相关 microRNAs以及24个mRNAs形象展现它们之间的相互作用。结论 circRNA可能作为miRNA分子海绵调控下游基因参与冠心病发病过程并作为潜在的血液生物标志物。     

冠心病患者血液外泌体mRNA、lncRNA及circRNA差异表达谱及竞争性内源RNA网络的构建

目的:通过生物信息学方法构建冠心病患者血液外泌体中的竞争性内源RNA(ceRNA)调控网络,探讨其发病机制.方法:在exoRbase数据库中下载冠心病患者和正常对照的血液外泌体测序数据,通过R语言分别对外泌体中mRNA、长链非编码RNA(lncRNA)、环状RNA(circRNA)的表达谱作差异表达分析,使用Tar-g...     

食管鳞癌差异表达基因鉴定及亚洲人食管鳞癌预后lncRNA功能分析

目的用生物信息学方法分析食管鳞癌(esophageal squamous cell carcinoma,ESCC)组织中转录组差异表达RNA,筛选和预测特异lncRNA的功能。方法通过TCGA数据库筛选ESCC差异表达基因并构建相关ceRNA网络,在GEO中对差异lncRNA进行验证,并对筛选出的差异lncRNA进行生存分析。利用GO、KEGG和蛋白互作网络进一步分析与预后相关lncRNA的功能。结果通过TCGA数据库共筛选出差异表达mRNA 2 064个,lncRNA 1 160个,miRNA 69个,并成功构建了lncRNA-miRNA-mRNA调控网络。GEO、TCGA共有差异表达lncRNA 26个,其中AC009264.1、PGM5-AS1及LINC00460与亚洲人ESCC患者生存相关。GO、KEGG、PPI分析表明这3个预后相关lncRNA可能参与ESCC的形成与进展。结论通过分析ESCC转录组测序数据,发现一批预后相关lncRNA,有望为ESCC的治疗和预后预测提供新的靶点与分子标志物。     

急性心肌梗死患者血浆外泌体mRNA表达谱分析

目的 比较分析急性心肌梗死(AMI)患者和非心源性胸痛(NCCP)患者血浆外泌体中mRNA的表达差异,并探讨差异表达mRNA对AMI发生发展可能的影响。方法 入选北京朝阳医院和内蒙古包头市中心医院NCCP患者和AMI患者各15例。提取入选者血浆外泌体及外泌体总RNA,高通量测序技术检测AMI患者和NCCP患者血浆中外泌体信使RNA(mRNA)的表达谱,筛选出AMI患者中差异表达的mRNA。对差异表达mRNA进行基因本体(GO)分析和京都基因与基因组百科全书(KEGG)信号通路分析。结果 提取的外泌体为粒径在30~200 nm之间的双层膜小囊泡,表达外泌体标志分子分化簇63(CD63)和热休克蛋白70(HSP70),而不表达甘油醛-3-磷酸脱氢酶(GAPDH),符合外泌体的特征。对入选AMI患者和NCCP患者血浆外泌体中的mRNA表达量进行检测,AMI患者血浆中外泌体转录本数量为64 258条,NCCP患者血浆中外泌体转录本数量为64 374条。其中差异表达的mRNA共1 800条(上调951条,下调849条)。GO和KEGG分析表明上述差异表达的mRNA参与了AMI的生物学调节功能和通路。结论 AMI患者血浆外泌体中mRNA的表达水平与NCCP组比较存在明显的差异,这些差异表达的外泌体mRNA可能在AMI的发生发展过程中发挥重要的作用。     

支气管肺发育不良中新型miRNA-TF-mRNA共调控网络的鉴定

目的筛选与新生儿支气管肺发育不良(BPD)发病相关的关键转录因子(TF)、微小核糖核酸(miRNA)和信使核糖核酸(mRNA), 并构建了调控网络。方法从高通量基因表达数据库GEO获取mRNA芯片数据集GSE108756, 筛选出的差异表达基因(DEGs)进行京都基因和基因百科全书(KEGG)、基因本体注释(GO)功能富集分析;参照HumanTFDB数据库获取与DEGs对应的TF后利用cytoHubba插件筛选出degree值前10的Hub TF;通过hTFtarget数据库找出Hub TF中7个TF所对应的靶基因;在GSE108756中获取7个TF及其靶基因所对应的探针表达量后做相关性分析, 筛选出最终纳入研究的6个Hub TF及所对应的正相关TF-mRNA关系队;利用Targetscan Human数据库获取靶向调控6个Hub TF的miRNAs, 并与miRNA芯片数据集GSE166762差异miRNAs取交集后匹配出负向调节的miRNA-TF关系队, 最后构建BPD患儿潜在miRNA-TF-mRNA调控网络, 进一步筛选出关键miRNA、mRNA。结果共筛选出201个差异表达基...     

心肌梗死相关miRNA-mRNA调控网络及其作用

目的 探讨心肌梗死相关的微小RNA(miRNA)-信使RNA(mRNA)调控网络,并分析其对心肌梗死发生发展的调控作用。方法 从基因表达数据库下载微阵列数据（GSE61741）,用R语言进行差异分析,并对获得的差异表达miRNA进行上游转录因子及下游靶基因的预测;从GEO中获取GSE66360数据集,用R语言进行差异分析,将差异表达基因与靶基因取交集获得目标基因;对目标基因进行基因本体（GO）生物学功能注释和京都基因与基因组百科全书（KEGG）通路富集分析,构建蛋白质相互作用（PPI）网络并筛选出Hub基因及核心miRNA。结果 共得到17个差异表达miRNA,其中4个表达上调、13个表达下调,其主要转录因子为2级POU结构域转录因子1、特异性蛋白1、早期生长反应1。差异表达miRNA靶基因与差异表达mRNA取交集共得到165个目标基因。GO富集分析发现其主要与细菌来源分子的反应、三级颗粒、细胞因子活性、趋化因子活性等生物过程和分子功能相关;KEGG通路富集分析显示目标基因主要聚集在TNF、IL-17、NF-κB等信号通路。miRNA-mRNA网络筛选出7个核心基因（JUN、CXCL8...     

小鼠日本血吸虫感染及吡喹酮治疗过程中全转录组及关键基因调控网络分析

目的　利用全转录组测序技术研究日本血吸虫感染及吡喹酮治疗过程中长链非编码RNA（lncRNA）⁃微小RNA（miRNA）⁃信使RNA（mRNA）的交互作用,分析其中发挥调控作用的关键基因网络。方法　110只C57BL/6小鼠随机分为对照组、感染组和治疗组,感染组和治疗组以腹部贴片法感染日本血吸虫尾蚴后,第3、6、8周分别取10只小鼠肝脏组织;治疗组在第8周后开始吡喹酮治疗,治疗后第2、4、6、8、10周分别取10只小鼠肝脏组织。所有肝脏样本提取总RNA并构建转录组文库,进行全转录组高通量测序,对显著变化的差异表达基因进行功能注释、基因本体（GO）功能富集分析、京都基因与基因组百科全书（KEGG）通路富集分析。应用R语言中Corrplot包和Himsc包对肝脏标本进行相关性分析,利用R语言中的MixOmics包和Himsc包对lncRNA⁃miRNA⁃mRNA进行多组学交互网络分析。结果　感染组与对照组间共有差异表达miRNA基因 1 176个、差异表达mRNA基因5 270个、差异表达lncRNA基因 2 682个;治疗组与感染组间共有差异表达miRNA基因1 289个、差异表达mRNA基因7个、差异表达lncRNA基因69个;治疗组与对照组间共有差异表达miRNA基因1 210个、差异表达mRNA基因4 456个、差异表达lncRNA基因2 016个。相关性分析显示,治疗组与对照组基因表达相关性更高。主成分分析显示,感染组与治疗组出现了明显分别聚类。具有显著相关性的基因主要富集在花生四烯酸代谢、异生分解代谢、不饱和脂肪酸代谢、异生代谢、长链脂肪酸代谢等24个GO条目和胆固醇代谢、酪氨酸代谢、亚油酸代谢、雷丁醇代谢、类固醇激素生物代谢等8条KEGG代谢途径。结论　Cyp2b9等23个mRNA和 Rmrpr等14个lncRNA处于基因调控网络核心位置,可能在血吸虫感染及吡喹酮治疗过程中发挥关键调控作用;miR⁃8105等9个miRNA具有作为血吸虫感染诊断分子标志物的潜力。     

羊急性心梗卸负荷模型miRNA表达差异的初步分析

目的对羊急性心梗卸负荷模型的micro RNA表达谱进行初步差异分析,探索LVAD卸负荷的调控机制。方法根据micro RNA表达谱筛选出差异表达miRNA,用靶基因预测软件PITA、mi Randa得到差异表达miRNA的靶基因,通过GO数据库和KEGG数据库对靶基因进行GO注释和KEGG pathway分析。结果筛选得到卸负荷组与对照组相同表达miRNA 3个,差异表达miRNA 22个。其中mi R-21、mi R-26a、mi R-30c、mi R-125b与心肌细胞凋亡调控相关,mi R-30a-3p可能与缺氧后心肌细胞自噬相关,mi R-218a、mi R-541-5p可能与肥厚性心肌调节相关,13个miRNA未见与心梗相关的报道。GO和KEGG分析发现差异miRNA靶基因富集的生物功能和信号通路与LVAD卸负荷作用密切相关。结论通过对micro RNA表达谱的差异分析,发现了9个参与卸负荷作用调节和13个未知功能的micro RNA表达,为进一步深入分析急性心梗的调控网络提供了一个新的线索。     

冠心病患者外周血外泌体中microRNA基因芯片的差异性表达

目的:通过基因芯片筛选并分析健康成年人与急性ST段抬高型心肌梗死(STEMI)患者、稳定型心绞痛(SA)患者外周血外泌体中microRNA的表达差异,寻找临床诊断和治疗冠心病的新靶点。方法:入选STEMI患者、SA患者和健康成年人各3例,采集受试者静脉血,通过超高速离心法提取血清中的外泌体,运用基因芯片技术对外泌体中的microRNA进行测序。两两对比,从中筛选出差异性表达的microRNA,对差异性表达的microRNA的靶基因进行GO功能富集分析和KEGG Pathway富集分析。结果:STEMI组、SA组和健康组外周血中外泌体所含有的microRNA表达有明显差异。SA组与健康组对比,miR-5195-3p、miR-328、miR-130a-3p上调表达差异较明显[FC(abs)2];SA组与STEMI组对比,miR-483-3p下调表达差异较明显[FC(abs)2];STEMI组与健康组对比,miR-4787-3p、miR-423-5p、miR-151b上调表达差异较明显[FC(abs)2],miR-140-3p、miR-29a-3p、miR-765、miR-939-5p下调表达较明显[FC(abs)2]。结论:STEMI患者、SA患者和健康成年人外周血中外泌体所含有的microRNA表达有显著差异,其中部分特异性的microRNA与心血管疾病的发生发展有着密切的关系,可以作为冠心病诊断和治疗的新靶标。     

Analysis of susceptibility genes and myocardial infarction risk correlation of ischemic cardiomyopathy based on bioinformatics

BackgroundThe present study was to investigated differential expressed genes (GEGs) in ischemic cardiomyopathy (ICM), and to construct regulation networks, and to study the correlation between myocardial infarction risk.MethodsData sets were downloaded from the Gene Expression Omnibus (GEO) to screen out messenger RNA (mRNA) and long non-coding RNA (lncRNA) differentially expressed between ICM samples and normal samples. Gene Ontology (GO) function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Differentially expressed mRNA and lncRNA were analyzed, and bioinformatics methods were used to predict and analyze microRNA (miRNA), and a competing endogenous RNA (Hub gene) regulatory network was constructed. Using the Limma software package in R language, DEGs of ICM were screened with non-heart failure donors as the control group under the conditions that the differential expression ratio was not less than 2 times, and the corrected P value was <0.05. The ClusterProfiler software package was used for GO enrichment analysis and KEGG enrichment analysis. The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) 11.0 online database was used to screen key genes for protein-protein interaction (PPI) network analysis.ResultsThe GO function analysis and KEGG pathway analysis showed that the DEGs were significantly enriched in metabolic pathways, oxidative phosphorylation, extracellular matrix receptor interactions, and other pathways, and were closely related to fibrosis, collagen catabolic process, and inflammatory response function, and a Hub gene regulatory network related to ICM lncRNA was constructed. Bioinformatics methods were used to effectively analyze the DEGs of ICM, and the Hub gene regulatory network of ICM was successfully constructed.ConclusionsThis study identified a certain risk correlation between ICM susceptibility genes and myocardial infarction.     

基于miRNA表达谱解析细粒棘球蚴病患者体内Th17/Treg失衡机制

目的　观察细粒棘球蚴病患者血清微小RNA（miRNA）表达水平、探讨miRNA对辅助性T 细胞17（Th17）/调节性T细胞（Treg）失衡的影响,以阐明细粒棘球蚴慢性感染并长期致病的机制。方法　提取细粒棘球蚴病患者与健康对照者血清总RNA,采用Illumina测序平台进行高通量测序。分别采用miRBase数据库和miRDeep2工具进行已知miRNA注释和新miRNA预测,并进行差异分析。采用miRanda软件和TargetScan软件分别预测差异表达miRNA靶基因后取交集,进行基因本体（GO）富集分析以及京都基因和基因组百科全书（KEGG）通路分析。在差异表达变化倍数居前20位的miRNA中,匹配可靶向决定Th17细胞和Treg细胞生成的关键转录因子（RORC和FOXP3）或重要调控通路（PI3K⁃Akt和mTOR通路）相关基因的miRNA。结果　细粒棘球蚴病患者与健康对照血清中共有53个差异表达miRNA,其中47个上调表达miRNA、6个下调表达miRNA。GO富集分析显示,差异表达miRNA功能涉及DNA转录翻译、细胞成分、细胞形态、神经发育及代谢分解等过程。KEGG富集分析显示,这些差异表达miRNA靶基因涉及的主要信号通路包括MAPK、PI3K⁃Akt、mTOR等信号通路。在差异表达变化倍数居前20位的miRNA中,有3个潜在靶向调控RORC的miRNA、15个潜在靶向PI3K⁃Akt、mTOR信号通路的miRNA。结论　细粒棘球蚴感染后可使患者血清miRNA表达谱出现明显改变,差异表达miRNA可能通过靶向Th17/Treg关键转录因子或PI3K⁃Akt、mTOR通路而导致Th17/Treg免疫失衡,进而利于细粒棘球蚴在宿主体内长期寄生并慢性致病。     

冠心病相关环状RNA调控机制及治疗的研究进展

环状RNA（circRNA）是一种非编码RNA,具有靶向调节小RNA（miRNA）或信使RNA（mRNA）的功能,参与动脉粥样硬化、免疫反应、血管新生、细胞凋亡、细胞增殖、细胞衰老和细胞自噬等多种冠心病（CHD）病理机制。基于circRNA构建的circRNA/miRNA/mRNA交互网络,有助于系统地、动态地反映CHD的发生发展。同时,通过药物干预或人工过表达/敲低circRNA的异常表达,以及circRNA序列编辑等方法,circRNA为今后CHD的靶向和精准治疗提供了新靶点和新策略。尽管如此,目前有关CHD的circRNA调控机制和治疗研究仍处于初级阶段,明确CHD circRNA生物标志物和治疗靶点仍任重而道远。     

Identification of a functional circRNA-miRNA-mRNA regulatory network in infantile hemangioma by bioinformatics analysis

Several circRNA have been reported to serve critical roles in various biological processes of human body. The present study aimed to build a circRNA-based competing endogenous RNA (ceRNA) network and explore the regulatory mechanisms of circRNA in infantile hemangiomas (IH). Differentially expressed circRNA, miRNA, and mRNA were downloaded from the gene expression synthesis (GEO) microarray database ({"type":"entrez-geo","attrs":{"text":"GSE98795","term_id":"98795"}}GSE98795, {"type":"entrez-geo","attrs":{"text":"GSE69136","term_id":"69136"}}GSE69136, and {"type":"entrez-geo","attrs":{"text":"GSE127487","term_id":"127487"}}GSE127487). Cancer-specific circRNA database (CSCD), miRDB and Targetscan were employed to predict the targets of RNA. A total of 855 DEcircRNAs, 69 differentially expressed miRNAs (DEmiRNAs), and 3233 differentially expressed mRNAs (DEmRNAs) appeared as genes that were aberrantly expressed in IH. The circRNA-miRNA-mRNA network was constructed based on 108 circRNAs, 7 miRNAs, 274 mRNAs in IH. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated hypoxia-inducible factors (HIF)-1 signaling pathway and Notch signaling pathway were significantly enriched in IH with being constructed a ceRNA regulatory network. Furthermore, protein-protein interaction (PPI) network and Cytoscape showed the top 10 hub genes that regulate angiogenesis, namely FBXW7, CBLB, HECW2, FBXO32, FBXL7, KLHL5, EP300, MAPK1, MEF2C, and PLCG1. Our findings provide a deeper understanding the circRNA-related ceRNA regulatory mechanism in IH. This study further perfected the circRNA-miRNA-mRNA regulatory network related to IH and explored the potential function of mRNA in this network. It provides more understanding for the circRNA-related ceRNA regulation mechanism in the pathogenesis of IH.     

大鼠颈动脉球囊损伤模型的竞争性内源RNA调控网络研究

目的构建大鼠颈动脉球囊损伤模型的竞争性内源RNA(competing endogenous RNA,ceRNA)调控网络,筛选血管新生内膜形成中的关键调控基因。方法首先建立大鼠颈动脉球囊损伤模型。将12只SD大鼠随机分为2组(每组6只):手术组,利用2F取栓球囊于左颈总动脉行球囊损伤术;假手术组:夹闭左颈总动脉,使血流阻断时间接近球囊损伤术操作时间。术后14 d取颈总动脉血管组织,提取总RNA,进行长链非编码RNA(long non-coding RNA,lncRNA)和信使mRNA(messenger RNA,mRNA)测序。应用生物信息学方法进行差异表达lncRNA和mRNA共表达分析、基因功能(Gene Ontology,GO)和信号通路(Pathway)分析;通过数据库预测微小RNA(microRNA,miRNA)与lncRNA及mRNA的结合关系,并从中筛选已报道在大鼠血管内膜增生过程中有生物学功能的miRNA相关的结合关系,得到最终的ceRNA网络。结果与假手术组相比,手术组鉴定出1731个差异表达的mRNAs和99个差异表达的lncRNAs;GO和Pathway分析显示,差异表达的mRNA主要参与调节免疫反应、细胞迁移、细胞黏附等。ceRNA分析构建了由46个mRNAs、18个lncRNAs和16个miRNAs组成的ceRNA网络,其中AABR07073245.1、Col6a3、AABR07071659.2和AABR07067310.2所介导的ceRNA调控轴可能在大鼠血管新生内膜形成中具有重要调控作用。结论本研究系统分析大鼠颈动脉球囊损伤模型表达谱,构建的ceRNA调控网络可能在大鼠血管内膜增生过程中具有重要调控作用,有望为动脉粥样硬化的防治提供新的靶点与分子标志物。     

Key factors and potential drug combinations of nonalcoholic steatohepatitis: Bioinformatic analysis and experimental validation-based study

BackgroundNonalcoholic fatty liver disease and its advanced stage, nonalcoholic steatohepatitis (NASH), are the major cause of hepatocellular carcinoma (HCC) and other end-stage liver disease. However, the potential mechanism and therapeutic strategies have not been clarified. This study aimed to identify potential roles of miRNA/mRNA axis in the pathogenesis and drug combinations in the treatment of NASH.MethodsMicroarray GSE59045 and GSE48452 were downloaded from the Gene Expression Omnibus and analyzed using R. Then we obtained differentially expressed genes (DE-genes). DAVID database was used for Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway analysis. Protein-protein interaction (PPI) networks were used for the identification of hub genes. We found upstream regulators of hub genes using miRTarBase. The expression and correlation of key miRNA and its targets were detected by qPCR. Drug Pair Seeker was employed to predict drug combinations against NASH. The expression of miRNA and hub genes in HCC was identified in the Cancer Genome Atlas database and Human Protein Atlas database.ResultsNinety-four DE-genes were accessed. GO and KEGG analysis showed that these predicted genes were linked to lipid metabolism. Eleven genes were identified as hub genes in PPI networks, and they were highly expressed in cells with vigorous lipid metabolism. hsa-miR-335-5p was the upstream regulator of 9 genes in the 11 hub genes, and it was identified as a key miRNA. The hub genes were highly expressed in NASH models, while hsa-miR-335-5p was lowly expressed. The correlation of miRNA-mRNA was established by qPCR. Functional verification indicated that hsa-miR-335-5p had inhibitory effect on the development of NASH. Finally, drug combinations were predicted and the expression of miRNA and hub genes in HCC was identified.ConclusionsIn the study, potential miRNA-mRNA pathways related to NASH were identified. Targeting these pathways may be novel strategies against NASH.